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De Sciscio ML, Nardi AN, Parisi G, Bulfaro G, Costanzo A, Gugole E, Exertier C, Freda I, Savino C, Vallone B, Montemiglio LC, D’Abramo M. Effect of Salts on the Conformational Dynamics of the Cytochrome P450 OleP. Molecules 2023; 28:molecules28020832. [PMID: 36677890 PMCID: PMC9867029 DOI: 10.3390/molecules28020832] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Cytochrome P450 OleP catalytic activity is strongly influenced by its structural dynamic conformational behavior. Here, we combine equilibrium-binding experiments with all-atom molecular dynamics simulations to clarify how different environments affect OleP conformational equilibrium between the open and the closed-catalytic competent-forms. Our data clearly show that at high-ionic strength conditions, the closed form is favored, and, very interestingly, different mechanisms, depending on the chemistry of the cations, can be used to rationalize such an effect.
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Affiliation(s)
- Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | | | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, IIT, 00185 Rome, Italy
| | - Giovanni Bulfaro
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Antonella Costanzo
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Elena Gugole
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
| | - Marco D’Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
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Exertier C, Sebastiani F, Freda I, Gugole E, Cerutti G, Parisi G, Montemiglio LC, Becucci M, Viappiani C, Bruno S, Savino C, Zamparelli C, Anselmi M, Abbruzzetti S, Smulevich G, Vallone B. Probing the Role of Murine Neuroglobin CDloop-D-Helix Unit in CO Ligand Binding and Structural Dynamics. ACS Chem Biol 2022; 17:2099-2108. [PMID: 35797699 PMCID: PMC9396615 DOI: 10.1021/acschembio.2c00172] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We produced a neuroglobin variant, namely, Ngb CDless,
with the
excised CDloop- and D-helix, directly joining the C- and E-helices.
The CDless variant retained bis-His hexacoordination, and we investigated
the role of the CDloop–D-helix unit in controlling the CO binding
and structural dynamics by an integrative approach based on X-ray
crystallography, rapid mixing, laser flash photolysis, resonance Raman
spectroscopy, and molecular dynamics simulations. Rapid mixing and
laser flash photolysis showed that ligand affinity was unchanged with
respect to the wild-type protein, albeit with increased on and off
constants for rate-limiting heme iron hexacoordination by the distal
His64. Accordingly, resonance Raman spectroscopy highlighted a more
open distal pocket in the CO complex that, in agreement with MD simulations,
likely involves His64 swinging inward and outward of the distal heme
pocket. Ngb CDless displays a more rigid overall structure with respect
to the wild type, abolishing the structural dynamics of the CDloop–D-helix
hypothesized to mediate its signaling role, and it retains ligand
binding control by distal His64. In conclusion, this mutant may represent
a tool to investigate the involvement of CDloop–D-helix in
neuroprotective signaling in a cellular or animal model.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Federico Sebastiani
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, 3227 Broadway, New York, New York 10027, United States
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, I-00161 Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
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Montemiglio LC, Gugole E, Freda I, Exertier C, D’Auria L, Chen CG, Nardi AN, Cerutti G, Parisi G, D’Abramo M, Savino C, Vallone B. Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics. Biomolecules 2021; 12:biom12010055. [PMID: 35053203 PMCID: PMC8774231 DOI: 10.3390/biom12010055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/01/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 12/16/2022] Open
Abstract
Substrate binding to the cytochrome P450 OleP is coupled to a large open-to-closed transition that remodels the active site, minimizing its exposure to the external solvent. When the aglycone substrate binds, a small empty cavity is formed between the I and G helices, the BC loop, and the substrate itself, where solvent molecules accumulate mediating substrate-enzyme interactions. Herein, we analyzed the role of this cavity in substrate binding to OleP by producing three mutants (E89Y, G92W, and S240Y) to decrease its volume. The crystal structures of the OleP mutants in the closed state bound to the aglycone 6DEB showed that G92W and S240Y occupied the cavity, providing additional contact points with the substrate. Conversely, mutation E89Y induces a flipped-out conformation of this amino acid side chain, that points towards the bulk, increasing the empty volume. Equilibrium titrations and molecular dynamic simulations indicate that the presence of a bulky residue within the cavity impacts the binding properties of the enzyme, perturbing the conformational space explored by the complexes. Our data highlight the relevance of this region in OleP substrate binding and suggest that it represents a key substrate-protein contact site to consider in the perspective of redirecting its activity towards alternative compounds.
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Affiliation(s)
- Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
| | - Elena Gugole
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
| | - Lucia D’Auria
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Cheng Giuseppe Chen
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Alessandro Nicola Nardi
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Gabriele Cerutti
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, IIT, 00185 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (C.G.C.); (A.N.N.); (M.D.)
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (L.C.M.); (C.E.)
- Correspondence: (C.S.); (B.V.); Tel.: +39-06-49910548 (C.S. & B.V.)
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy; (E.G.); (I.F.); (L.D.); (G.C.)
- Correspondence: (C.S.); (B.V.); Tel.: +39-06-49910548 (C.S. & B.V.)
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Exertier C, Montemiglio LC, Freda I, Gugole E, Parisi G, Savino C, Vallone B. Neuroglobin, clues to function and mechanism. Mol Aspects Med 2021; 84:101055. [PMID: 34876274 DOI: 10.1016/j.mam.2021.101055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/09/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
Neuroglobin is expressed in vertebrate brain and belongs to a branch of the globin family that diverged early in evolution. Sequence conservation and presence in nervous cells of several taxa suggests a relevant role in the nervous system, with tight structural restraints. Twenty years after its discovery, a rich scientific literature provides convincing evidence of the involvement of neuroglobin in sustaining neuron viability in physiological and pathological conditions however, a full and conclusive picture of its specific function, or set of functions is still lacking. The difficulty of unambiguously assigning a precise mechanism and biochemical role to neuroglobin might arise from the participation to one or more cell mechanism that redundantly guarantee the functioning of the highly specialized and metabolically demanding central nervous system of vertebrates. Here we collect findings and hypotheses arising from recent biochemical, biophysical, structural, in cell and in vivo experimental work on neuroglobin, aiming at providing an overview of the most recent literature. Proteins are said to have jobs and hobbies, it is possible that, in the case of neuroglobin, evolution has selected for it more than one job, and support to cover for its occasional failings. Disentangling the mechanisms and roles of neuroglobin is thus a challenging task that might be achieved by considering data from different disciplines and experimental approaches.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, 00161, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy.
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
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Maffei M, Montemiglio LC, Vitagliano G, Fedele L, Sellathurai S, Bucci F, Compagnone M, Chiarini V, Exertier C, Muzi A, Roscilli G, Vallone B, Marra E. The Nuts and Bolts of SARS-CoV-2 Spike Receptor-Binding Domain Heterologous Expression. Biomolecules 2021; 11:1812. [PMID: 34944456 PMCID: PMC8699011 DOI: 10.3390/biom11121812] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 10/28/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 is a highly infectious disease caused by a newly emerged coronavirus (SARS-CoV-2) that has rapidly progressed into a pandemic. This unprecedent emergency has stressed the significance of developing effective therapeutics to fight the current and future outbreaks. The receptor-binding domain (RBD) of the SARS-CoV-2 surface Spike protein is the main target for vaccines and represents a helpful "tool" to produce neutralizing antibodies or diagnostic kits. In this work, we provide a detailed characterization of the native RBD produced in three major model systems: Escherichia coli, insect and HEK-293 cells. Circular dichroism, gel filtration chromatography and thermal denaturation experiments indicated that recombinant SARS-CoV-2 RBD proteins are stable and correctly folded. In addition, their functionality and receptor-binding ability were further evaluated through ELISA, flow cytometry assays and bio-layer interferometry.
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Affiliation(s)
- Mariano Maffei
- Evvivax Biotech, Via di Castel Romano 100, 00128 Rome, Italy;
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology (IBPM), National Research Council, c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy;
| | - Grazia Vitagliano
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
| | - Luigi Fedele
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
| | - Shaila Sellathurai
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
| | - Federica Bucci
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
| | | | - Valerio Chiarini
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
| | - Cécile Exertier
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (C.E.); (B.V.)
| | - Alessia Muzi
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
| | - Giuseppe Roscilli
- Evvivax Biotech, Via di Castel Romano 100, 00128 Rome, Italy;
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
| | - Beatrice Vallone
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (C.E.); (B.V.)
| | - Emanuele Marra
- Evvivax Biotech, Via di Castel Romano 100, 00128 Rome, Italy;
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy; (G.V.); (L.F.); (S.S.); (F.B.); (V.C.); (A.M.)
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Cerutti G, Gugole E, Montemiglio LC, Turbé-Doan A, Chena D, Navarro D, Lomascolo A, Piumi F, Exertier C, Freda I, Vallone B, Record E, Savino C, Sciara G. Crystal structure and functional characterization of an oligosaccharide dehydrogenase from Pycnoporus cinnabarinus provides insights into fungal breakdown of lignocellulose. Biotechnol Biofuels 2021; 14:161. [PMID: 34294139 PMCID: PMC8296622 DOI: 10.1186/s13068-021-02003-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/23/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Fungal glucose dehydrogenases (GDHs) are FAD-dependent enzymes belonging to the glucose-methanol-choline oxidoreductase superfamily. These enzymes are classified in the "Auxiliary Activity" family 3 (AA3) of the Carbohydrate-Active enZymes database, and more specifically in subfamily AA3_2, that also includes the closely related flavoenzymes aryl-alcohol oxidase and glucose 1-oxidase. Based on sequence similarity to known fungal GDHs, an AA3_2 enzyme active on glucose was identified in the genome of Pycnoporus cinnabarinus, a model Basidiomycete able to completely degrade lignin. RESULTS In our work, substrate screening and functional characterization showed an unexpected preferential activity of this enzyme toward oligosaccharides containing a β(1→3) glycosidic bond, with the highest efficiency observed for the disaccharide laminaribiose. Despite its sequence similarity to GDHs, we defined a novel enzymatic activity, namely oligosaccharide dehydrogenase (ODH), for this enzyme. The crystallographic structures of ODH in the sugar-free form and in complex with glucose and laminaribiose unveiled a peculiar saccharide recognition mechanism which is not shared with previously characterized AA3 oxidoreductases and accounts for ODH preferential activity toward oligosaccharides. The sugar molecules in the active site of ODH are mainly stabilized through CH-π interactions with aromatic residues rather than through hydrogen bonds with highly conserved residues, as observed instead for the fungal glucose dehydrogenases and oxidases characterized to date. Finally, three sugar-binding sites were identified on ODH external surface, which were not previously observed and might be of importance in the physiological scenario. CONCLUSIONS Structure-function analysis of ODH is consistent with its role as an auxiliary enzyme in lignocellulose degradation and unveils yet another enzymatic function within the AA3 family of the Carbohydrate-Active enZymes database. Our findings allow deciphering the molecular determinants of substrate binding and provide insight into the physiological role of ODH, opening new perspectives to exploit biodiversity for lignocellulose transformation into fuels and chemicals.
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Affiliation(s)
- Gabriele Cerutti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, 10029, USA
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Linda Celeste Montemiglio
- Consiglio Nazionale delle Ricerche (CNR) Institute of Molecular Biology and Pathology, P.le A. Moro 5, 00185, Rome, Italy
| | - Annick Turbé-Doan
- INRAE, Aix Marseille Université, BBF UMR1163 Biodiversité et Biotechnologie Fongiques, 163 Avenue de Luminy, 13009, Marseille, France
| | - Dehbia Chena
- INRAE, Aix Marseille Université, BBF UMR1163 Biodiversité et Biotechnologie Fongiques, 163 Avenue de Luminy, 13009, Marseille, France
| | - David Navarro
- INRAE, Aix Marseille Université, BBF UMR1163 Biodiversité et Biotechnologie Fongiques, 163 Avenue de Luminy, 13009, Marseille, France
| | - Anne Lomascolo
- INRAE, Aix Marseille Université, BBF UMR1163 Biodiversité et Biotechnologie Fongiques, 163 Avenue de Luminy, 13009, Marseille, France
| | - François Piumi
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, UMR1161 Virologie, Maisons-Alfort, France
- INRAE, Aix Marseille Université, BBF UMR1163 Biodiversité et Biotechnologie Fongiques, 163 Avenue de Luminy, 13009, Marseille, France
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
- Consiglio Nazionale delle Ricerche (CNR) Institute of Molecular Biology and Pathology, P.le A. Moro 5, 00185, Rome, Italy
| | - Eric Record
- INRAE, Aix Marseille Université, BBF UMR1163 Biodiversité et Biotechnologie Fongiques, 163 Avenue de Luminy, 13009, Marseille, France
| | - Carmelinda Savino
- Consiglio Nazionale delle Ricerche (CNR) Institute of Molecular Biology and Pathology, P.le A. Moro 5, 00185, Rome, Italy.
| | - Giuliano Sciara
- INRAE, Aix Marseille Université, BBF UMR1163 Biodiversité et Biotechnologie Fongiques, 163 Avenue de Luminy, 13009, Marseille, France.
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7
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Parisi G, Freda I, Exertier C, Cecchetti C, Gugole E, Cerutti G, D’Auria L, Macone A, Vallone B, Savino C, Montemiglio LC. Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate. Biomolecules 2020; 10:biom10101411. [PMID: 33036250 PMCID: PMC7600006 DOI: 10.3390/biom10101411] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 11/22/2022] Open
Abstract
The cytochrome P450 OleP catalyzes the epoxidation of aliphatic carbons on both the aglycone 8.8a-deoxyoleandolide (DEO) and the monoglycosylated L-olivosyl-8.8a-deoxyoleandolide (L-O-DEO) intermediates of oleandomycin biosynthesis. We investigated the substrate versatility of the enzyme. X-ray and equilibrium binding data show that the aglycone DEO loosely fits the OleP active site, triggering the closure that prepares it for catalysis only on a minor population of enzyme. The open-to-closed state transition allows solvent molecules to accumulate in a cavity that forms upon closure, mediating protein–substrate interactions. In silico docking of the monoglycosylated L-O-DEO in the closed OleP–DEO structure shows that the L-olivosyl moiety can be hosted in the same cavity, replacing solvent molecules and directly contacting structural elements involved in the transition. X-ray structures of aglycone-bound OleP in the presence of L-rhamnose confirm the cavity as a potential site for sugar binding. All considered, we propose L-O-DEO as the optimal substrate of OleP, the L-olivosyl moiety possibly representing the molecular wedge that triggers a more efficient structural response upon substrate binding, favoring and stabilizing the enzyme closure before catalysis. OleP substrate versatility is supported by structural solvent molecules that compensate for the absence of a glycosyl unit when the aglycone is bound.
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Affiliation(s)
- Giacomo Parisi
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Current affiliation: Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161 Rome, Italy
| | - Ida Freda
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
| | - Cécile Exertier
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
| | - Cristina Cecchetti
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Current affiliation: Department of Life Sciences Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Elena Gugole
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
| | - Gabriele Cerutti
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Current affiliation: Zuckerman Mind Brain Behavior Institute, Columbia University, 3227 Broadway, New York, NY 10027, USA
| | - Lucia D’Auria
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (L.D.); (A.M.)
| | - Alberto Macone
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (L.D.); (A.M.)
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti and Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; (G.P.); (I.F.); (C.E.); (C.C.); (E.G.); (G.C.); (B.V.)
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
- Correspondence: (C.S.); (L.C.M.)
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
- Correspondence: (C.S.); (L.C.M.)
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8
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Di Rienzo L, Milanetti E, Testi C, Montemiglio LC, Baiocco P, Boffi A, Ruocco G. A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction. Comput Struct Biotechnol J 2020; 18:2678-2686. [PMID: 33101606 PMCID: PMC7548301 DOI: 10.1016/j.csbj.2020.09.020] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/24/2022] Open
Abstract
Protein-protein interactions regulate almost all cellular functions and rely on a fine tune of surface amino acids properties involved on both molecular partners. The disruption of a molecular association can be caused even by a single residue mutation, often leading to a pathological modification of a biochemical pathway. Therefore the evaluation of the effects of amino acid substitutions on binding, and the ad hoc design of protein-protein interfaces, is one of the biggest challenges in computational biology. Here, we present a novel strategy for computational mutation and optimization of protein-protein interfaces. Modeling the interaction surface properties using the Zernike polynomials, we describe the shape and electrostatics of binding sites with an ordered set of descriptors, making possible the evaluation of complementarity between interacting surfaces. With a Monte Carlo approach, we obtain protein mutants with controlled molecular complementarities. Applying this strategy to the relevant case of the interaction between Ferritin and Transferrin Receptor, we obtain a set of Ferritin mutants with increased or decreased complementarity. The extensive molecular dynamics validation of the method results confirms its efficacy, showing that this strategy represents a very promising approach in designing correct molecular interfaces.
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Affiliation(s)
- Lorenzo Di Rienzo
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Claudia Testi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | | | - Paola Baiocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Biochemical Sciences ‘A. Rossi Fanelli’ Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Boffi
- Department of Biochemical Sciences ‘A. Rossi Fanelli’ Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
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9
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Kiraga Ł, Cerutti G, Braniewska A, Strzemecki D, Sas Z, Boffi A, Savino C, Montemiglio LC, Turnham D, Seaton G, Bonamore A, Clarkson R, Dabkowski AM, Paisey SJ, Taciak B, Kucharzewska P, Rygiel TP, Król M. Biodistribution PET/CT Study of Hemoglobin-DFO- 89Zr Complex in Healthy and Lung Tumor-Bearing Mice. Int J Mol Sci 2020; 21:ijms21144991. [PMID: 32679799 PMCID: PMC7404105 DOI: 10.3390/ijms21144991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/05/2020] [Accepted: 07/11/2020] [Indexed: 01/26/2023] Open
Abstract
Proteins, as a major component of organisms, are considered the preferred biomaterials for drug delivery vehicles. Hemoglobin (Hb) has been recently rediscovered as a potential drug carrier, but its use for biomedical applications still lacks extensive investigation. To further explore the possibility of utilizing Hb as a potential tumor targeting drug carrier, we examined and compared the biodistribution of Hb in healthy and lung tumor-bearing mice, using for the first time 89Zr labelled Hb in a positron emission tomography (PET) measurement. Hb displays a very high conjugation yield in its fast and selective reaction with the maleimide-deferoxamine (DFO) bifunctional chelator. The high-resolution X-ray structure of the Hb-DFO complex demonstrated that cysteine β93 is the sole attachment moiety to the αβ-protomer of Hb. The Hb-DFO complex shows quantitative uptake of 89Zr in solution as determined by radiochromatography. Injection of 0.03 mg of Hb-DFO-89Zr complex in healthy mice indicates very high radioactivity in liver, followed by spleen and lungs, whereas a threefold increased dosage results in intensification of PET signal in kidneys and decreased signal in liver and spleen. No difference in biodistribution pattern is observed between naïve and tumor-bearing mice. Interestingly, the liver Hb uptake did not decrease upon clodronate-mediated macrophage depletion, indicating that other immune cells contribute to Hb clearance. This finding is of particular interest for rapidly developing clinical immunology and projects aiming to target, label or specifically deliver agents to immune cells.
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Affiliation(s)
- Łukasz Kiraga
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
| | - Gabriele Cerutti
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, 00-185 Rome, Italy; (G.C.); (A.B.); (A.B.)
| | - Agata Braniewska
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Damian Strzemecki
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Zuzanna Sas
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Alberto Boffi
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, 00-185 Rome, Italy; (G.C.); (A.B.); (A.B.)
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, 00-185 Rome, Italy; (C.S.); (L.C.M.)
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, 00-185 Rome, Italy; (C.S.); (L.C.M.)
| | - Daniel Turnham
- European Cancer Stem Cell Research Institute (ECSCRI), School of Biosciences, Haydn Ellis Building, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (D.T.); (G.S.); (R.C.)
| | - Gillian Seaton
- European Cancer Stem Cell Research Institute (ECSCRI), School of Biosciences, Haydn Ellis Building, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (D.T.); (G.S.); (R.C.)
| | - Alessandra Bonamore
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, 00-185 Rome, Italy; (G.C.); (A.B.); (A.B.)
| | - Richard Clarkson
- European Cancer Stem Cell Research Institute (ECSCRI), School of Biosciences, Haydn Ellis Building, Cardiff University, Cardiff CF24 4HQ, Wales, UK; (D.T.); (G.S.); (R.C.)
| | - Adam M. Dabkowski
- Wales Research & Diagnostic PET Imaging Centre (PETIC), School of Medicine, Heath Park, Cardiff University, Cardiff CF14 4XN, Wales, UK; (A.M.D.); (S.J.P.)
| | - Stephen J. Paisey
- Wales Research & Diagnostic PET Imaging Centre (PETIC), School of Medicine, Heath Park, Cardiff University, Cardiff CF14 4XN, Wales, UK; (A.M.D.); (S.J.P.)
| | - Bartłomiej Taciak
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
| | - Paulina Kucharzewska
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
| | - Tomasz P. Rygiel
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; (A.B.); (D.S.); (Z.S.); (T.P.R.)
| | - Magdalena Król
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland; (L.K.); (B.T.); (P.K.)
- Correspondence: ; Tel.: +48-22-59-362-59
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10
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Milazzo L, Exertier C, Becucci M, Freda I, Montemiglio LC, Savino C, Vallone B, Smulevich G. Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy. FEBS J 2020; 287:4082-4097. [PMID: 32034988 DOI: 10.1111/febs.15241] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/17/2023]
Abstract
Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly-loop40-48 and Gly-loop44-47 ), the F106A mutant, and the double Gly-loop44-47 /F106A mutant. Their ferric resonance Raman spectra in solution and in crystals are almost identical. In the high-frequency region, the identification of a double set of core size marker bands indicates the presence of two 6-coordinate low spin species. The resonance Raman data, together with the corresponding crystal structures, indicate the presence of two neuroglobin conformers with a reversed (A conformer) or a canonical (B conformer) heme insertion orientation. With the identification of the marker bands corresponding to each conformer, the data indicate that the B conformer increases at the expense of the A form, predominantly in the Gly-loop44-47 /F106A double mutant, as confirmed by X-ray crystallography. This is the first time that a reversed heme insertion has been identified by resonance Raman in a native 6-coordinate low-spin heme protein. This diagnostic tool could be extended to other heme proteins in order to detect heme orientational disorder, which are likely to be correlated to functionally relevant heme dynamics. DATABASE: Crystallographic structure: structural data are deposited in the Protein Data Bank under the 6RA6 PDB entry.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy.,European Laboratory for Non-Linear Spectroscopy - LENS, Florence, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Linda Celeste Montemiglio
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | | | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
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11
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Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prangé T, Brunori M, Colloc’h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCrJ 2019; 6:832-842. [PMID: 31576217 PMCID: PMC6760443 DOI: 10.1107/s2052252519008157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Life and Environmental Sciences, New York–Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli–IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Avella
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy
| | - Cécile Exertier
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thierry Prangé
- CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France
| | - Maurizio Brunori
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nathalie Colloc’h
- ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France
| | - Beatrice Vallone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
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12
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Montemiglio LC, Testi C, Ceci P, Falvo E, Pitea M, Savino C, Arcovito A, Peruzzi G, Baiocco P, Mancia F, Boffi A, des Georges A, Vallone B. Cryo-EM structure of the human ferritin-transferrin receptor 1 complex. Nat Commun 2019; 10:1121. [PMID: 30850661 PMCID: PMC6408514 DOI: 10.1038/s41467-019-09098-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [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: 09/18/2018] [Accepted: 02/13/2019] [Indexed: 12/31/2022] Open
Abstract
Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion and epitopes on CD71 for interaction with transferrin and pathogenic hosts were identified. Here, we provide the molecular basis of the CD71 ectodomain-human ferritin interaction by determining the 3.9 Å resolution single-particle cryo-electron microscopy structure of their complex and by validating our structural findings in a cellular context. The contact surfaces between the heavy-chain ferritin and CD71 largely overlap with arenaviruses and Plasmodium vivax binding regions in the apical part of the receptor ectodomain. Our data account for transferrin-independent binding of ferritin to CD71 and suggest that select pathogens may have adapted to enter cells by mimicking the ferritin access gate. The human transferrin receptor 1 (CD71) is a transmembrane protein responsible for iron uptake. Here the authors present the 3.9 Å resolution cryo-EM structure of the CD71 ectodomain-human ferritin (H-Ft) complex and find that H-Ft binds a CD71 region different from the transferrin one that overlaps with the surface recognized by select pathogens.
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Affiliation(s)
- Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Claudia Testi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy.,Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Pierpaolo Ceci
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Elisabetta Falvo
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Martina Pitea
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Largo F. Vito 1, 00168, Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161, Rome, Italy
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Russ Berrie Pavilion, Columbia University Medical Center, 1150 St Nicholas Ave, New York, NY, 10032, USA
| | - Alberto Boffi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy
| | - Amédée des Georges
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY, 10031, USA. .,Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. .,Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Beatrice Vallone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro 5, 00185, Rome, Italy. .,Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
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13
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Parisi G, Montemiglio LC, Giuffrè A, Macone A, Scaglione A, Cerutti G, Exertier C, Savino C, Vallone B. Substrate-induced conformational change in cytochrome P450 OleP. FASEB J 2018; 33:1787-1800. [PMID: 30207799 DOI: 10.1096/fj.201800450rr] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The regulation of cytochrome P450 activity is often achieved by structural transitions induced by substrate binding. We describe the conformational transition experienced upon binding by the P450 OleP, an epoxygenase involved in oleandomycin biosynthesis. OleP bound to the substrate analog 6DEB crystallized in 2 forms: one with an ensemble of open and closed conformations in the asymmetric unit and another with only the closed conformation. Characterization of OleP-6DEB binding kinetics, also using the P450 inhibitor clotrimazole, unveiled a complex binding mechanism that involves slow conformational rearrangement with the accumulation of a spectroscopically detectable intermediate where 6DEB is bound to open OleP. Data reported herein provide structural snapshots of key precatalytic steps in the OleP reaction and explain how structural rearrangements induced by substrate binding regulate activity.-Parisi, G., Montemiglio, L. C., Giuffrè, A., Macone, A., Scaglione, A., Cerutti, G., Exertier, C., Savino, C., Vallone, B. Substrate-induced conformational change in cytochrome P450 OleP.
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Affiliation(s)
- Giacomo Parisi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Linda Celeste Montemiglio
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Alessandro Giuffrè
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Alberto Macone
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Antonella Scaglione
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Gabriele Cerutti
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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14
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Calisti L, Trabuco MC, Boffi A, Testi C, Montemiglio LC, des Georges A, Benni I, Ilari A, Taciak B, Białasek M, Rygiel T, Król M, Baiocco P, Bonamore A. Engineered ferritin for lanthanide binding. PLoS One 2018; 13:e0201859. [PMID: 30102720 PMCID: PMC6089422 DOI: 10.1371/journal.pone.0201859] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 06/07/2018] [Accepted: 07/23/2018] [Indexed: 11/18/2022] Open
Abstract
Ferritin H-homopolymers have been extensively used as nanocarriers for diverse applications in the targeted delivery of drugs and imaging agents, due to their unique ability to bind the transferrin receptor (CD71), highly overexpressed in most tumor cells. In order to incorporate novel fluorescence imaging properties, we have fused a lanthanide binding tag (LBT) to the C-terminal end of mouse H-chain ferritin, HFt. The HFt-LBT possesses one high affinity Terbium binding site per each of the 24 subunits provided by six coordinating aminoacid side chains and a tryptophan residue in its close proximity and is thus endowed with strong FRET sensitization properties. Accordingly, the characteristic Terbium emission band at 544 nm for the HFt-LBT Tb(III) complex was detectable upon excitation of the tag enclosed at two order of magnitude higher intensity with respect to the wtHFt protein. X-ray data at 2.9 Å and cryo-EM at 7 Å resolution demonstrated that HFt-LBT is correctly assembled as a 24-mer both in crystal and in solution. On the basis of the intrinsic Tb(III) binding properties of the wt protein, 32 additional Tb(III) binding sites, located within the natural iron binding sites of the protein, were identified besides the 24 Tb(III) ions coordinated to the LBTs. HFt-LBT Tb(III) was demonstrated to be actively uptaken by selected tumor cell lines by confocal microscopy and FACS analysis of their FITC derivatives, although direct fluorescence from Terbium emission could not be singled out with conventional, 295-375 nm, fluorescence excitation.
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Affiliation(s)
- Lorenzo Calisti
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | | | - Alberto Boffi
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Claudia Testi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Amédée des Georges
- The City University of New York Advanced Science Research Center, New York, NY
| | - Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Bartłomiej Taciak
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Maciej Białasek
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
| | - Tomasz Rygiel
- Cellis Ltd., Warsaw, Poland
- Department of Immunology, Center for Biostructure Research, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Król
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- * E-mail:
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
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15
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Scaglione A, Monteonofrio L, Parisi G, Cecchetti C, Siepi F, Rinaldo C, Giorgi A, Verzili D, Zamparelli C, Savino C, Soddu S, Vallone B, Montemiglio LC. Effects of Y361-auto-phosphorylation on structural plasticity of the HIPK2 kinase domain. Protein Sci 2017; 27:725-737. [PMID: 29277937 DOI: 10.1002/pro.3367] [Citation(s) in RCA: 3] [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: 07/26/2017] [Revised: 11/21/2017] [Accepted: 12/13/2017] [Indexed: 12/30/2022]
Abstract
The dual-specificity activity of the homeodomain interacting protein kinase 2 (HIPK2) is regulated by cis-auto-phosphorylation of tyrosine 361 (Y361) on the activation loop. Inhibition of this process or substitution of Y361 with nonphosphorylatable amino acid residues result in aberrant HIPK2 forms that show altered functionalities, pathological-like cellular relocalization, and accumulation into cytoplasmic aggresomes. Here, we report an in vitro characterization of wild type HIPK2 kinase domain and of two mutants, one at the regulating Y361 (Y361F, mimicking a form of HIPK2 lacking Y361 phosphorylation) and another at the catalytic lysine 228 (K228A, inactivating the enzyme). Gel filtration and thermal denaturation analyzes along with equilibrium binding experiments and kinase assays performed in the presence or absence of ATP-competitors were performed. The effects induced by mutations on overall stability, oligomerization and activity support the existence of different conformations of the kinase domain linked to Y361 phosphorylation. In addition, our in vitro data are consistent with both the cross-talk between the catalytic site and the activation loop of HIPK2 and the aberrant activities and accumulation previously reported for the Y361 nonphosphorylated HIPK2 in mammalian cells.
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Affiliation(s)
- Antonella Scaglione
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Laura Monteonofrio
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy
| | - Giacomo Parisi
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Cristina Cecchetti
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Francesca Siepi
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy
| | - Cinzia Rinaldo
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy.,CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, Rome, 00185, Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Daniela Verzili
- CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, Rome, 00185, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Carmelinda Savino
- CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, Rome, 00185, Italy
| | - Silvia Soddu
- Unit of Cellular Networks and Molecular Therapeutic Targets, Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute - IRCCS, Via Elio Chianesi, 53, Rome, 00144, Italy
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
| | - Linda Celeste Montemiglio
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome.,Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli", Sapienza Università di Roma, P.le A. Moro 5, 00185, Italy, Rome
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16
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Scaglione A, Fullone MR, Montemiglio LC, Parisi G, Zamparelli C, Vallone B, Savino C, Grgurina I. Structure of the adenylation domain Thr1 involved in the biosynthesis of 4-chlorothreonine in Streptomyces sp. OH-5093-protein flexibility and molecular bases of substrate specificity. FEBS J 2017; 284:2981-2999. [PMID: 28704585 DOI: 10.1111/febs.14163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 05/19/2017] [Accepted: 07/10/2017] [Indexed: 12/13/2022]
Abstract
We determined the crystal structure of Thr1, the self-standing adenylation domain involved in the nonribosomal-like biosynthesis of free 4-chlorothreonine in Streptomyces sp. OH-5093. Thr1 shows two monomers in the crystallographic asymmetric unit with different relative orientations of the C- and N-terminal subdomains both in the presence of substrates and in the unliganded form. Cocrystallization with substrates, adenosine 5'-triphosphate and l-threonine, yielded one monomer containing the two substrates and the other in complex with l-threonine adenylate, locked in a postadenylation state. Steady-state kinetics showed that Thr1 activates l-Thr and its stereoisomers, as well as d-Ala, l- and d-Ser, albeit with lower efficiency. Modeling of these substrates in the active site highlighted the molecular bases of substrate discrimination. This work provides the first crystal structure of a threonine-activating adenylation enzyme, a contribution to the studies on conformational rearrangement in adenylation domains and on substrate recognition in nonribosomal biosynthesis. DATABASE Structural data are available in the Protein Data Bank under the accession number 5N9W and 5N9X.
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Affiliation(s)
- Antonella Scaglione
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Maria Rosaria Fullone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Giacomo Parisi
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Carlotta Zamparelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR - National Research Council of Italy, Rome, Italy
| | - Ingeborg Grgurina
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Italy
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17
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Scaglione A, Montemiglio LC, Parisi G, Asteriti IA, Bruni R, Cerutti G, Testi C, Savino C, Mancia F, Lavia P, Vallone B. Subcellular localization of the five members of the human steroid 5α-reductase family. Biochim Open 2017; 4:99-106. [PMID: 29082129 PMCID: PMC5656259 DOI: 10.1016/j.biopen.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In humans the steroid 5α-reductase (SRD5A) family comprises five integral membrane enzymes that carry out reduction of a double bond in lipidic substrates: Δ4-3-keto steroids, polyprenol and trans-enoyl CoA. The best-characterized reaction is the conversion of testosterone into the more potent dihydrotestosterone carried out by SRD5A1-2. Some controversy exists on their possible nuclear or endoplasmic reticulum localization. We report the cloning and transient expression in HeLa cells of the five members of the human steroid 5α-reductase family as both N- and C-terminus green fluorescent protein tagged protein constructs. Following the intrinsic fluorescence of the tag, we have determined that the subcellular localization of these enzymes is in the endoplasmic reticulum, upon expression in HeLa cells. The presence of the tag at either end of the polypeptide chain can affect protein expression and, in the case of trans enoyl-CoA reductase, it induces the formation of protein aggregates. All members of human testosterone 5α-reductase family were expressed in HeLa cells. Subcellular localization of SRD5A proteins in the endoplasmic reticulum is reported. The effect of GFP tagging at N- or C-term on SRD5A proteins expression was assessed. The TECRL gene is expressed for the first time and its product localizes in the ER.
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Affiliation(s)
- Antonella Scaglione
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti Dept. of Biochemical Sciences, Sapienza University of Rome
| | - Giacomo Parisi
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy
| | | | - Renato Bruni
- New York Consortium on Membrane Protein Structure, New York, NY 10027, USA
| | - Gabriele Cerutti
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy
| | - Claudia Testi
- Center for Life Nano Science@Sapienza, IIT, V.le Regina Elena 291, Rome I-00185, Italy
| | | | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | | | - Beatrice Vallone
- Dept. of Biochemical Sciences, Sapienza University of Rome, P.le A.Moro 5, 00185, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti Dept. of Biochemical Sciences, Sapienza University of Rome.,Schaefer Research Scholar at Columbia University and Fellow of the Italian Academy for Advanced Studies in America at Columbia University
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18
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de Turris V, Cardoso Trabuco M, Peruzzi G, Boffi A, Testi C, Vallone B, Celeste Montemiglio L, Georges AD, Calisti L, Benni I, Bonamore A, Baiocco P. Humanized archaeal ferritin as a tool for cell targeted delivery. Nanoscale 2017; 9:647-655. [PMID: 27942679 DOI: 10.1039/c6nr07129e] [Citation(s) in RCA: 23] [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] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Human ferritins have been extensively studied to be used as nanocarriers for diverse applications and could represent a convenient alternative for targeted delivery of anticancer drugs and imaging agents. However, the most relevant limitation to their applications is the need for highly acidic experimental conditions during the initial steps of particle/cargo assembly, a process that could affect both drug stability and the complete reassembly of the ferritin cage. To overcome this issue the unique assembly of Archaeoglobus fulgidus ferritin was genetically engineered by changing a surface exposed loop of 12 amino acids connecting B and C helices to mimic the sequence of the analogous human H-chain ferritin loop. This new chimeric protein was shown to maintain the unique, cation linked, association-dissociation properties of Archaeoglobus fulgidus ferritin occurring at neutral pH values, while exhibiting the typical human H-homopolymer recognition by the transferrin receptor TfR1. The chimeric protein was confirmed to be actively and specifically internalized by HeLa cells, thus representing a unique nanotechnological tool for cell-targeted delivery of possible payloads for diagnostic or therapeutic purposes. Moreover, it was demonstrated that the 12 amino acids' loop is necessary and sufficient for binding to the transferrin receptor. The three-dimensional structure of the humanized Archaeoglobus ferritin has been obtained both as crystals by X-ray diffraction and in solution by cryo-EM.
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Affiliation(s)
- Valeria de Turris
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
| | | | - Giovanna Peruzzi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
| | - Alberto Boffi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy. and Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro, 7, 00185, Rome, Italy
| | - Claudia Testi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
| | - Beatrice Vallone
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro, 7, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Amédée Des Georges
- The City University of New York Advanced Science Research Center 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - Lorenzo Calisti
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy
| | - Paola Baiocco
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, Rome 00161, Italy.
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19
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Barteri M, De Carolis R, Marinelli F, Tomassetti G, Montemiglio LC. Effects of microwaves (900 MHz) on peroxidase systems: A comparison between lactoperoxidase and horseradish peroxidase. Electromagn Biol Med 2015; 35:126-33. [PMID: 25577980 DOI: 10.3109/15368378.2014.1002135] [Citation(s) in RCA: 2] [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] [Indexed: 11/13/2022]
Abstract
This work shows the effects of exposure to an electromagnetic field at 900 MHz on the catalytic activity of the enzymes lactoperoxidase (LPO) and horseradish peroxidase (HRP). Experimental evidence that irradiation causes conformational changes of the active sites and influences the formation and stability of the intermediate free radicals is documented by measurements of enzyme kinetics, circular dichroism spectroscopy (CD) and cyclic voltammetry.
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Affiliation(s)
- Mario Barteri
- a Department of Chemistry , "Sapienza" University of Rome , Rome , Italy
| | - Roberta De Carolis
- b National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) , Rome , Italy
| | - Fiorenzo Marinelli
- c National Research Council of Italy (CNR), Instituto di Genetica Molecolare (IGM) , Bologna , Italy.,d SC Laboratory of Muscoloskeletal Cell Biology, Istituto Ortopedico Rizzoli (IOR) , Bologna , Italy
| | - Goliardo Tomassetti
- e Institute of Radioastronomy, Italian National Institute for Astrophysics (INAF) , Bologna , Italy
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20
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Montemiglio LC, Macone A, Ardiccioni C, Avella G, Vallone B, Savino C. Redirecting P450 EryK Specificity by Rational Site-Directed Mutagenesis. Biochemistry 2013; 52:3678-87. [DOI: 10.1021/bi400223j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Linda Celeste Montemiglio
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Alberto Macone
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Chiara Ardiccioni
- Departments of Physiology & Cellular Biophysics, Columbia University College of Physicians & Surgeons, Russ Berrie Pavilion, 1150 St. Nicholas Avenue, New York, New York 10032, United States
| | - Giovanna Avella
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Carmelinda Savino
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
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21
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Montemiglio LC, Gianni S, Vallone B, Savino C. Azole Drugs Trap Cytochrome P450 EryK in Alternative Conformational States,. Biochemistry 2010; 49:9199-206. [DOI: 10.1021/bi101062v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linda Celeste Montemiglio
- Department of Biochemical Sciences, “Sapienza” University of Rome and CNR Institute of Molecular Biology and Pathology, P. le A. Moro 5, 00185 Rome, Italy
| | - Stefano Gianni
- Department of Biochemical Sciences, “Sapienza” University of Rome and CNR Institute of Molecular Biology and Pathology, P. le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences, “Sapienza” University of Rome and CNR Institute of Molecular Biology and Pathology, P. le A. Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Department of Biochemical Sciences, “Sapienza” University of Rome and CNR Institute of Molecular Biology and Pathology, P. le A. Moro 5, 00185 Rome, Italy
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