1
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Coletta M, Bolognesi M, Ascenzi P. Heme is pivotal for life. J Inorg Biochem 2024; 250:112423. [PMID: 37953207 DOI: 10.1016/j.jinorgbio.2023.112423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Affiliation(s)
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Paolo Ascenzi
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Roma, Italy.
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2
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Ascenzi P, Bolognesi M, Guertin M, Moens L. Jonathan B. Wittenberg (1923-2023). J Inorg Biochem 2023:112396. [PMID: 37838607 DOI: 10.1016/j.jinorgbio.2023.112396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2023]
Affiliation(s)
- Paolo Ascenzi
- Department of Science, Roma Tre University, 00146 Roma, Italy.
| | | | - Michel Guertin
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec G1V 0A6, Canada.
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium.
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3
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Grandi A, Tomasi M, Ullah I, Bertelli C, Vanzo T, Accordini S, Gagliardi A, Zanella I, Benedet M, Corbellari R, Di Lascio G, Tamburini S, Caproni E, Croia L, Ravà M, Fumagalli V, Di Lucia P, Marotta D, Sala E, Iannacone M, Kumar P, Mothes W, Uchil PD, Cherepanov P, Bolognesi M, Pizzato M, Grandi G. Immunogenicity and Pre-Clinical Efficacy of an OMV-Based SARS-CoV-2 Vaccine. Vaccines (Basel) 2023; 11:1546. [PMID: 37896949 PMCID: PMC10610814 DOI: 10.3390/vaccines11101546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
The vaccination campaign against SARS-CoV-2 relies on the world-wide availability of effective vaccines, with a potential need of 20 billion vaccine doses to fully vaccinate the world population. To reach this goal, the manufacturing and logistic processes should be affordable to all countries, irrespective of economical and climatic conditions. Outer membrane vesicles (OMVs) are bacterial-derived vesicles that can be engineered to incorporate heterologous antigens. Given the inherent adjuvanticity, such modified OMVs can be used as vaccines to induce potent immune responses against the associated proteins. Here, we show that OMVs engineered to incorporate peptides derived from the receptor binding motif (RBM) of the spike protein from SARS-CoV-2 elicit an effective immune response in vaccinated mice, resulting in the production of neutralizing antibodies (nAbs) with a titre higher than 1:300. The immunity induced by the vaccine is sufficient to protect the animals from intranasal challenge with SARS-CoV-2, preventing both virus replication in the lungs and the pathology associated with virus infection. Furthermore, we show that OMVs can be effectively decorated with the RBM of the Omicron BA.1 variant and that such engineered OMVs induce nAbs against Omicron BA.1 and BA.5, as measured using the pseudovirus neutralization infectivity assay. Importantly, we show that the RBM438-509 ancestral-OMVs elicited antibodies which efficiently neutralize in vitro both the homologous ancestral strain, the Omicron BA.1 and BA.5 variants with a neutralization titre ranging from 1:100 to 1:1500, suggesting its potential use as a vaccine targeting diverse SARS-CoV-2 variants. Altogether, given the convenience associated with the ease of engineering, production and distribution, our results demonstrate that OMV-based SARS-CoV-2 vaccines can be a crucial addition to the vaccines currently available.
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Affiliation(s)
- Alberto Grandi
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy; (A.G.); (A.G.); (M.B.); (G.D.L.); (E.C.)
- BiOMViS Srl, Via Fiorentina 1, 53100 Siena, Italy
| | - Michele Tomasi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Irfan Ullah
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06520, USA; (I.U.); (W.M.); (P.D.U.)
| | - Cinzia Bertelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Teresa Vanzo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Silvia Accordini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Assunta Gagliardi
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy; (A.G.); (A.G.); (M.B.); (G.D.L.); (E.C.)
| | - Ilaria Zanella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Mattia Benedet
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy; (A.G.); (A.G.); (M.B.); (G.D.L.); (E.C.)
| | - Riccardo Corbellari
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Gabriele Di Lascio
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy; (A.G.); (A.G.); (M.B.); (G.D.L.); (E.C.)
| | - Silvia Tamburini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Elena Caproni
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy; (A.G.); (A.G.); (M.B.); (G.D.L.); (E.C.)
| | - Lorenzo Croia
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Micol Ravà
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.R.); (V.F.); (P.D.L.); (D.M.); (E.S.); (M.I.)
| | - Valeria Fumagalli
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.R.); (V.F.); (P.D.L.); (D.M.); (E.S.); (M.I.)
- Vita-Salute San Raffaele University, Via Olgettina 58, 00132 Milan, Italy
| | - Pietro Di Lucia
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.R.); (V.F.); (P.D.L.); (D.M.); (E.S.); (M.I.)
| | - Davide Marotta
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.R.); (V.F.); (P.D.L.); (D.M.); (E.S.); (M.I.)
- Vita-Salute San Raffaele University, Via Olgettina 58, 00132 Milan, Italy
| | - Eleonora Sala
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.R.); (V.F.); (P.D.L.); (D.M.); (E.S.); (M.I.)
- Vita-Salute San Raffaele University, Via Olgettina 58, 00132 Milan, Italy
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.R.); (V.F.); (P.D.L.); (D.M.); (E.S.); (M.I.)
- Vita-Salute San Raffaele University, Via Olgettina 58, 00132 Milan, Italy
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Priti Kumar
- Department of Microbial Pathogenesis, School of Medicine, Yale University, New Haven, CT 06510, USA;
| | - Walther Mothes
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06520, USA; (I.U.); (W.M.); (P.D.U.)
- Department of Microbial Pathogenesis, School of Medicine, Yale University, New Haven, CT 06510, USA;
| | - Pradeep D. Uchil
- Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT 06520, USA; (I.U.); (W.M.); (P.D.U.)
- Department of Microbial Pathogenesis, School of Medicine, Yale University, New Haven, CT 06510, USA;
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
| | - Martino Bolognesi
- Biosciences Department, University of Milan, Via Celoria 26, 20133 Milan, Italy;
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; (M.T.); (C.B.); (T.V.); (S.A.); (I.Z.); (R.C.); (S.T.); (L.C.)
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4
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Puri S, Schulte T, Chaves-Sanjuan A, Mazzini G, Caminito S, Pappone C, Anastasia L, Milani P, Merlini G, Bolognesi M, Nuvolone M, Palladini G, Ricagno S. The Cryo-EM STRUCTURE of Renal Amyloid Fibril Suggests Structurally Homogeneous Multiorgan Aggregation in AL Amyloidosis. J Mol Biol 2023; 435:168215. [PMID: 37516426 DOI: 10.1016/j.jmb.2023.168215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/15/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Immunoglobulin light chain amyloidosis (AL) is caused by the aberrant production of amyloidogenic light chains (LC) that accumulate as amyloid deposits in vital organs. Distinct LC sequences in each patient yield distinct amyloid structures. However different tissue microenvironments may also cause identical protein precursors to adopt distinct amyloid structures. To address the impact of the tissue environment on the structural polymorphism of amyloids, we extracted fibrils from the kidney of an AL patient (AL55) whose cardiac amyloid structure was previously determined by our group. Here we show that the 4.0 Å resolution cryo-EM structure of the renal fibril is virtually identical to that reported for the cardiac fibril. These results provide the first structural evidence that LC amyloids independently deposited in different organs of the same AL patient share a common fold.
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Affiliation(s)
- Sarita Puri
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy. https://twitter.com/@Saritapuri1504
| | - Tim Schulte
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy. https://twitter.com/@timpaul81
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Pediatric Research Center Fondazione R.E. Invernizzi and NOLIMITS Center, Università degli Studi di Milano, Milan, Italy. https://twitter.com/@ChavesSanjuan
| | - Giulia Mazzini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Serena Caminito
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Carlo Pappone
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; Faculty of Medicine, University of Vita-Salute San Raffaele, 20132 Milan, Italy; Arrhythmia and Electrophysiology Department, IRCCS Policlinico San Donato, San Donato, 20097 Milan, Italy
| | - Luigi Anastasia
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy; Faculty of Medicine, University of Vita-Salute San Raffaele, 20132 Milan, Italy. https://twitter.com/@skinski74
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Pediatric Research Center Fondazione R.E. Invernizzi and NOLIMITS Center, Università degli Studi di Milano, Milan, Italy. https://twitter.com/@Martinobologne2
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefano Ricagno
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy; Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy.
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5
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Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega M, Isupov M, Harmer N, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo M, Contestabile R, Vallone B, Tramonti A, Montemiglio L. Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR. Nucleic Acids Res 2023; 51:8237-8254. [PMID: 37378428 PMCID: PMC10450172 DOI: 10.1093/nar/gkad552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5'-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors.
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Affiliation(s)
- Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Anna Barile
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy
| | - Mirella Vivoli Vega
- School of Biochemistry, University of Bristol, University Walk, BS8 1TD Bristol, UK
| | - Michail N Isupov
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Elena Gugole
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Paolo Swuec
- Cryo-Electron Microscopy Core Facility, Human Technopole, Milano 20157, Italy
| | - Martino Bolognesi
- Department of Biosciences, Pediatric Clinical Research Center Romeo ed Enrica Invernizzi and NOLIMITS, University of Milano, Milano 20133, Italy
| | - Anita Scipioni
- Department of Chemistry, Sapienza, University of Rome, Rome 00185, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Martino Luigi Di Salvo
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
| | - Roberto Contestabile
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, University of Rome, Rome 00185, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza, University of Rome, Rome 00185, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
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6
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Pesce A, Barmpidi K, Dewilde S, Estarellas C, Moens L, Bolognesi M, Luque FJ, Nardini M. Structural and dynamic characterization of the hexa-coordinated globin from Spisula solidissima. J Inorg Biochem 2023; 246:112289. [PMID: 37354606 DOI: 10.1016/j.jinorgbio.2023.112289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023]
Abstract
High energy consumption in the nervous system requires a continuous supply of O2. This role is assisted by proteins from the globin super-family in the nerve cells of invertebrates, where 'nerve hemoglobins' (nHbs) are mainly present at mM concentrations and exhibit oxygen affinities comparable to those of vertebrate myoglobins. To gain insight into the structural bases of this function, we report the crystal structure of nHb from the Atlantic surf clam Spisula solidissima (SsHb), previously suggested to display a bis-histidyl hexa-coordinated heme in the deoxy state, high O2 affinity, and ligand binding cooperativity when assayed in situ. The crystallized protein forms a dimer through packing of a 4-helix bundle involving helices E and F of each subunit. The SsHb 'classic' globin fold displays bis-histidyl (His71(E7) and His103(F8)) hexa-coordination of the heme-Fe atom, with structural and dynamics variations found in the inter-helix hinge regions. Molecular Dynamics simulations of both monomeric and dimeric species in the bis-histidyl hexa-coordinated, deoxy penta-coordinated, and O2-bound hexa-coordinated states reveal distinct structural rearrangements at the interface between subunits in the dimer; these would affect the magnitude of the conformational fluctuations observed between monomer and dimer, and the topology of cavities within the protein matrix and at the interface. These results point to a distal site opening mechanism allowing access of the exogenous ligand to the heme and cast hypotheses on the dimer interface structural and dynamic properties that may support ligand binding cooperativity in dimeric SsHb.
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Affiliation(s)
- Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, I-16146 Genova, Italy
| | - Katerina Barmpidi
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Institut de Biomedicina (IBUB) and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Institut de Biomedicina (IBUB) and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milan, Italy
| | - Francisco Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Institut de Biomedicina (IBUB) and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milan, Italy.
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7
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Grandi A, Tomasi M, Ullah I, Bertelli C, Vanzo T, Accordini S, Gagliardi A, Zanella I, Benedet M, Corbellari R, Lascio GD, Tamburini S, Caproni E, Croia L, Ravà M, Fumagalli V, Lucia PD, Marotta D, Sala E, Iannacone M, Kumar P, Mothes W, Uchil PD, Cherepanov P, Bolognesi M, Pizzato M, Grandi G. Immunogenicity and pre-clinical efficacy of an OMV-based SARS-CoV-2 vaccine. Res Sq 2023:rs.3.rs-2788726. [PMID: 37292970 PMCID: PMC10246226 DOI: 10.21203/rs.3.rs-2788726/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The vaccination campaign against SARS-CoV-2 relies on the world-wide availability of effective vaccines, with a potential need of 20 billion vaccine doses to fully vaccinate the world population. To reach this goal, the manufacturing and logistic processes should be affordable to all countries, irrespectively of economical and climatic conditions. Outer membrane vesicles (OMV) are bacterial-derived vesicles that can be engineered to incorporate heterologous antigens. Given the inherent adjuvanticity, such modified OMV can be used as vaccine to induce potent immune responses against the associated protein. Here we show that OMVs engineered to incorporate peptides derived from the receptor binding motif (RBM) of the spike protein from SARS-CoV-2 elicit an effective immune response in vaccinated mice, resulting in the production of neutralizing antibodies (nAbs). The immunity induced by the vaccine is sufficient to protect the animals from intranasal challenge with SARS-CoV-2, preventing both virus replication in the lungs and the pathology associated with virus infection. Furthermore, we show that OMVs can be effectively decorated with the RBM of the Omicron BA.1 variant and that such engineered OMVs induced nAbs against Omicron BA.1 and BA.5, as judged by pseudovirus infectivity assay. Importantly, we show that the RBM438-509 ancestral-OMVs elicited antibodies which efficiently neutralized in vitro both the homologous ancestral strain, the Omicron BA.1 and BA.5 variants, suggesting its potential use as a pan SARS-CoV-2 vaccine. Altogether, given the convenience associated with ease of engineering, production and distribution, our results demonstrate that OMV-based SARS-CoV-2 vaccines can be a crucial addition to the vaccines currently available.
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Affiliation(s)
- Alberto Grandi
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100, Siena, Italy
- BiOMViS Srl, Via Fiorentina 1, 53100, Siena Italy
| | - Michele Tomasi
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cinzia Bertelli
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Teresa Vanzo
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Silvia Accordini
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Assunta Gagliardi
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Ilaria Zanella
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Mattia Benedet
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Riccardo Corbellari
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | | | - Silvia Tamburini
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Elena Caproni
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100, Siena, Italy
| | - Lorenzo Croia
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Micol Ravà
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, 20132 Milan, Italy
| | - Valeria Fumagalli
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Pietro Di Lucia
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, 20132 Milan, Italy
| | - Davide Marotta
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Eleonora Sala
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Matteo Iannacone
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Diseases, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- IRCCS San Raffaele Scientific Institute, Experimental Imaging Center, 20132 Milan, Italy
| | - Priti Kumar
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Walther Mothes
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pradeep D. Uchil
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Peter Cherepanov
- The Francis Crick Institute, Chromatin Structure and Mobile DNA Laboratory, London, UK
| | | | - Massimo Pizzato
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
| | - Guido Grandi
- University of Trento, CIBIO Department, Via Sommarive 9, 28123, Trento Italy
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8
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Milazzo FM, Chaves-Sanjuan A, Minenkova O, Santapaola D, Anastasi AM, Battistuzzi G, Chiapparino C, Rosi A, Merlo Pich E, Albertoni C, Marra E, Luberto L, Viollet C, Spagnoli LG, Riccio A, Rossi A, Santoro MG, Ballabio F, Paissoni C, Camilloni C, Bolognesi M, De Santis R. Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery. Mol Ther 2023; 31:362-373. [PMID: 36114671 PMCID: PMC9476359 DOI: 10.1016/j.ymthe.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/31/2022] [Accepted: 09/12/2022] [Indexed: 02/07/2023] Open
Abstract
The uneven worldwide vaccination coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emergence of variants escaping immunity call for broadly effective and easily deployable therapeutic agents. We have previously described the human single-chain scFv76 antibody, which recognizes SARS-CoV-2 Alpha, Beta, Gamma and Delta variants. We now show that scFv76 also neutralizes the infectivity and fusogenic activity of the Omicron BA.1 and BA.2 variants. Cryoelectron microscopy (cryo-EM) analysis reveals that scFv76 binds to a well-conserved SARS-CoV-2 spike epitope, providing the structural basis for its broad-spectrum activity. We demonstrate that nebulized scFv76 has therapeutic efficacy in a severe hACE2 transgenic mouse model of coronavirus disease 2019 (COVID-19) pneumonia, as shown by body weight and pulmonary viral load data. Counteraction of infection correlates with inhibition of lung inflammation, as observed by histopathology and expression of inflammatory cytokines and chemokines. Biomarkers of pulmonary endothelial damage were also significantly reduced in scFv76-treated mice. The results support use of nebulized scFv76 for COVID-19 induced by any SARS-CoV-2 variants that have emerged so far.
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Affiliation(s)
- Ferdinando M Milazzo
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; Cryo-EM Lab, Pediatric Research Center, Fondazione Romeo e Enrica Invernizzi, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Olga Minenkova
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy
| | - Daniela Santapaola
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy
| | - Anna M Anastasi
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy
| | | | - Caterina Chiapparino
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy
| | - Antonio Rosi
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy
| | - Emilio Merlo Pich
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy
| | | | | | - Laura Luberto
- Takis Srl, Via di Castel Romano 100, 00128 Rome, Italy
| | - Cécile Viollet
- Texcell, Génavenir 5, Rue Pierre Fontaine 1, 91058 Evry Cedex, France
| | - Luigi G Spagnoli
- Histo-Cyto Service Srl, Via Bernardino Ramazzini 93, 00151 Rome, Italy
| | - Anna Riccio
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Antonio Rossi
- Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, 00133 Rome, Italy
| | - M Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Federico Ballabio
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Cristina Paissoni
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Carlo Camilloni
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; Cryo-EM Lab, Pediatric Research Center, Fondazione Romeo e Enrica Invernizzi, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Rita De Santis
- Biotechnology R&D, Alfasigma SpA, Via Pontina Km 30.400, Pomezia, 00071 Rome, Italy.
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9
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Schulte T, Chaves-Sanjuan A, Mazzini G, Speranzini V, Lavatelli F, Ferri F, Palizzotto C, Mazza M, Milani P, Nuvolone M, Vogt AC, Vogel M, Palladini G, Merlini G, Bolognesi M, Ferro S, Zini E, Ricagno S. Cryo-EM structure of ex vivo fibrils associated with extreme AA amyloidosis prevalence in a cat shelter. Nat Commun 2022; 13:7041. [PMID: 36396658 PMCID: PMC9672049 DOI: 10.1038/s41467-022-34743-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
AA amyloidosis is a systemic disease characterized by deposition of misfolded serum amyloid A protein (SAA) into cross-β amyloid in multiple organs in humans and animals. AA amyloidosis occurs at high SAA serum levels during chronic inflammation. Prion-like transmission was reported as possible cause of extreme AA amyloidosis prevalence in captive animals, e.g. 70% in cheetah and 57-73% in domestic short hair (DSH) cats kept in zoos and shelters, respectively. Herein, we present the 3.3 Å cryo-EM structure of AA amyloid extracted post-mortem from the kidney of a DSH cat with renal failure, deceased in a shelter with extreme disease prevalence. The structure reveals a cross-β architecture assembled from two 76-residue long proto-filaments. Despite >70% sequence homology to mouse and human SAA, the cat SAA variant adopts a distinct amyloid fold. Inclusion of an eight-residue insert unique to feline SAA contributes to increased amyloid stability. The presented feline AA amyloid structure is fully compatible with the 99% identical amino acid sequence of amyloid fragments of captive cheetah.
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Affiliation(s)
- Tim Schulte
- grid.419557.b0000 0004 1766 7370Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy
| | - Antonio Chaves-Sanjuan
- grid.4708.b0000 0004 1757 2822Department of Biosciences, Università degli Studi di Milano, Milan, Italy ,grid.4708.b0000 0004 1757 2822Pediatric Research Center Fondazione R.E. Invernizzi and NOLIMITS Center, Università degli Studi di Milano, Milan, Italy
| | - Giulia Mazzini
- grid.8982.b0000 0004 1762 5736Department of Molecular Medicine, University of Pavia, Pavia, Italy ,grid.419425.f0000 0004 1760 3027Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentina Speranzini
- grid.4708.b0000 0004 1757 2822Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Francesca Lavatelli
- grid.8982.b0000 0004 1762 5736Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Filippo Ferri
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara Italy
| | - Carlo Palizzotto
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara Italy
| | - Maria Mazza
- grid.425427.20000 0004 1759 3180Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, S.C. Diagnostica Specialistica, Via Bologna 148, 10154 Torino, Italy
| | - Paolo Milani
- grid.8982.b0000 0004 1762 5736Department of Molecular Medicine, University of Pavia, Pavia, Italy ,grid.419425.f0000 0004 1760 3027Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mario Nuvolone
- grid.8982.b0000 0004 1762 5736Department of Molecular Medicine, University of Pavia, Pavia, Italy ,grid.419425.f0000 0004 1760 3027Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Anne-Cathrine Vogt
- grid.5734.50000 0001 0726 5157Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland ,grid.411656.10000 0004 0479 0855Department of Rheumatology and Immunology, University Hospital Bern, 3010 Bern, Switzerland
| | - Monique Vogel
- grid.5734.50000 0001 0726 5157Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland ,grid.411656.10000 0004 0479 0855Department of Rheumatology and Immunology, University Hospital Bern, 3010 Bern, Switzerland
| | - Giovanni Palladini
- grid.8982.b0000 0004 1762 5736Department of Molecular Medicine, University of Pavia, Pavia, Italy ,grid.419425.f0000 0004 1760 3027Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giampaolo Merlini
- grid.8982.b0000 0004 1762 5736Department of Molecular Medicine, University of Pavia, Pavia, Italy ,grid.419425.f0000 0004 1760 3027Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Martino Bolognesi
- grid.4708.b0000 0004 1757 2822Department of Biosciences, Università degli Studi di Milano, Milan, Italy ,grid.4708.b0000 0004 1757 2822Pediatric Research Center Fondazione R.E. Invernizzi and NOLIMITS Center, Università degli Studi di Milano, Milan, Italy
| | - Silvia Ferro
- grid.5608.b0000 0004 1757 3470Department of Comparative Biomedicine and Food Sciences, University of Padova, viale dell’Università 16, 35020 Legnaro, Padua Italy
| | - Eric Zini
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara Italy ,grid.5608.b0000 0004 1757 3470Department of Animal Medicine, Production and Health, University of Padua, viale dell’Università 16, 35020 Legnaro, Padua Italy ,grid.7400.30000 0004 1937 0650Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Stefano Ricagno
- grid.419557.b0000 0004 1766 7370Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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10
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Bolognesi M, Rossi L, Biagi A, Coccia M, Sticozzi C, Comastri G, Aschieri D. P24 WEAREBLE CARDIOVERTER – DEFIBRILLATOR : UTILITY AND USER FRIENDLINESS. Eur Heart J Suppl 2022. [DOI: 10.1093/eurheartj/suac012.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Worldwide, cardiovascular disease are still a major mode of death, being sudden arrhythmic death (SCD)25 % of total death. Implantable cardioverter defibrillator (ICD) is an effective weapon for SCD prevention in high risk patients with reasonable expectation of survival with good functional status for >1 year. However sometimes the risk of SCD can be transient, so the use of a wearable cardioverter defibrillator (WCD) is considered.
Methods
We considered consecutively 40 patients discharged from our cardiology department of Piacenza and Castel san Giovanni that, for potentially transient high risk of SCD, weared a WCD from August 2017 to September 2021, after a systematic education session lasting 30 – 45 minutes. They are followed through remote monitoring.
Results
Out of 40 patients, with average age 66 years old and average left ventricular ejection fraction (LVEF) 29%, 88% were males, 70 % suffered from arterial hypertension, 32% diabetes mellitus, 17,5 % peripheral vascular disease, 35 % chronic renal failure, 55% heart failure, 7,5% previous stroke. 56% of these patients weared WCD for severe systolic disfunction in ischemic cardiac disease after recent myocardial infarction, after percutaneous coronary intervention or coronary artery bypass graft, 7% after removal of an infected ICD, 9 % whilst awaiting completion of diagnostic tests (chanalopathies/right arrhythmogenic ventricular cardiomyopathy), 34% after newly diagnosed cardiomyopathy.The patients were discharged in high risk mode of SCD with WCD protection.The average wearing time of WCD was 51 days and 22,98 hours daily. We received 953 trasmissions, with 21 events: 7 ventricular tachicardia, 4 Sopraventricular tachicardia and 5 T wave oversensing .Neither inappropriate shock and neither death were detected .After wearing time and after clinical evaluation, only 52% of patients were subjected to ICD implantation.
Conclusions
In our experience we may consider that WCD use is effective, safe and with a good adherence in all patients, considering wearing time. The WCD allows saving resources with less hospitalization time.
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Affiliation(s)
- M Bolognesi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE, CASTEL SAN GIOVANNI; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - L Rossi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE, CASTEL SAN GIOVANNI; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - A Biagi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE, CASTEL SAN GIOVANNI; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - M Coccia
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE, CASTEL SAN GIOVANNI; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - C Sticozzi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE, CASTEL SAN GIOVANNI; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - G Comastri
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE, CASTEL SAN GIOVANNI; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - D Aschieri
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE, CASTEL SAN GIOVANNI; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
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11
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Bolognesi M, Iconomu E, Armentano C, Turchio P, Petrini M, Moderato L, Michieletti E, Aschieri D. P303 A CASE OF MYOPERICARDITIS AFTER II DOSE COVID 19 MRNA VACCINE IN YOUNG MALE. Eur Heart J Suppl 2022. [PMCID: PMC9383961 DOI: 10.1093/eurheartj/suac012.291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
COVID 19 disease caused devasting health consequences from March 2020. The development of effective vaccines against SARs COV 2 is an important weapon to defeat this virus. However rare cases of vaccines complications have been reported including myopericarditis above all in young males that we have to follow strictly and to begin right therapy as soon as possible. Data regarding specific therapy about mypericarditis after COVid 19 vaccine are scanty. We report a case of 16 years old male with no health problems, admitted in emergency department with chest pain relieved by sitting posistion and persistent fever rised 24 h after receiving his second dose of mRNA COVID 19 vaccineA 12 lead ECG showed normal sinusal rhythm without ST changes. On admission the complete blood cells count was normal, PCR was high: 5,92 mg/dl and troponin I at high sensivity was elevated: 9249 ml/L. The patient was hospitalized in our cardiology department with suspected myopericarditis. Ecocardiography TT showed normal left ventricular ejection fraction and no pericardial effusion. We began immediately non steroidal anti inflammatory therapy at high dose (ibuprofen 600 mg x 3/die and colchicine 1 mg/die) with conseguently reduction of chest painfuls symptoms. We also began ACEi therapy. On the advice of of the infectious disease specialist we added in the 5 th day methilprednisolone 25 mg/die in consideration of an excessive acute inflammatory response and we observed a clinical improvement with an indices of inflammation reduction. Cardiac magnetic resonance (CMR) performed after 3 day in T2 weighted images showed intramyocardial and subepicardial hyperintensity localized to the mid and apical lateral, basal infero lateral, distal anterior segment, as myocardial edema. Furthermore after Injection of contrast: subepicardial late gadolinium enhancement in the same segment. Minimum (4 mm) pericardial effusion. The clinical setting was attributable as symptoms, elevated troponin above upper limit of normal, in absence of other identifiable cause of symptoms and findings, to confirmed case of acute myocarditis after vaccine in according to the “CDC case definitions”. Myocarditis after mRNA COVID 19 vaccination affect above all young males with mild and multifocal forms with risks and benefits in favour of vaccines. However we need to identify them for an early therapy. In these setting of myocarditis an early use of corticosteroids can be provided.
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Affiliation(s)
| | - E Iconomu
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | | | - P Turchio
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - M Petrini
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | - L Moderato
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
| | | | - D Aschieri
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA
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12
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Bolognesi M, Rossi L, Biagi A, Coccia M, Sticozzi C, Comastri G, Aschieri D. C7 WEARABLE CARDIOVERTER – DEFIBRILLATOR IN PATIENTS WITH HIGH RISK OF SUDDEN CARDIAC DEATH: IS IT USEFUL A PATIENT SELECTION? Eur Heart J Suppl 2022. [DOI: 10.1093/eurheartj/suac011.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background
The wearable cardioverter defibrillator (WCD) is considered in patients with increased risk of sudden cardiac death (SDC), in which implanted cardiac defibrillator (ICD) is temporary not definitively indicated. A few registry confirmed efficacy and safety of WCD and left ventricular ejection fraction recovery (LEVS)after wearing time.
Methods
We considered in our study 40 consecutively patients that used WCD in Piacenza and Castel San Giovanni Cardiology Department from August 2017 to September 2021 with recent acute myocardial infarction, newly diagnosed cardiomyopathy, primary arrhythmias syndrome awaiting diagnostic completation. They were followed by remore monitoring. The primary outcome were: the need of ICD implantation or not indication to ICD at the of the wearing time, We analyzed clinical variables related to primary outcome.
Results
Out of 40 patients, average age 66 years, average LEVS media 29%±12,5,88% were males, 32% suffered from diabetes mellitus, 35% renal failure, 55% acute and chronic heart failure, 10% previous ischemic stroke, 17% atrial fibrillation (AF), 12% cardiac arrest (ACC) after STEMI onset, 20% ventricular tachicardia (VT). 27% of these patients took amiodarone,92% beta blockers and 82% ACEi.The average wearing time of WCD was 51 days and 22,96 hours dailyAt the end of this period 48% of patients didn‘t receive ICD implantation for increasing LEVS.We evaluated clinical variables related to primary outcome with Chi Square test and Student’s t test.There weren’t significant difference regarding primary outcome between ischemic disease and other cardiophaties. The presence of AF, previous stroke, renal failure, hypertension, diabetes mellitus was more but not significant in ICD group. No significant age difference(66.8±14.1 vs 66.3±11.8, p = 0,6) neither FEVS (29.4±11.6 vs 29.5±12.7, p = 0,8) was in patients that received ICD versus not received .The clinical variables related to primary outcome only were: ACC after STEMI onset and amiodarone therapy.
Conclusions
In our study of patients with WCD, the percentage of LEVS increase is consistent with European registries. A few clinical variables may be related to ICD indication. Further studies can be useful to identify patients who need more of WCD for a lack of LEVS improvement.
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Affiliation(s)
- M Bolognesi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE DI CASTEL SAN GIOVANNI, CASTEL SAN GIOVANNI
| | - L Rossi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE DI CASTEL SAN GIOVANNI, CASTEL SAN GIOVANNI
| | - A Biagi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE DI CASTEL SAN GIOVANNI, CASTEL SAN GIOVANNI
| | - M Coccia
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE DI CASTEL SAN GIOVANNI, CASTEL SAN GIOVANNI
| | - C Sticozzi
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE DI CASTEL SAN GIOVANNI, CASTEL SAN GIOVANNI
| | - G Comastri
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE DI CASTEL SAN GIOVANNI, CASTEL SAN GIOVANNI
| | - D Aschieri
- OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE GUGLIELMO DI SALICETO, PIACENZA; OSPEDALE CIVILE DI CASTEL SAN GIOVANNI, CASTEL SAN GIOVANNI
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13
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Quilici G, Berardi A, Fabris C, Ghitti M, Punta M, Gourlay LJ, Bolognesi M, Musco G. Solution Structure of the BPSL1445 Protein of Burkholderia pseudomallei Reveals the SYLF Domain Three-Dimensional Fold. ACS Chem Biol 2022; 17:230-239. [PMID: 34968022 DOI: 10.1021/acschembio.1c00886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The SYLF domain is an evolutionary conserved protein domain with phosphatidylinositol binding ability, whose three-dimensional structure is unknown. Here, we present the solution structure and the dynamics characterization of the SYLF domain of the bacterial BPSL1445 protein. BPSL1445 is a seroreactive antigen and a diagnostic marker of Burkholderia pseudomallei, the etiological agent of melioidosis, a severe infectious disease in the tropics. The BPSL1445 SYLF domain (BPSL1445-SYLF) consists of a β-barrel core, with two flexible loops protruding out of the barrel and three helices packing on its surface. Our structure allows for a more precise definition of the boundaries of the SYLF domain compared to the previously reported one and suggests common ancestry with bacterial EipA domains. We also demonstrate by phosphatidyl-inositol phosphate arrays and nuclear magnetic resonance titrations that BPSL1445-SYLF weakly interacts with phosphoinositides, thus supporting lipid binding abilities of this domain also in prokaryotes.
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Affiliation(s)
- Giacomo Quilici
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Andrea Berardi
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Chantal Fabris
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Michela Ghitti
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Marco Punta
- Unit of Immunogenetics, Leukemia Genomics and Immunobiology and Center for Omics Sciences, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Louise J. Gourlay
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milan, Italy
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Laboratory, I.R.C.C.S. Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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14
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Nardini M, Pesce A, Bolognesi M. Truncated (2/2) hemoglobin: Unconventional structures and functional roles in vivo and in human pathogenesis. Mol Aspects Med 2021; 84:101049. [PMID: 34776271 DOI: 10.1016/j.mam.2021.101049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022]
Abstract
Truncated hemoglobins (trHbs) build a sub-class of the globin family, found in eubacteria, cyanobacteria, unicellular eukaryotes, and in higher plants; among these, selected human pathogens are found. The trHb fold is based on a 2/2 α-helical sandwich, consisting of a simplified and reduced-size version of the classical 3/3 α-helical sandwich of vertebrate and invertebrate globins. Phylogenetic analysis indicates that trHbs further branch into three groups: group I (or trHbN), group II (or trHbO), and group III (or trHbP), each group being characterized by specific structural features. Among these, a protein matrix tunnel, or a cavity system implicated in diatomic ligand diffusion through the protein matrix, is typical of group I and group II, respectively. In general, a highly intertwined network of hydrogen bonds stabilizes the heme bound ligand, despite variability of the heme distal residues in the different trHb groups. Notably, some organisms display genes from more than one trHb group, suggesting that trHbN, trHbO, and trHbP may support different functions in vivo, such as detoxification of reactive nitrogen and oxygen species, respiration, oxygen storage/sensoring, thus aiding survival of an invading microorganism. Here, structural features and proposed functions of trHbs from human pathogens are reviewed.
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Affiliation(s)
- Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
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15
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Saponaro A, Bauer D, Giese MH, Swuec P, Porro A, Gasparri F, Sharifzadeh AS, Chaves-Sanjuan A, Alberio L, Parisi G, Cerutti G, Clarke OB, Hamacher K, Colecraft HM, Mancia F, Hendrickson WA, Siegelbaum SA, DiFrancesco D, Bolognesi M, Thiel G, Santoro B, Moroni A. Gating movements and ion permeation in HCN4 pacemaker channels. Mol Cell 2021; 81:2929-2943.e6. [PMID: 34166608 PMCID: PMC8294335 DOI: 10.1016/j.molcel.2021.05.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/27/2021] [Indexed: 10/31/2022]
Abstract
The HCN1-4 channel family is responsible for the hyperpolarization-activated cation current If/Ih that controls automaticity in cardiac and neuronal pacemaker cells. We present cryoelectron microscopy (cryo-EM) structures of HCN4 in the presence or absence of bound cAMP, displaying the pore domain in closed and open conformations. Analysis of cAMP-bound and -unbound structures sheds light on how ligand-induced transitions in the channel cytosolic portion mediate the effect of cAMP on channel gating and highlights the regulatory role of a Mg2+ coordination site formed between the C-linker and the S4-S5 linker. Comparison of open/closed pore states shows that the cytosolic gate opens through concerted movements of the S5 and S6 transmembrane helices. Furthermore, in combination with molecular dynamics analyses, the open pore structures provide insights into the mechanisms of K+/Na+ permeation. Our results contribute mechanistic understanding on HCN channel gating, cyclic nucleotide-dependent modulation, and ion permeation.
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Affiliation(s)
- Andrea Saponaro
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniel Bauer
- Department of Biology, TU-Darmstadt, Darmstadt, Germany
| | - M Hunter Giese
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Paolo Swuec
- Department of Biosciences, University of Milan, Milan, Italy; Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milan, Milan, Italy
| | | | | | | | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milan, Milan, Italy; Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milan, Milan, Italy
| | - Laura Alberio
- Department of Biosciences, University of Milan, Milan, Italy; Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Giacomo Parisi
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Gabriele Cerutti
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA; Department of Anesthesiology, Columbia University, New York, NY, USA
| | - Kay Hamacher
- Department of Biology, TU-Darmstadt, Darmstadt, Germany
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Wayne A Hendrickson
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Steven A Siegelbaum
- Department of Neuroscience, Zuckerman Institute, Columbia University, New York, NY, USA
| | - Dario DiFrancesco
- Department of Biosciences, University of Milan, Milan, Italy; Institute of Biophysics-Milano, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Milan, Italy; Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milan, Milan, Italy
| | - Gerhard Thiel
- Department of Biology, TU-Darmstadt, Darmstadt, Germany
| | - Bina Santoro
- Department of Neuroscience, Zuckerman Institute, Columbia University, New York, NY, USA.
| | - Anna Moroni
- Department of Biosciences, University of Milan, Milan, Italy; Institute of Biophysics-Milano, Consiglio Nazionale delle Ricerche, Rome, Italy.
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16
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De Benedetti S, Di Pisa F, Fassi EMA, Cretich M, Musicò A, Frigerio R, Mussida A, Bombaci M, Grifantini R, Colombo G, Bolognesi M, Grande R, Zanchetta N, Gismondo MR, Mileto D, Mancon A, Gourlay LJ. Structure, Immunoreactivity, and In Silico Epitope Determination of SmSPI S. mansoni Serpin for Immunodiagnostic Application. Vaccines (Basel) 2021; 9:vaccines9040322. [PMID: 33915716 PMCID: PMC8066017 DOI: 10.3390/vaccines9040322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
The human parasitic disease Schistosomiasis is caused by the Schistosoma trematode flatworm that infects freshwaters in tropical regions of the world, particularly in Sub-Saharan Africa, South America, and the Far-East. It has also been observed as an emerging disease in Europe, due to increased immigration. In addition to improved therapeutic strategies, it is imperative to develop novel, rapid, and sensitive diagnostic tests that can detect the Schistosoma parasite, allowing timely treatment. Present diagnosis is difficult and involves microscopy-based detection of Schistosoma eggs in the feces. In this context, we present the 3.22 Å resolution crystal structure of the circulating antigen Serine protease inhibitor from S. mansoni (SmSPI), and we describe it as a potential serodiagnostic marker. Moreover, we identify three potential immunoreactive epitopes using in silico-based epitope mapping methods. Here, we confirm effective immune sera reactivity of the recombinant antigen, suggesting the further investigation of the protein and/or its predicted epitopes as serodiagnostic Schistosomiasis biomarkers.
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Affiliation(s)
- Stefano De Benedetti
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
| | - Flavio Di Pisa
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
| | - Enrico Mario Alessandro Fassi
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Angelo Musicò
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Roberto Frigerio
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Alessandro Mussida
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), Via Mario Bianco 9, 20131 Milano, Italy; (E.M.A.F.); (M.C.); (A.M.); (R.F.); (A.M.)
| | - Mauro Bombaci
- Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.B.); (R.G.)
| | - Renata Grifantini
- Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.B.); (R.G.)
| | - Giorgio Colombo
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy;
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
- Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133 Milano, Italy
| | - Romualdo Grande
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Nadia Zanchetta
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Maria Rita Gismondo
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
- Clinical Microbiology, Virology and Bioemergency Unit, Department of Biomedical and Clinical Sciences, Luigi Sacco Hospital, University of Milan, 20157 Milan, Italy
| | - Davide Mileto
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Alessandro Mancon
- UOC Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze ASST FBF Sacco, 20157 Milano, Italy; (R.G.); (N.Z.); (M.R.G.); (D.M.); (A.M.)
| | - Louise Jane Gourlay
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (S.D.B.); (F.D.P.); (M.B.)
- Correspondence: ; Tel.: +39-(0)2-5031-4914
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17
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Grinzato A, Albanese P, Marotta R, Swuec P, Saracco G, Bolognesi M, Zanotti G, Pagliano C. High-Light versus Low-Light: Effects on Paired Photosystem II Supercomplex Structural Rearrangement in Pea Plants. Int J Mol Sci 2020; 21:E8643. [PMID: 33207833 PMCID: PMC7698171 DOI: 10.3390/ijms21228643] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/14/2020] [Indexed: 11/24/2022] Open
Abstract
In plant grana thylakoid membranes Photosystem II (PSII) associates with a variable number of antenna proteins (LHCII) to form different types of supercomplexes (PSII-LHCII), whose organization is dynamically adjusted in response to light cues, with the C2S2 more abundant in high-light and the C2S2M2 in low-light. Paired PSII-LHCII supercomplexes interacting at their stromal surface from adjacent thylakoid membranes were previously suggested to mediate grana stacking. Here, we present the cryo-electron microscopy maps of paired C2S2 and C2S2M2 supercomplexes isolated from pea plants grown in high-light and low-light, respectively. These maps show a different rotational offset between the two supercomplexes in the pair, responsible for modifying their reciprocal interaction and energetic connectivity. This evidence reveals a different way by which paired PSII-LHCII supercomplexes can mediate grana stacking at diverse irradiances. Electrostatic stromal interactions between LHCII trimers almost completely overlapping in the paired C2S2 can be the main determinant by which PSII-LHCII supercomplexes mediate grana stacking in plants grown in high-light, whereas the mutual interaction of stromal N-terminal loops of two facing Lhcb4 subunits in the paired C2S2M2 can fulfil this task in plants grown in low-light. The high-light induced accumulation of the Lhcb4.3 protein in PSII-LHCII supercomplexes has been previously reported. Our cryo-electron microscopy map at 3.8 Å resolution of the C2S2 supercomplex isolated from plants grown in high-light suggests the presence of the Lhcb4.3 protein revealing peculiar structural features of this high-light-specific antenna important for photoprotection.
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Affiliation(s)
- Alessandro Grinzato
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58 B, 35121 Padova, Italy; (A.G.); (G.Z.)
| | - Pascal Albanese
- Applied Science and Technology Department–BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy; (P.A.); (G.S.)
| | - Roberto Marotta
- Center for Convergent Technologies, Electron Microscopy Facility, Istituto Italiano di Tecnologia—IIT, Via Morego 30, 16163 Genova, Italy;
| | - Paolo Swuec
- Department of BioSciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (P.S.); (M.B.)
- Cryo-Electron Microscopy Facility, Human Technopole, Via Cristina Belgioioso 171, 20157 Milano, Italy
| | - Guido Saracco
- Applied Science and Technology Department–BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy; (P.A.); (G.S.)
| | - Martino Bolognesi
- Department of BioSciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (P.S.); (M.B.)
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58 B, 35121 Padova, Italy; (A.G.); (G.Z.)
| | - Cristina Pagliano
- Applied Science and Technology Department–BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144 Torino, Italy; (P.A.); (G.S.)
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18
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Pederzoli R, Tarantino D, Gourlay LJ, Chaves-Sanjuan A, Bolognesi M. Detecting the nature and solving the crystal structure of a contaminant protein from an opportunistic pathogen. Acta Crystallogr F Struct Biol Commun 2020; 76:392-397. [PMID: 32880586 PMCID: PMC7470038 DOI: 10.1107/s2053230x20010626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/02/2020] [Indexed: 03/26/2023] Open
Abstract
The unintentional crystallization of contaminant proteins in the place of target recombinant proteins is sporadically reported, despite the availability of stringent expression/purification protocols and of software for the detection of contaminants. Typically, the contaminant protein originates from the expression organism (for example Escherichia coli), but in rare circumstances contaminants from different sources have been reported. Here, a case of contamination from a Serratia bacterial strain that occurred while attempting to crystallize an unrelated protein from Burkholderia pseudomallei (overexpressed in E. coli) is presented. The contamination led to the unintended crystallization and structure analysis of a cyanase hydratase from a bacterial strain of the Serratia genus, an opportunistic enterobacterium that grows under conditions similar to those of E. coli and that is found in a variety of habitats, including the laboratory environment. In this context, the procedures that were adopted to identify the contaminant based on crystallographic data only are presented and the crystal structure of Serrata spp. cyanase hydratase is briefly discussed.
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Affiliation(s)
- Riccardo Pederzoli
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Delia Tarantino
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Louise J. Gourlay
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
- Invernizzi Pediatric Research Center, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
- Invernizzi Pediatric Research Center, University of Milano, Via Celoria 26, 20133 Milano, Italy
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19
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Giordano D, Pesce A, Vermeylen S, Abbruzzetti S, Nardini M, Marchesani F, Berghmans H, Seira C, Bruno S, Javier Luque F, di Prisco G, Ascenzi P, Dewilde S, Bolognesi M, Viappiani C, Verde C. Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions. Comput Struct Biotechnol J 2020; 18:2132-2144. [PMID: 32913582 PMCID: PMC7451756 DOI: 10.1016/j.csbj.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/10/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
While the functions of the recently discovered cytoglobin, ubiquitously expressed in vertebrate tissues, remain uncertain, Antarctic fish provide unparalleled models to study novel protein traits that may arise from cold adaptation. We report here the spectral, ligand-binding and enzymatic properties (peroxynitrite isomerization, nitrite-reductase activity) of cytoglobin-1 from two Antarctic fish, Chaenocephalus aceratus and Dissostichus mawsoni, and present the crystal structure of D. mawsoni cytoglobin-1. The Antarctic cytoglobins-1 display high O2 affinity, scarcely compatible with an O2-supply role, a slow rate constant for nitrite-reductase activity, and do not catalyze peroxynitrite isomerization. Compared with mesophilic orthologues, the cold-adapted cytoglobins favor binding of exogenous ligands to the hexa-coordinated bis-histidyl species, a trait related to their higher rate constant for distal-His/heme-Fe dissociation relative to human cytoglobin. At the light of a remarkable 3D-structure conservation, the observed differences in ligand-binding kinetics may reflect Antarctic fish cytoglobin-1 specific features in the dynamics of the heme distal region and of protein matrix cavities, suggesting adaptation to functional requirements posed by the cold environment. Taken together, the biochemical and biophysical data presented suggest that in Antarctic fish, as in humans, cytoglobin-1 unlikely plays a role in O2 transport, rather it may be involved in processes such as NO detoxification.
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Key Words
- C.aceCygb-1*, Mutant of C.aceCygb-1
- C.aceCygb-1, Cytoglobin-1 of C. aceratus
- CO, Carbon monoxide
- CYGB, Human Cygb
- Cold-adaptation
- Cygb, Cytoglobin
- Cygb-1, Cytoglobin 1
- Cygb-2, Cytoglobin 2
- Cygbh, Hexa-coordinated bis-histidyl species
- Cygbp, Penta-coordinated Cygb
- Cytoglobin
- D.mawCygb-1*, Mutant of D.mawCygb-1
- D.mawCygb-1, Cytoglobin-1 of D. mawsoni
- DTT, Dithiothreitol
- Hb, Hemoglobin
- Ligand properties
- MD, Molecular Dynamics
- Mb, Myoglobin
- NGB, Human neuroglobin
- NO dioxygenase
- NO, Nitric oxide
- RNS, Reactive Nitrogen Species
- ROS, Reactive Oxygen Species
- X-ray structure
- p50, O2 partial pressure required to achieve half saturation
- rms, Root-mean square
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, I-16121 Genova, Italy
| | - Stijn Vermeylen
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Francesco Marchesani
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Constantí Seira
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
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20
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De Simone G, di Masi A, Vita GM, Polticelli F, Pesce A, Nardini M, Bolognesi M, Ciaccio C, Coletta M, Turilli ES, Fasano M, Tognaccini L, Smulevich G, Abbruzzetti S, Viappiani C, Bruno S, Ascenzi P. Mycobacterial and Human Nitrobindins: Structure and Function. Antioxid Redox Signal 2020; 33:229-246. [PMID: 32295384 DOI: 10.1089/ars.2019.7874] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Aims: Nitrobindins (Nbs) are evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom. The physiological role(s) of Nbs is almost unknown. Here, the structural and functional properties of ferric Mycobacterium tuberculosis Nb (Mt-Nb(III)) and ferric Homo sapiens Nb (Hs-Nb(III)) have been investigated and compared with those of ferric Arabidopsis thaliana Nb (At-Nb(III), Rhodnius prolixus nitrophorins (Rp-NP(III)s), and mammalian myoglobins. Results: Data here reported demonstrate that Mt-Nb(III), At-Nb(III), and Hs-Nb(III) share with Rp-NP(III)s the capability to bind selectively nitric oxide, but display a very low reactivity, if any, toward histamine. Data obtained overexpressing Hs-Nb in human embryonic kidney 293 cells indicate that Hs-Nb localizes mainly in the cytoplasm and partially in the nucleus, thanks to a nuclear localization sequence encompassing residues Glu124-Leu154. Human Hs-Nb corresponds to the C-terminal domain of the human nuclear protein THAP4 suggesting that Nb may act as a sensor possibly modulating the THAP4 transcriptional activity residing in the N-terminal region. Finally, we provide strong evidence that both Mt-Nb(III) and Hs-Nb(III) are able to scavenge peroxynitrite and to protect free l-tyrosine against peroxynitrite-mediated nitration. Innovation: Data here reported suggest an evolutionarily conserved function of Nbs related to their role as nitric oxide sensors and components of antioxidant systems. Conclusion: Human THAP4 may act as a sensing protein that couples the heme-based Nb(III) reactivity with gene transcription. Mt-Nb(III) seems to be part of the pool of proteins required to scavenge reactive nitrogen and oxygen species produced by the host during the immunity response.
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Affiliation(s)
| | | | | | - Fabio Polticelli
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy.,Istituto Nazionale di Fisica Nucleare, Sezione di Roma Tre, Roma, Italy
| | | | - Marco Nardini
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Milano, Italy.,Centro di Ricerche Pediatriche R.E. Invernizzi, Università di Milano, Milano, Italy
| | - Chiara Ciaccio
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
| | - Emily Samuela Turilli
- Dipartimento di Scienza ed Alta Tecnologia, Università dell'Insubria, Busto Arsizio, Italy
| | - Mauro Fasano
- Dipartimento di Scienza ed Alta Tecnologia, Università dell'Insubria, Busto Arsizio, Italy
| | - Lorenzo Tognaccini
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Sesto Fiorentino, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Sesto Fiorentino, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy
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21
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Visentin C, Musso L, Broggini L, Bonato F, Russo R, Moriconi C, Bolognesi M, Miranda E, Dallavalle S, Passarella D, Ricagno S. Embelin as Lead Compound for New Neuroserpin Polymerization Inhibitors. Life (Basel) 2020; 10:life10070111. [PMID: 32664592 PMCID: PMC7400170 DOI: 10.3390/life10070111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/25/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Familial encephalopathy with neuroserpin inclusion bodies (FENIB) is a severe and lethal neurodegenerative disease. Upon specific point mutations in the SERPINI1gene-coding for the human protein neuroserpin (NS) the resulting pathologic NS variants polymerize and accumulate within the endoplasmic reticulum of neurons in the central nervous system. To date, embelin (EMB) is the only known inhibitor of NS polymerization in vitro. This molecule is capable of preventing NS polymerization and dissolving preformed polymers. Here, we show that lowering EMB concentration results in increasing size of NS oligomers in vitro. Moreover, we observe that in cells expressing NS, the polymerization of G392E NS is reduced, but this effect is mediated by an increased proteasomal degradation rather than polymerization impairment. For these reasons we designed a systematic chemical evolution of the EMB scaffold aimed to improve its anti-polymerization properties. The effect of EMB analogs against NS polymerization was assessed in vitro. None of the EMB analogs displayed an anti-polymerization activity better than the one reported for EMB, indicating that the EMB–NS interaction surface is very specific and highly optimized. Thus, our results indicate that EMB is, to date, still the best candidate for developing a treatment against NS polymerization.
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Affiliation(s)
- Cristina Visentin
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (M.B.)
| | - Loana Musso
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Via Celoria, 2, 20133 Milan, Italy; (L.M.); (S.D.)
| | - Luca Broggini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (M.B.)
| | - Francesca Bonato
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milan, Italy; (F.B.); (D.P.)
| | - Rosaria Russo
- Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Via Fratelli Cervi, 93, 20090 Segrate, Italy;
| | - Claudia Moriconi
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Rome, Italy; (C.M.); (E.M.)
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (M.B.)
| | - Elena Miranda
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Rome, Italy; (C.M.); (E.M.)
- Istituto Pasteur—Cenci Bolognetti Foundation, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Sabrina Dallavalle
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Via Celoria, 2, 20133 Milan, Italy; (L.M.); (S.D.)
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milan, Italy; (F.B.); (D.P.)
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (M.B.)
- Correspondence: ; Tel.: +39-02-5031-4914
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22
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Visentin C, Broggini L, Sala BM, Russo R, Barbiroli A, Santambrogio C, Nonnis S, Dubnovitsky A, Bolognesi M, Miranda E, Achour A, Ricagno S. Glycosylation Tunes Neuroserpin Physiological and Pathological Properties. Int J Mol Sci 2020; 21:E3235. [PMID: 32375228 PMCID: PMC7247563 DOI: 10.3390/ijms21093235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 02/03/2023] Open
Abstract
Neuroserpin (NS) is a member of the serine protease inhibitors superfamily. Specific point mutations are responsible for its accumulation in the endoplasmic reticulum of neurons that leads to a pathological condition named familial encephalopathy with neuroserpin inclusion bodies (FENIB). Wild-type NS presents two N-glycosylation chains and does not form polymers in vivo, while non-glycosylated NS causes aberrant polymer accumulation in cell models. To date, all in vitro studies have been conducted on bacterially expressed NS, de facto neglecting the role of glycosylation in the biochemical properties of NS. Here, we report the expression and purification of human glycosylated NS (gNS) using a novel eukaryotic expression system, LEXSY. Our results confirm the correct N-glycosylation of wild-type gNS. The fold and stability of gNS are not altered compared to bacterially expressed NS, as demonstrated by the circular dichroism and intrinsic tryptophan fluorescence assays. Intriguingly, gNS displays a remarkably reduced polymerisation propensity compared to non-glycosylated NS, in keeping with what was previously observed for wild-type NS in vivo and in cell models. Thus, our results support the relevance of gNS as a new in vitro tool to study the molecular bases of FENIB.
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Affiliation(s)
- Cristina Visentin
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (B.M.S.); (M.B.)
| | - Luca Broggini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (B.M.S.); (M.B.)
| | - Benedetta Maria Sala
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (B.M.S.); (M.B.)
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden;
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Rosaria Russo
- Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Via Fratelli Cervi, 93, 20090 Segrate, Italy;
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l′Ambiente, Università degli Studi di Milano, Via Celoria, 2, 20133 Milan, Italy;
| | - Carlo Santambrogio
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza dell’Ateneo Nuovo, 1, 20126 Milan, Italy;
| | - Simona Nonnis
- Departimento di Medicina Veterinaria, Università degli Studi di Milano, Via dell’Università, 6, 26900 Lodi, Italy;
| | - Anatoly Dubnovitsky
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Rheumatology, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden;
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (B.M.S.); (M.B.)
| | - Elena Miranda
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, and Istituto Pasteur - Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Rome, Italy;
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden;
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, 20133 Milan, Italy; (C.V.); (L.B.); (B.M.S.); (M.B.)
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23
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Germani F, Nardini M, De Schutter A, Cuypers B, Berghmans H, Van Hauwaert ML, Bruno S, Mozzarelli A, Moens L, Van Doorslaer S, Bolognesi M, Pesce A, Dewilde S. Structural and Functional Characterization of the Globin-Coupled Sensors of Azotobacter vinelandii and Bordetella pertussis. Antioxid Redox Signal 2020; 32:378-395. [PMID: 31559835 DOI: 10.1089/ars.2018.7690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aims: Structural and functional characterization of the globin-coupled sensors (GCSs) from Azotobacter vinelandii (AvGReg) and Bordetella pertussis (BpeGReg). Results: Ultraviolet/visible and resonance Raman spectroscopies confirm the presence in AvGReg and BpeGReg of a globin domain capable of reversible gaseous ligand binding. In AvGReg, an influence of the transmitter domain on the heme proximal region of the globin domain can be seen, and k'CO is higher than for other GCSs. The O2 binding kinetics suggests the presence of an open and a closed conformation. As for BpeGReg, the fully oxygenated AvGReg show a very high diguanylate cyclase activity. The carbon monoxide rebinding to BpeGReg indicates that intra- and intermolecular interactions influence the ligand binding. The globin domains of both proteins (AvGReg globin domain and BpeGRegGb with cysteines (Cys16, 45, 114, 154) mutated to serines [BpeGReg-Gb*]) share the same GCS fold, a similar proximal but a different distal side structure. They homodimerize through a G-H helical bundle as in other GCSs. However, BpeGReg-Gb* shows also a second dimerization mode. Innovation: This article extends our knowledge on the GCS proteins and contributes to a better understanding of the GCSs role in the formation of bacterial biofilms. Conclusions:AvGReg and BpeGReg conform to the GCS family, share a similar overall structure, but they have different properties in terms of the ligand binding. In particular, AvGReg shows an open and a closed conformation that in the latter form will very tightly bind oxygen. BpeGReg has only one closed conformation. In both proteins, it is the fully oxygenated GCS form that catalyzes the production of the second messenger.
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Affiliation(s)
- Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | - Amy De Schutter
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Wilrijk, Belgium
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parma, Italy
| | | | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | | | | | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
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24
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Swuec P, Chaves-Sanjuan A, Camilloni C, Vanoni MA, Bolognesi M. Cryo-EM Structures of Azospirillum brasilense Glutamate Synthase in Its Oligomeric Assemblies. J Mol Biol 2019; 431:4523-4526. [PMID: 31473159 DOI: 10.1016/j.jmb.2019.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 10/26/2022]
Abstract
Bacterial NADPH-dependent glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate. GltS functional unit hosts an α-subunit (αGltS) and a β-subunit (βGltS) that assemble in different αβ oligomers in solution. Here, we present the cryo-electron microscopy structures of Azospirillum brasilense GltS in four different oligomeric states (α4β3, α4β4, α6β4 and α6β6, in the 3.5- to 4.1-Å resolution range). Our study provides a comprehensive GltS model that details the inter-protomeric assemblies and allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S]+1,+2 clusters within βGltS.
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Affiliation(s)
- Paolo Swuec
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Antonio Chaves-Sanjuan
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Maria Antonietta Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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25
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Swuec P, Lavatelli F, Tasaki M, Paissoni C, Rognoni P, Maritan M, Brambilla F, Milani P, Mauri P, Camilloni C, Palladini G, Merlini G, Ricagno S, Bolognesi M. Cryo-EM structure of cardiac amyloid fibrils from an immunoglobulin light chain AL amyloidosis patient. Nat Commun 2019; 10:1269. [PMID: 30894521 PMCID: PMC6427027 DOI: 10.1038/s41467-019-09133-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
Systemic light chain amyloidosis (AL) is a life-threatening disease caused by aggregation and deposition of monoclonal immunoglobulin light chains (LC) in target organs. Severity of heart involvement is the most important factor determining prognosis. Here, we report the 4.0 Å resolution cryo-electron microscopy map and molecular model of amyloid fibrils extracted from the heart of an AL amyloidosis patient with severe amyloid cardiomyopathy. The helical fibrils are composed of a single protofilament, showing typical 4.9 Å stacking and cross-β architecture. Two distinct polypeptide stretches (total of 77 residues) from the LC variable domain (Vl) fit the fibril density. Despite Vl high sequence variability, residues stabilizing the fibril core are conserved through different cardiotoxic Vl, highlighting structural motifs that may be common to misfolding-prone LCs. Our data shed light on the architecture of LC amyloids, correlate amino acid sequences with fibril assembly, providing the grounds for development of innovative medicines.
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Affiliation(s)
- Paolo Swuec
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Francesca Lavatelli
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Masayoshi Tasaki
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy.,Department of Morphological and Physiological Sciences, Graduate School of Health Sciences,, Kumamoto University, 4-24-1 Kuhonji, Kumamoto, 862-0976, Japan.,Department of Neurology, Graduate School of Medical Sciences, 1-1-1, Honjo, Kumamoto, 860-0811, Japan
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Paola Rognoni
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Martina Maritan
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Francesca Brambilla
- Institute for Biomedical Technologies-CNR, Via Fratelli Cervi 93, 20090, Segrate, Italy
| | - Paolo Milani
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Pierluigi Mauri
- Institute for Biomedical Technologies-CNR, Via Fratelli Cervi 93, 20090, Segrate, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Giovanni Palladini
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Giampaolo Merlini
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, and Department of Molecular Medicine, University of Pavia, P.le Golgi 19, 27100, Pavia, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy. .,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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26
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Uruburu M, Mastrangelo E, Bolognesi M, Ferrara S, Bertoni G, Milani M. Structural and functional characterization of TgpA, a critical protein for the viability of Pseudomonas aeruginosa. J Struct Biol 2019; 205:18-25. [PMID: 30599211 DOI: 10.1016/j.jsb.2018.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/29/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen associated with severe diseases, such as cystic fibrosis. During an extensive search for novel essential genes, we identified tgpA (locus PA2873) in P. aeruginosa PAO1, as a gene playing a critical role in bacterial viability. TgpA, the translated protein, is an internal membrane protein with a periplasmic soluble domain, predicted to be endowed with a transglutaminase-like fold, hosting the Cys404, His448, and Asp464 triad. We report here that Cys404 mutation hampers the essential role of TgpA in granting P. aeruginosa viability. Moreover, we present the crystal structure of the TgpA periplasmic domain at 1.6 Å resolution as a first step towards structure-activity analysis of a new potential target for the discovery of antibacterial compounds.
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Affiliation(s)
- Mónica Uruburu
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Eloise Mastrangelo
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133 Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; Centro di Ricerca Pediatrica R.E. Invernizzi, Università di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy.
| | - Mario Milani
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133 Milano, Italy.
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27
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Maritan M, Ambrosetti A, Oberti L, Barbiroli A, Diomede L, Romeo M, Lavatelli F, Sormanni P, Palladini G, Bolognesi M, Merlini G, Ricagno S. Modulating the cardiotoxic behaviour of immunoglobulin light chain dimers through point mutations. Amyloid 2019; 26:105-106. [PMID: 31343361 DOI: 10.1080/13506129.2019.1583185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Martina Maritan
- a Department of Bioscience, University of Milan , Milan , Italy
| | | | - Luca Oberti
- a Department of Bioscience, University of Milan , Milan , Italy
| | - Alberto Barbiroli
- b Department of Nutritional Science, University of Milan , Milan , Italy
| | - Luisa Diomede
- c IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Milano , Italy
| | - Margherita Romeo
- c IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri" , Milano , Italy
| | - Francesca Lavatelli
- d Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo , Pavia , Italy
| | - Pietro Sormanni
- e Department of Chemistry, University of Cambridge , Cambridge , UK
| | - Giovanni Palladini
- d Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo , Pavia , Italy
| | | | - Giampaolo Merlini
- d Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo , Pavia , Italy
| | - Stefano Ricagno
- a Department of Bioscience, University of Milan , Milan , Italy
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28
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Oberti L, Maritan M, Rognoni P, Barbiroli A, Lavatelli F, Russo R, Palladini G, Bolognesi M, Merlini G, Ricagno S. The concurrency of several biophysical traits links immunoglobulin light chains with toxicity in AL amyloidosis. Amyloid 2019; 26:107-108. [PMID: 31343357 DOI: 10.1080/13506129.2019.1583187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Luca Oberti
- a Department of Bioscience, University of Milan , Milan , Italy
| | - Martina Maritan
- a Department of Bioscience, University of Milan , Milan , Italy
| | - Paola Rognoni
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | - Alberto Barbiroli
- c DeFENS - Department of Food, Environmental and Nutritional Sciences, University of Milan , Milan , Italy
| | - Francesca Lavatelli
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | - Rosaria Russo
- d Department of Physiopathology and Transplantation, University of Milan , Milan , Italy
| | - Giovanni Palladini
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | | | - Giampaolo Merlini
- b Department of Molecular Medicine, Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, University of Pavia , Pavia , Italy
| | - Stefano Ricagno
- a Department of Bioscience, University of Milan , Milan , Italy
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29
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Capelli R, Peri C, Villa R, Nithichanon A, Conchillo-Solé O, Yero D, Gagni P, Chiari M, Lertmemongkolchai G, Cretich M, Daura X, Bolognesi M, Colombo G, Gourlay LJ. BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design against Burkholderia pseudomallei. Antibodies (Basel) 2018; 7:antib7030026. [PMID: 31544878 PMCID: PMC6640674 DOI: 10.3390/antib7030026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 11/24/2022] Open
Abstract
Due to significant advances in computational biology, protein prediction, together with antigen and epitope design, have rapidly moved from conventional methods, based on experimental approaches, to in silico-based bioinformatics methods. In this context, we report a reverse vaccinology study that identified a panel of 104 candidate antigens from the Gram-negative bacterial pathogen Burkholderia pseudomallei, which is responsible for the disease melioidosis. B. pseudomallei can cause fatal sepsis in endemic populations in the tropical regions of the world and treatment with antibiotics is mostly ineffective. With the aim of identifying potential vaccine candidates, we report the experimental validation of predicted antigen and type I fimbrial subunit, BPSL1626, which we show is able to recognize and bind human antibodies from the sera of Burkholderia infected patients and to stimulate T-lymphocytes in vitro. The prerequisite for a melioidosis vaccine, in fact, is that both antibody- and cell-mediated immune responses must be triggered. In order to reveal potential antigenic regions of the protein that may aid immunogen re-design, we also report the crystal structure of BPSL1626 at 1.9 Å resolution on which structure-based epitope predictions were based. Overall, our data suggest that BPSL1626 and three epitope regions here-identified can represent viable candidates as potential antigenic molecules.
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Affiliation(s)
- Riccardo Capelli
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
- Center for Complexity and Biosystems and Dipartimento di Fisica, Università degli Studi di Milano and INFN, 20133 Milano, Italy.
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Riccardo Villa
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Arnone Nithichanon
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Oscar Conchillo-Solé
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
| | - Daniel Yero
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
| | - Paola Gagni
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Ganjana Lertmemongkolchai
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Cryo Electron-Microscopy Laboratory, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy.
- Department of Chemistry, Università di Pavia, 27100 Pavia, Italy.
| | - Louise J Gourlay
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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Le Marchand T, de Rosa M, Salvi N, Sala BM, Andreas LB, Barbet-Massin E, Sormanni P, Barbiroli A, Porcari R, Sousa Mota C, de Sanctis D, Bolognesi M, Emsley L, Bellotti V, Blackledge M, Camilloni C, Pintacuda G, Ricagno S. Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity. Nat Commun 2018; 9:1658. [PMID: 29695721 PMCID: PMC5916882 DOI: 10.1038/s41467-018-04078-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins. The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.
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Affiliation(s)
- Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Matteo de Rosa
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Nicola Salvi
- Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France
| | - Benedetta Maria Sala
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133, Milano, Italy
| | - Riccardo Porcari
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK
| | | | | | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133, Milano, Italy
| | - Lyndon Emsley
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Vittorio Bellotti
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.
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31
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De Vitis V, Nakhnoukh C, Pinto A, Contente ML, Barbiroli A, Milani M, Bolognesi M, Molinari F, Gourlay LJ, Romano D. A stereospecific carboxyl esterase from Bacillus coagulans hosting nonlipase activity within a lipase-like fold. FEBS J 2018; 285:903-914. [PMID: 29278448 DOI: 10.1111/febs.14368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/30/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022]
Abstract
Microbial carboxylesterases are important biocatalysts that selectively hydrolyze an extensive range of esters. Here, we report the biochemical and structural characterization of an atypical carboxylesterase from Bacillus coagulans (BCE), endowed with high enantioselectivity toward different 1,2-O-isopropylideneglycerol (IPG or solketal) esters. BCE efficiently catalyzes the production of enantiopure (S)-IPG, a chiral building block for the synthesis of β-blockers, glycerophospholipids, and prostaglandins; efficient hydrolysis was observed up to 65 °C. To gain insight into the mechanistic bases of such enantioselectivity, we solved the crystal structures of BCE in apo- and glycerol-bound forms at resolutions of 1.9 and 1.8 Å, respectively. In silico docking studies on the BCE structure confirmed that IPG esters with small acyl chains (≤ C6) were easily accommodated in the active site pocket, indicating that small conformational changes are necessary to accept longer substrates. Furthermore, docking studies suggested that enantioselectivity may be due to an improved stabilization of the tetrahedral reaction intermediate for the S-enantiomer. Contrary to the above functional data implying nonlipolytic functions, BCE displays a lipase-like 3D structure that hosts a "lid" domain capping the main entrance to the active site. In lipases the lid mediates catalysis through interfacial activation, a process that we did not observe for BCE. Overall, we present the functional-structural properties of an atypical carboxyl esterase that has nonlipase-like functions, yet possesses a lipase-like 3D fold. Our data provide original enzymatic information in view of BCE applications as an inexpensive, efficient biocatalyst for the production of enantiopure (S)-IPG. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank (www.rcsb.org) under accession numbers 5O7G (apo-BCE) and 5OLU (glycerol-bound BCE).
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Affiliation(s)
- Valerio De Vitis
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | | | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Martina L Contente
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy.,School of Chemistry, University of Nottingham, UK
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Mario Milani
- Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Department of Biosciences, Università degli Studi di Milano, Italy.,Biophysics Institute, National Research Council c/o, Department of Biosciences, Università degli Studi di Milano, Italy.,Pediatric Research Center "Romeo e Enrica Invernizzi", Cryo Electron Microscopy Laboratory, University of Milano, Italy
| | - Francesco Molinari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
| | - Louise J Gourlay
- Department of Biosciences, Università degli Studi di Milano, Italy
| | - Diego Romano
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Italy
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Capelli R, Matterazzo E, Amabili M, Peri C, Gori A, Gagni P, Chiari M, Lertmemongkolchai G, Cretich M, Bolognesi M, Colombo G, Gourlay LJ. Designing Probes for Immunodiagnostics: Structural Insights into an Epitope Targeting Burkholderia Infections. ACS Infect Dis 2017; 3:736-743. [PMID: 28707874 DOI: 10.1021/acsinfecdis.7b00080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Structure-based epitope prediction drives the design of diagnostic peptidic probes to reveal specific antibodies elicited in response to infections. We previously identified a highly immunoreactive epitope from the peptidoglycan-associated lipoprotein (Pal) antigen from Burkholderia pseudomallei, which could also diagnose Burkholderia cepacia infections. Here, considering the high phylogenetic conservation within Burkholderia species, we ask whether cross-reactivity can be reciprocally displayed by the synthetic epitope from B. cenocepacia. We perform comparative analyses of the conformational preferences and diagnostic performances of the corresponding epitopes from the two Burkholderia species when presented in the context of the full-length proteins or as isolated peptides. The effects of conformation on the diagnostic potential and cross-reactivity of Pal peptide epitopes are rationalized on the basis of the 1.8 Å crystal structure of B. cenocepacia Pal and through computational analyses. Our results are discussed in the context of designing new diagnostic molecules for the early detection of infectious diseases.
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Affiliation(s)
- Riccardo Capelli
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
- Center
for Complexity and Biosystems and Dipartimento di Fisica, Università degli Studi di Milano and INFN, Via Celoria 16, 20133 Milano, Italy
| | - Elena Matterazzo
- Department
of Biosciences, Università degli Studi di Milano, Via
Celoria 26, Milano, 20133, Italy
| | - Marco Amabili
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
- Department
of Biosciences, Università degli Studi di Milano, Via
Celoria 26, Milano, 20133, Italy
| | - Claudio Peri
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
| | - Alessandro Gori
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
| | - Paola Gagni
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
| | - Marcella Chiari
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
| | - Ganjana Lertmemongkolchai
- Center
for Research and Development of Medical Diagnostic Laboratories (CMDL),
Faculty of Associated Medical Sciences, Khon Kaen University, 40002, Khon Kaen, Thailand
| | - Marina Cretich
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
| | - Martino Bolognesi
- Department
of Biosciences, Università degli Studi di Milano, Via
Celoria 26, Milano, 20133, Italy
- Pediatric
Clinical Research Center “Romeo ed Enrica Invernizzi”,
Cryo Electron-Microscopy Laboratory, Università degli Studi di Milano, Milano, 20133, Italy
| | - Giorgio Colombo
- Istituto
di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco 9, 20131 Milano, Italy
| | - Louise J. Gourlay
- Department
of Biosciences, Università degli Studi di Milano, Via
Celoria 26, Milano, 20133, Italy
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Gourlay L, Peri C, Bolognesi M, Colombo G. Structure and Computation in Immunoreagent Design: From Diagnostics to Vaccines. Trends Biotechnol 2017; 35:1208-1220. [PMID: 28739221 DOI: 10.1016/j.tibtech.2017.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022]
Abstract
Novel immunological tools for efficient diagnosis and treatment of emerging infections are urgently required. Advances in the diagnostic and vaccine development fields are continuously progressing, with reverse vaccinology and structural vaccinology (SV) methods for antigen identification and structure-based antigen (re)design playing increasingly relevant roles. SV, in particular, is predicted to be the front-runner in the future development of diagnostics and vaccines targeting challenging diseases such as AIDS and cancer. We review state-of-the-art methodologies for structure-based epitope identification and antigen design, with specific applicative examples. We highlight the implications of such methods for the engineering of biomolecules with improved immunological properties, potential diagnostic and/or therapeutic uses, and discuss the perspectives of structure-based rational design for the production of advanced immunoreagents.
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Affiliation(s)
- Louise Gourlay
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università di Milano, Milan, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy.
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Gori A, Bolognesi M, Colombo G, Gourlay LJ. Structural Vaccinology for Melioidosis Vaccine Design and Immunodiagnostics. Curr Trop Med Rep 2017. [DOI: 10.1007/s40475-017-0117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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de Rosa M, Halabelian L, Barbiroli A, Bolognesi M, Bellotti V, Ricagno S. An Asp to Asn mutation is a toxic trigger in beta-2 microglobulin: structure and biophysics. Amyloid 2017; 24:15-16. [PMID: 28434301 DOI: 10.1080/13506129.2016.1272450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Matteo de Rosa
- a Department of Biosciences , University of Milan, Milan , Italy.,b CNR Biophysics Institute , Milan , Italy
| | - Levon Halabelian
- a Department of Biosciences , University of Milan, Milan , Italy
| | | | | | - Vittorio Bellotti
- d Center for Amyloidosis and Acute Phase proteins, UCL , London , UK
| | - Stefano Ricagno
- a Department of Biosciences , University of Milan, Milan , Italy
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Tarantino D, Cannalire R, Mastrangelo E, Croci R, Querat G, Barreca ML, Bolognesi M, Manfroni G, Cecchetti V, Milani M. Targeting flavivirus RNA dependent RNA polymerase through a pyridobenzothiazole inhibitor. Antiviral Res 2016; 134:226-235. [PMID: 27649989 DOI: 10.1016/j.antiviral.2016.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 12/31/2022]
Abstract
RNA dependent RNA polymerases (RdRp) are essential enzymes for flavivirus replication. Starting from an in silico docking analysis we identified a pyridobenzothiazole compound, HeE1-2Tyr, able to inhibit West Nile and Dengue RdRps activity in vitro, which proved effective against different flaviviruses in cell culture. Crystallographic data show that HeE1-2Tyr binds between the fingers domain and the priming loop of Dengue virus RdRp (Site 1). Conversely, enzyme kinetics, binding studies and mutational analyses suggest that, during the catalytic cycle and assembly of the RdRp-RNA complex, HeE1-2Tyr might be hosted in a distinct binding site (Site 2). RdRp mutational studies, driven by in silico docking analysis, allowed us to locate the inhibition Site 2 in the thumb domain. Taken together, our results provide innovative concepts for optimization of a new class of anti-flavivirus compounds.
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Affiliation(s)
- Delia Tarantino
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy
| | - Rolando Cannalire
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Perugia, Italy
| | - Eloise Mastrangelo
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy
| | - Romina Croci
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Gilles Querat
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille university - IRD 190 - Inserm 1207 - EHESP), & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Maria Letizia Barreca
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Perugia, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy
| | - Giuseppe Manfroni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Perugia, Italy.
| | - Violetta Cecchetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Perugia, Italy
| | - Mario Milani
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-IBF, Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy.
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Camilloni C, Sala BM, Sormanni P, Porcari R, Corazza A, De Rosa M, Zanini S, Barbiroli A, Esposito G, Bolognesi M, Bellotti V, Vendruscolo M, Ricagno S. Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability. Sci Rep 2016; 6:25559. [PMID: 27150430 PMCID: PMC4858664 DOI: 10.1038/srep25559] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/20/2016] [Indexed: 01/27/2023] Open
Abstract
A wide range of human diseases is associated with mutations that, destabilizing proteins native state, promote their aggregation. However, the mechanisms leading from folded to aggregated states are still incompletely understood. To investigate these mechanisms, we used a combination of NMR spectroscopy and molecular dynamics simulations to compare the native state dynamics of Beta-2 microglobulin (β2m), whose aggregation is associated with dialysis-related amyloidosis, and its aggregation-resistant mutant W60G. Our results indicate that W60G low aggregation propensity can be explained, beyond its higher stability, by an increased average protection of the aggregation-prone residues at its surface. To validate these findings, we designed β2m variants that alter the aggregation-prone exposed surface of wild-type and W60G β2m modifying their aggregation propensity. These results allowed us to pinpoint the role of dynamics in β2m aggregation and to provide a new strategy to tune protein aggregation by modulating the exposure of aggregation-prone residues.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.,Department of Chemistry and Institute for Advanced Study, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching, Germany
| | - Benedetta Maria Sala
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Riccardo Porcari
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London NW3 2PF, UK
| | - Alessandra Corazza
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, 33100 Udine, Italy
| | - Matteo De Rosa
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Stefano Zanini
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, 33100 Udine, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milano, Italy
| | - Gennaro Esposito
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, 33100 Udine, Italy.,Science and Math Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAE
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy.,CIMAINA and CNR Istituto di Biofisica, c/o Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Vittorio Bellotti
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London NW3 2PF, UK
| | | | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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Gori A, Peri C, Quilici G, Nithichanon A, Gaudesi D, Longhi R, Gourlay L, Bolognesi M, Lertmemongkolchai G, Musco G, Colombo G. Flexible vs Rigid Epitope Conformations for Diagnostic- and Vaccine-Oriented Applications: Novel Insights from the Burkholderia pseudomallei BPSL2765 Pal3 Epitope. ACS Infect Dis 2016; 2:221-30. [PMID: 27623032 DOI: 10.1021/acsinfecdis.5b00118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Peptides seldom retain stable conformations if separated from their native protein structure. In an immunological context, this potentially affects the development of selective peptide-based bioprobes and, from a vaccine perspective, poses inherent limits in the elicitation of cross-reactive antibodies by candidate epitopes. Here, a 1,4-disubstituted-1,2,3-triazole-mediated stapling strategy was used to stabilize the native α-helical fold of the Pal3 peptidic epitope from the protein antigen PalBp (BPSL2765) from Burkholderia pseudomallei, the etiological agent of melioidosis. Whereas Pal3 shows no propensity to fold outside its native protein context, the engineered peptide (Pal3H) forms a stable α-helix, as assessed by MD, NMR, and CD structural analyses. Importantly, Pal3H shows an enhanced ability to discriminate between melioidosis patient subclasses in immune sera reactivity tests, demonstrating the potential of the stapled peptide for diagnostic purposes. With regard to antibody elicitation and related bactericidal activities, the linear peptide is shown to elicit a higher response. On these bases, we critically discuss the implications of epitope structure engineering for diagnostic- and vaccine-oriented applications.
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Affiliation(s)
- Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Giacomo Quilici
- Biomolecular NMR Laboratory,
Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, 20132 Milan, Italy
| | - Arnone Nithichanon
- Center for Research and Development of
Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical
Sciences, Khon Kaen University, 40002, Khon Kaen, Thailand
| | - Davide Gaudesi
- Biomolecular NMR Laboratory,
Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, 20132 Milan, Italy
| | - Renato Longhi
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Louise Gourlay
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, 20133, Milan, Italy
- CNR-IBF and Cimaina,
c/o Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Ganjana Lertmemongkolchai
- Center for Research and Development of
Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical
Sciences, Khon Kaen University, 40002, Khon Kaen, Thailand
| | - Giovanna Musco
- Biomolecular NMR Laboratory,
Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, 20132 Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
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Champion OL, Gourlay LJ, Scott AE, Lassaux P, Conejero L, Perletti L, Hemsley C, Prior J, Bancroft G, Bolognesi M, Titball RW. Immunisation with proteins expressed during chronic murine melioidosis provides enhanced protection against disease. Vaccine 2016; 34:1665-71. [PMID: 26917010 DOI: 10.1016/j.vaccine.2016.02.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/29/2016] [Accepted: 02/15/2016] [Indexed: 11/20/2022]
Abstract
There is an urgent need for an effective vaccine against human disease caused by Burkholderia pseudomallei, and although a wide range of candidates have been tested in mice none provide high level protection. We considered this might reflect the inability of these vaccine candidates to protect against chronic disease. Using Q-RT PCR we have identified 6 genes which are expressed in bacteria colonising spleens and lungs of chronically infected mice. Three of the genes (BPSL1897, BPSL3369 and BPSL2287) have been expressed in Escherichia coli and the encoded proteins purified. We have also included BPSL2765, a protein known to induce immune responses associated with a reduced incidence of chronic/recurrent disease in humans. Immunisation of mice with a combination of these antigens resulted in the induction of antibody responses against all of the proteins. Compared with mice immunised with capsular polysaccharide or LolC protein, mice immunised with the combination of chronic stage antigens showed enhanced protection against experimental disease in mice.
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Affiliation(s)
- Olivia L Champion
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Louise J Gourlay
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Andrew E Scott
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Patricia Lassaux
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Laura Conejero
- London School of Hygiene and Tropical Medicine, Keppler Street, London WC1E 7HT, UK
| | - Lucia Perletti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Claudia Hemsley
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Joann Prior
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK; Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Gregory Bancroft
- London School of Hygiene and Tropical Medicine, Keppler Street, London WC1E 7HT, UK
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Milan 20133, Italy; Consiglio Nazionale delle Ricerche, Institute of Biophysics, University of Milan, Milan 20133, Italy
| | - Richard W Titball
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
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40
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Saga G, Sessa F, Barbiroli A, Santambrogio C, Russo R, Sala M, Raccosta S, Martorana V, Caccia S, Noto R, Moriconi C, Miranda E, Grandori R, Manno M, Bolognesi M, Ricagno S. Embelin binds to human neuroserpin and impairs its polymerisation. Sci Rep 2016; 6:18769. [PMID: 26732982 PMCID: PMC4702122 DOI: 10.1038/srep18769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/26/2015] [Indexed: 01/07/2023] Open
Abstract
Neuroserpin (NS) is a serpin inhibitor of tissue plasminogen activator (tPA) in the brain. The polymerisation of NS pathologic mutants is responsible for a genetic dementia known as familial encephalopathy with neuroserpin inclusion bodies (FENIB). So far, a pharmacological treatment of FENIB, i.e. an inhibitor of NS polymerisation, remains an unmet challenge. Here, we present a biophysical characterisation of the effects caused by embelin (EMB a small natural compound) on NS conformers and NS polymerisation. EMB destabilises all known NS conformers, specifically binding to NS molecules with a 1:1 NS:EMB molar ratio without unfolding the NS fold. In particular, NS polymers disaggregate in the presence of EMB, and their formation is prevented. The NS/EMB complex does not inhibit tPA proteolytic activity. Both effects are pharmacologically relevant: firstly by inhibiting the NS polymerisation associated to FENIB, and secondly by potentially antagonizing metastatic processes facilitated by NS activity in the brain.
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Affiliation(s)
- Giorgia Saga
- Dipartimento di Bioscienze and CIMAINA, Università degli Studi di Milano, Milan, Italy
| | - Fabio Sessa
- Dipartimento di Bioscienze and CIMAINA, Università degli Studi di Milano, Milan, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l′Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Carlo Santambrogio
- Dipartimento di Biotecnologie e Bioscienze, Università Milano-Bicocca, Milan, Italy
| | - Rosaria Russo
- Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di MilanoItaly
| | - Michela Sala
- Dipartimento di Biotecnologie e Bioscienze, Università Milano-Bicocca, Milan, Italy
| | - Samuele Raccosta
- Istituto di Biofisica, National Research Council of Italy, Palermo, Italy
| | - Vincenzo Martorana
- Istituto di Biofisica, National Research Council of Italy, Palermo, Italy
| | - Sonia Caccia
- Dipartimento di Biotecnologie Mediche e Medicina traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Rosina Noto
- Istituto di Biofisica, National Research Council of Italy, Palermo, Italy
| | - Claudia Moriconi
- Dipartimento di Biologia e Biotecnologie Charles Darwin, and Istituto Pasteur – Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Elena Miranda
- Dipartimento di Biologia e Biotecnologie Charles Darwin, and Istituto Pasteur – Fondazione Cenci-Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Rita Grandori
- Dipartimento di Biotecnologie e Bioscienze, Università Milano-Bicocca, Milan, Italy
| | - Mauro Manno
- Istituto di Biofisica, National Research Council of Italy, Palermo, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze and CIMAINA, Università degli Studi di Milano, Milan, Italy
- Istituto di Biofisica, National Research Council of Italy, c/o Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze and CIMAINA, Università degli Studi di Milano, Milan, Italy
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41
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De Henau S, Tilleman L, Vangheel M, Luyckx E, Trashin S, Pauwels M, Germani F, Vlaeminck C, Vanfleteren JR, Bert W, Pesce A, Nardini M, Bolognesi M, De Wael K, Moens L, Dewilde S, Braeckman BP. A redox signalling globin is essential for reproduction in Caenorhabditis elegans. Nat Commun 2015; 6:8782. [PMID: 26621324 PMCID: PMC4686822 DOI: 10.1038/ncomms9782] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 10/02/2015] [Indexed: 12/17/2022] Open
Abstract
Moderate levels of reactive oxygen species (ROS) are now recognized as redox signalling molecules. However, thus far, only mitochondria and NADPH oxidases have been identified as cellular sources of ROS in signalling. Here we identify a globin (GLB-12) that produces superoxide, a type of ROS, which serves as an essential signal for reproduction in C. elegans. We find that GLB-12 has an important role in the regulation of multiple aspects in germline development, including germ cell apoptosis. We further describe how GLB-12 displays specific molecular, biochemical and structural properties that allow this globin to act as a superoxide generator. In addition, both an intra- and extracellular superoxide dismutase act as key partners of GLB-12 to create a transmembrane redox signal. Our results show that a globin can function as a driving factor in redox signalling, and how this signal is regulated at the subcellular level by multiple control layers.
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Affiliation(s)
- Sasha De Henau
- Department of Biology, Ghent University, Ghent B-9000, Belgium
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | | | - Evi Luyckx
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | - Stanislav Trashin
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Martje Pauwels
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | | | | | - Wim Bert
- Department of Biology, Ghent University, Ghent B-9000, Belgium
| | - Alessandra Pesce
- Department of Physics, University of Genova, Genova I-16146, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano I-20133, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Milano I-20133, Italy
- CNR-IBF and CIMAINA, University of Milano, Milano I-20133, Italy
| | - Karolien De Wael
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
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42
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de Rosa M, Barbiroli A, Giorgetti S, Mangione PP, Bolognesi M, Ricagno S. Decoding the Structural Bases of D76N ß2-Microglobulin High Amyloidogenicity through Crystallography and Asn-Scan Mutagenesis. PLoS One 2015; 10:e0144061. [PMID: 26625273 PMCID: PMC4666650 DOI: 10.1371/journal.pone.0144061] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/12/2015] [Indexed: 11/19/2022] Open
Abstract
D76N is the first natural variant of human β-2 microglobulin (β2m) so far identified. Contrary to the wt protein, this mutant readily forms amyloid fibres in physiological conditions, leading to a systemic and severe amyloidosis. Although the Asp76Asn mutant has been extensively characterized, the molecular bases of its instability and aggregation propensity remain elusive. In this work all Asp residues of human β2m were individually substituted to Asn; D-to-N mutants (D34N, D38N, D53N, D59N, D96N and D98N) were characterised in terms of thermodynamic stability and aggregation propensity. Moreover, crystal structures of the D38N, D53N, D59N and D98N variants were solved at high-resolution (1.24–1.70 Å). Despite showing some significant variations in their thermal stabilities, none showed the dramatic drop in melting temperature (relative to the wt protein) as observed for the pathogenic mutant. Consistently, none of the variants here described displayed any increase in aggregation propensity under the experimental conditions tested. The crystal structures confirmed that D-to-N mutations are generally well tolerated, and lead only to minor reorganization of the side chains in close proximity of the mutated residue. D38N is the only exception, where backbone readjustments and a redistribution of the surface electrostatic charges are observed. Overall, our results suggest that neither removing negative charges at sites 34, 38, 53, 59, 96 and 98, nor the difference in β2m pI, are the cause of the aggressive phenotype observed in D76N. We propose that the dramatic effects of the D76N natural mutation must be linked to effects related to the crucial location of this residue within the β2m fold.
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Affiliation(s)
- Matteo de Rosa
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Sofia Giorgetti
- Dipartimento di Medicina Molecolare, Istituto di Biochimica “A. Castellani”, Università di Pavia, Via Taramelli 3/b, 27100, Pavia, Italy
| | - Patrizia P. Mangione
- Dipartimento di Medicina Molecolare, Istituto di Biochimica “A. Castellani”, Università di Pavia, Via Taramelli 3/b, 27100, Pavia, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy
- CIMAINA and CNR-Istituto di Biofisica, c/o Università di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy
- * E-mail:
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43
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Pesce A, Bustamante JP, Bidon-Chanal A, Boechi L, Estrin DA, Luque FJ, Sebilo A, Guertin M, Bolognesi M, Ascenzi P, Nardini M. The N-terminal pre-A region of Mycobacterium tuberculosis 2/2HbN promotes NO-dioxygenase activity. FEBS J 2015; 283:305-22. [PMID: 26499089 DOI: 10.1111/febs.13571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/09/2015] [Accepted: 08/16/2015] [Indexed: 01/24/2023]
Abstract
UNLABELLED A unique defense mechanisms by which Mycobacterium tuberculosis protects itself from nitrosative stress is based on the O2 -dependent NO-dioxygenase (NOD) activity of truncated hemoglobin 2/2HbN (Mt2/2HbN). The NOD activity largely depends on the efficiency of ligand migration to the heme cavity through a two-tunnel (long and short) system; recently, it was also correlated with the presence at the Mt2/2HbN N-terminus of a short pre-A region, not conserved in most 2/2HbNs, whose deletion results in a drastic reduction of NO scavenging. In the present study, we report the crystal structure of Mt2/2HbN-ΔpreA, lacking the pre-A region, at a resolution of 1.53 Å. We show that removal of the pre-A region results in long range effects on the protein C-terminus, promoting the assembly of a stable dimer, both in the crystals and in solution. In the Mt2/2HbN-ΔpreA dimer, access of heme ligands to the short tunnel is hindered. Molecular dynamics simulations show that the long tunnel branch is the only accessible pathway for O2 -ligand migration to/from the heme, and that the gating residue Phe(62)E15 partly restricts the diameter of the tunnel. Accordingly, kinetic measurements indicate that the kon value for peroxynitrite isomerization by Mt2/2HbN-ΔpreA-Fe(III) is four-fold lower relative to the full-length protein, and that NO scavenging by Mt2/2HbN-ΔpreA-Fe(II)-O2 is reduced by 35-fold. Therefore, we speculate that Mt2/2HbN evolved to host the pre-A region as a mechanism for preventing dimerization, thus reinforcing the survival of the microorganism against the reactive nitrosative stress in macrophages. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank under accession number 5AB8.
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Affiliation(s)
| | - Juan P Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Francisco Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Anne Sebilo
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Michel Guertin
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Italy.,CNR-IBF and CIMAINA, University of Milan, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, Roma Tre University, Rome, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milan, Italy
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Gourlay LJ, Peano C, Deantonio C, Perletti L, Pietrelli A, Villa R, Matterazzo E, Lassaux P, Santoro C, Puccio S, Sblattero D, Bolognesi M. Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen BPSL2063. ACTA ACUST UNITED AC 2015; 71:2227-35. [PMID: 26527140 DOI: 10.1107/s1399004715015680] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022]
Abstract
The 1.8 Å resolution crystal structure of a conserved domain of the potential Burkholderia pseudomallei antigen and trimeric autotransporter BPSL2063 is presented as a structural vaccinology target for melioidosis vaccine development. Since BPSL2063 (1090 amino acids) hosts only one conserved domain, and the expression/purification of the full-length protein proved to be problematic, a domain-filtering library was generated using β-lactamase as a reporter gene to select further BPSL2063 domains. As a result, two domains (D1 and D2) were identified and produced in soluble form in Escherichia coli. Furthermore, as a general tool, a genomic open reading frame-filtering library from the B. pseudomallei genome was also constructed to facilitate the selection of domain boundaries from the entire ORFeome. Such an approach allowed the selection of three potential protein antigens that were also produced in soluble form. The results imply the further development of ORF-filtering methods as a tool in protein-based research to improve the selection and production of soluble proteins or domains for downstream applications such as X-ray crystallography.
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Affiliation(s)
- Louise J Gourlay
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Cecilia Deantonio
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy
| | - Lucia Perletti
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Alessandro Pietrelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Riccardo Villa
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Elena Matterazzo
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Patricia Lassaux
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Claudio Santoro
- Department of Health Sciences and IRCAD, University of Eastern Piedmont, Via Solaroli 17, 28100 Novara, Italy
| | - Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Italy
| | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, Via Weiss 2, 34128 Trieste, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
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45
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Quilici G, Berardi A, Gaudesi D, Gourlay LJ, Bolognesi M, Musco G. Backbone and side-chain (1)H, (15)N, (13)C assignment and secondary structure of BPSL1445 from Burkholderia pseudomallei. Biomol NMR Assign 2015; 9:347-350. [PMID: 25893672 DOI: 10.1007/s12104-015-9607-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
BPSL1445 is a lipoprotein produced by the Gram-negative bacterium Burkholderia pseudomallei (B. pseudomallei), the etiological agent of melioidosis. Immunodetection assays against sera patients using protein microarray suggest BPSL1445 involvement in melioidosis. Herein we report backbone, side chain NMR assignment and secondary structure for the recombinant protein.
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Affiliation(s)
- Giacomo Quilici
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Andrea Berardi
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Davide Gaudesi
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Louise J Gourlay
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy.
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46
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Halabelian L, Relini A, Barbiroli A, Penco A, Bolognesi M, Ricagno S. A covalent homodimer probing early oligomers along amyloid aggregation. Sci Rep 2015; 5:14651. [PMID: 26420657 PMCID: PMC4588566 DOI: 10.1038/srep14651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/02/2015] [Indexed: 11/20/2022] Open
Abstract
Early oligomers are crucial in amyloid aggregation; however, due to their transient nature they are among the least structurally characterized species. We focused on the amyloidogenic protein beta2-microglobulin (β2m) whose early oligomers are still a matter of debate. An intermolecular interaction between D strands of facing β2m molecules was repeatedly observed, suggesting that such interface may be relevant for β2m dimerization. In this study, by mutating Ser33 to Cys, and assembling the disulphide-stabilized β2m homodimer (DimC33), such DD strand interface was locked. Although the isolated DimC33 display a stability similar to wt β2m under native conditions, it shows enhanced amyloid aggregation propensity. Three distinct crystal structures of DimC33 suggest that dimerization through the DD interface is instrumental for enhancing DimC33 aggregation propensity. Furthermore, the crystal structure of DimC33 in complex with the amyloid-specific dye Thioflavin-T pinpoints a second interface, which likely participates in the first steps of β2m aggregation. The present data provide new insight into β2m early steps of amyloid aggregation.
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Affiliation(s)
- Levon Halabelian
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Annalisa Relini
- Dipartimento di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy
| | - Amanda Penco
- Dipartimento di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.,CIMAINA e Istituto CNR di Biofisica, Milano, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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47
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Pesce P, Cecchetto L, Brocco S, Bolognesi M, Sodhi K, Abraham NG, Sacerdoti D. Characterization of a murine model of cardiorenal syndrome type 1 by high-resolution Doppler sonography. J Ultrasound 2015; 18:229-35. [PMID: 26261465 PMCID: PMC4529411 DOI: 10.1007/s40477-014-0129-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/14/2014] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT Cardiorenal syndrome type 1 (CRS-1) is the acute kidney disfunction caused by an acute worsening of cardiac function. CRS-1 is the consequence of renal vasoconstriction secondary to renin-angiotensin system (RAS) activation. No animal models of CRS-1 are described in literature. PURPOSE To characterize a murine model of CRS-1 by using a high-resolution ultrasound echo-color Doppler system (VEVO2100). MATERIALS Post-ischemic heart failure was induced by coronary artery ligation (LAD) in seven CD1 mice. Fifteen and thirty days after surgery, mice underwent cardiac and renal echo-color Doppler. Serum creatinine and plasma renin activity were measured after killing. Animals were compared to seven CD1 control mice. RESULTS Heart failure with left ventricle dilatation (end diastolic area, p < 0.05 vs. controls) and significantly reduced ejection fraction (EF; p < 0.01 vs. controls) was evident 15 days after LAD. We measured a significant renal vasoconstriction in infarcted mice characterized by increased renal pulsatility index (PI; p < 0.05 vs. controls) associated to increased creatinine and renin levels (p < 0.05 vs. controls). CONCLUSIONS The mice model of LAD is a good model of CRS-1 evaluable by Doppler sonography and characterized by renal vasoconstriction due to the activation of the renin-angiotensin system secondary to heart failure.
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Affiliation(s)
- P. Pesce
- />Department of Medicine (DIMED), University of Padova, Padua, Italy
| | - L. Cecchetto
- />Department of Medicine (DIMED), University of Padova, Padua, Italy
| | - S. Brocco
- />Department of Medicine (DIMED), University of Padova, Padua, Italy
| | - M. Bolognesi
- />Department of Medicine (DIMED), University of Padova, Padua, Italy
| | - K. Sodhi
- />Department of Medicine, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755 USA
| | - N. G. Abraham
- />Department of Medicine, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755 USA
| | - D. Sacerdoti
- />Department of Medicine (DIMED), University of Padova, Padua, Italy
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48
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Nithichanon A, Rinchai D, Gori A, Lassaux P, Peri C, Conchillio-Solé O, Ferrer-Navarro M, Gourlay LJ, Nardini M, Vila J, Daura X, Colombo G, Bolognesi M, Lertmemonkolchai G. Sequence- and Structure-Based Immunoreactive Epitope Discovery for Burkholderia pseudomallei Flagellin. PLoS Negl Trop Dis 2015. [PMID: 26222657 PMCID: PMC4519301 DOI: 10.1371/journal.pntd.0003917] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative bacterium responsible for melioidosis, a serious and often fatal infectious disease that is poorly controlled by existing treatments. Due to its inherent resistance to the major antibiotic classes and its facultative intracellular pathogenicity, an effective vaccine would be extremely desirable, along with appropriate prevention and therapeutic management. One of the main subunit vaccine candidates is flagellin of Burkholderia pseudomallei (FliCBp). Here, we present the high resolution crystal structure of FliCBp and report the synthesis and characterization of three peptides predicted to be both B and T cell FliCBp epitopes, by both structure-based in silico methods, and sequence-based epitope prediction tools. All three epitopes were shown to be immunoreactive against human IgG antibodies and to elicit cytokine production from human peripheral blood mononuclear cells. Furthermore, two of the peptides (F51-69 and F270-288) were found to be dominant immunoreactive epitopes, and their antibodies enhanced the bactericidal activities of purified human neutrophils. The epitopes derived from this study may represent potential melioidosis vaccine components. Melioidosis is an infectious disease caused by Burkolderia pseudomallei that poses a major public health problem in Southeast Asia and northern Australia. This bacterium is difficult to treat due to its intrinsic resistance to antibiotics, poor diagnosis, and the lack of a licensed vaccine. Vaccine safety is a prime concern, therefore recombinant protein subunit and/or peptide vaccine components, may represent safer alternatives. In this context, we targeted one of the main subunit vaccine candidates tested to date, flagellin from B. pseudomallei (FliCBp) that comprises the flagellar filament that mediates bacterial motility. Based on the knowledge that activation of both cell-mediated and antibody-mediated responses must be addressed in a melioidosis vaccine, we identified B and T cell immunoreactive peptides from FliCBp, using both sequence-based and structure-based computational prediction programs, for further in vitro immunological testing. Our data confirm the accuracy of sequence-based epitope prediction tools, and two structure-based methods applied to the FliCBp crystal structure (here-described), in predicting both T- and B-cell epitopes. Moreover, we identified two epitope peptides with significant joint T-cell and B-cell activities for further development as melioidosis vaccine components.
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Affiliation(s)
- Arnone Nithichanon
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Darawan Rinchai
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Patricia Lassaux
- Department of Biosciences, CIMAINA and CNR Institute of Biophysics, University of Milan, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Oscar Conchillio-Solé
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mario Ferrer-Navarro
- Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Louise J. Gourlay
- Department of Biosciences, CIMAINA and CNR Institute of Biophysics, University of Milan, Milan, Italy
| | - Marco Nardini
- Department of Biosciences, CIMAINA and CNR Institute of Biophysics, University of Milan, Milan, Italy
| | - Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, CIMAINA and CNR Institute of Biophysics, University of Milan, Milan, Italy
| | - Ganjana Lertmemonkolchai
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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49
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Giordano D, Pesce A, Boechi L, Bustamante JP, Caldelli E, Howes BD, Riccio A, di Prisco G, Nardini M, Estrin D, Smulevich G, Bolognesi M, Verde C. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. FEBS J 2015; 282:2948-65. [PMID: 26040838 DOI: 10.1111/febs.13335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/17/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022]
Abstract
Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two α-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21 Å resolution) shows typical features of group-II truncated hemoglobins, namely the two-on-two α-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | | | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Juan Pablo Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Elena Caldelli
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Barry D Howes
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Alessia Riccio
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
| | - Dario Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Giulietta Smulevich
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Italy.,CNR-Institute of Biophysics and CIMAINA, University of Milano, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy.,Department of Biology, Roma 3 University, Italy
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50
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Tilleman L, Abbruzzetti S, Ciaccio C, De Sanctis G, Nardini M, Pesce A, Desmet F, Moens L, Van Doorslaer S, Bruno S, Bolognesi M, Ascenzi P, Coletta M, Viappiani C, Dewilde S. Structural Bases for the Regulation of CO Binding in the Archaeal Protoglobin from Methanosarcina acetivorans. PLoS One 2015; 10:e0125959. [PMID: 26047471 PMCID: PMC4457829 DOI: 10.1371/journal.pone.0125959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 03/28/2015] [Indexed: 12/02/2022] Open
Abstract
Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20)101 was mutated to Ser). The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the “more reactive” and “less reactive” conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60)B9, Tyr(61)B10, and Phe(93)E11. Trp(60)B9 and Tyr(61)B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93)E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60)B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60)B9, Tyr(61)B10, and Phe(93)E11 play a role in regulating heme/ligand affinity.
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Affiliation(s)
- Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Giampiero De Sanctis
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | | | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Stefano Bruno
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | - Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Cristiano Viappiani
- Department of Physics and Earth Sciences, University of Parma, Parma, Italy
- * E-mail: (SD); (CV)
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- * E-mail: (SD); (CV)
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