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Kliza KW, Song W, Pinzuti I, Schaubeck S, Kunzelmann S, Kuntin D, Fornili A, Pandini A, Hofmann K, Garnett JA, Stieglitz B, Husnjak K. N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling. Cell Death Discov 2024; 10:183. [PMID: 38643192 PMCID: PMC11032371 DOI: 10.1038/s41420-024-01913-8] [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: 01/14/2024] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/22/2024] Open
Abstract
Signalling through TNFR1 modulates proinflammatory gene transcription and programmed cell death, and its impairment causes autoimmune diseases and cancer. NEDD4-binding protein 1 (N4BP1) is a critical suppressor of proinflammatory cytokine production that acts as a regulator of innate immune signalling and inflammation. However, our current understanding about the molecular properties that enable N4BP1 to exert its suppressive potential remain limited. Here, we show that N4BP1 is a novel linear ubiquitin reader that negatively regulates NFκB signalling by its unique dimerization-dependent ubiquitin-binding module that we named LUBIN. Dimeric N4BP1 strategically positions two non-selective ubiquitin-binding domains to ensure preferential recognition of linear ubiquitin. Under proinflammatory conditions, N4BP1 is recruited to the nascent TNFR1 signalling complex, where it regulates duration of proinflammatory signalling in LUBIN-dependent manner. N4BP1 deficiency accelerates TNFα-induced cell death by increasing complex II assembly. Under proapoptotic conditions, caspase-8 mediates proteolytic processing of N4BP1, resulting in rapid degradation of N4BP1 by the 26 S proteasome, and acceleration of apoptosis. In summary, our findings demonstrate that N4BP1 dimerization creates a novel type of ubiquitin reader that selectively recognises linear ubiquitin which enables the timely and coordinated regulation of TNFR1-mediated inflammation and cell death.
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Affiliation(s)
- Katarzyna W Kliza
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany.
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany.
| | - Wei Song
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Irene Pinzuti
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Simone Schaubeck
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - David Kuntin
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany
- Department of Biology, University of York, Wentworth Way, York, UK
| | - Arianna Fornili
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - Benjamin Stieglitz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
| | - Koraljka Husnjak
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany.
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2
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans. bioRxiv 2023:2023.12.10.570962. [PMID: 38106198 PMCID: PMC10723406 DOI: 10.1101/2023.12.10.570962] [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] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual dynamic trimer arrangement with a positively charged external surface and a negatively charged solvent exposed internal cavity. Through Molecular Dynamics (MD) simulations, we show how the GAG chondroitin-4-sulphate associates with the Lcl-CTD surface via unique binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Anna K. Antonovic
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E. McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Carlton O. Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giulia Mastroianni
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M. Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Arianna Fornili
- School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, UK
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3
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Sonne A, Antonovic AK, Melhedegaard E, Akter F, Andersen JL, Jungbluth H, Witting N, Vissing J, Zanoteli E, Fornili A, Ochala J. Abnormal myosin post-translational modifications and ATP turnover time associated with human congenital myopathy-related RYR1 mutations. Acta Physiol (Oxf) 2023; 239:e14035. [PMID: 37602753 PMCID: PMC10909445 DOI: 10.1111/apha.14035] [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: 05/30/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
AIM Conditions related to mutations in the gene encoding the skeletal muscle ryanodine receptor 1 (RYR1) are genetic muscle disorders and include congenital myopathies with permanent weakness, as well as episodic phenotypes such as rhabdomyolysis/myalgia. Although RYR1 dysfunction is the primary mechanism in RYR1-related disorders, other downstream pathogenic events are less well understood and may include a secondary remodeling of major contractile proteins. Hence, in the present study, we aimed to investigate whether congenital myopathy-related RYR1 mutations alter the regulation of the most abundant contractile protein, myosin. METHODS We used skeletal muscle tissues from five patients with RYR1-related congenital myopathy and compared those with five controls and five patients with RYR1-related rhabdomyolysis/myalgia. We then defined post-translational modifications on myosin heavy chains (MyHCs) using LC/MS. In parallel, we determined myosin relaxed states using Mant-ATP chase experiments and performed molecular dynamics (MD) simulations. RESULTS LC/MS revealed two additional phosphorylations (Thr1309-P and Ser1362-P) and one acetylation (Lys1410-Ac) on the β/slow MyHC of patients with congenital myopathy. This method also identified six acetylations that were lacking on MyHC type IIa of these patients (Lys35-Ac, Lys663-Ac, Lys763-Ac, Lys1171-Ac, Lys1360-Ac, and Lys1733-Ac). MD simulations suggest that modifying myosin Ser1362 impacts the protein structure and dynamics. Finally, Mant-ATP chase experiments showed a faster ATP turnover time of myosin heads in the disordered-relaxed conformation. CONCLUSIONS Altogether, our results suggest that RYR1 mutations have secondary negative consequences on myosin structure and function, likely contributing to the congenital myopathic phenotype.
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Affiliation(s)
- Alexander Sonne
- Department of Biomedical Sciences, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Anna Katarina Antonovic
- Department of Chemistry, School of Physical and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Elise Melhedegaard
- Department of Biomedical Sciences, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Fariha Akter
- Department of Chemistry, School of Physical and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Jesper L. Andersen
- Department of Orthopaedic Surgery, Institute of Sports Medicine CopenhagenCopenhagen University Hospital, Bispebjerg and FrederiksbergCopenhagenDenmark
- Center for Healthy Aging, Department of Clinical MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Heinz Jungbluth
- Department of Paediatric NeurologyEvelina London Children's HospitalLondonUK
- Randall Centre for Cell and Molecular Biophysics, Muscle Signalling Section, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Nanna Witting
- Copenhagen Neuromuscular Center, Department of NeurologyUniversity of CopenhagenCopenhagenDenmark
| | - John Vissing
- Copenhagen Neuromuscular Center, Department of NeurologyUniversity of CopenhagenCopenhagenDenmark
| | - Edmar Zanoteli
- Departamento de Neurologia, Faculdade de Medicina, Hospital das ClínicasUniversidade de São PauloSão PauloBrazil
| | - Arianna Fornili
- Department of Chemistry, School of Physical and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Julien Ochala
- Department of Biomedical Sciences, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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4
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Akter F, Ochala J, Fornili A. Binding pocket dynamics along the recovery stroke of human β-cardiac myosin. PLoS Comput Biol 2023; 19:e1011099. [PMID: 37200380 DOI: 10.1371/journal.pcbi.1011099] [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] [Received: 12/05/2022] [Revised: 05/31/2023] [Accepted: 04/12/2023] [Indexed: 05/20/2023] Open
Abstract
The druggability of small-molecule binding sites can be significantly affected by protein motions and conformational changes. Ligand binding, protein dynamics and protein function have been shown to be closely interconnected in myosins. The breakthrough discovery of omecamtiv mecarbil (OM) has led to an increased interest in small molecules that can target myosin and modulate its function for therapeutic purposes (myosin modulators). In this work, we use a combination of computational methods, including steered molecular dynamics, umbrella sampling and binding pocket tracking tools, to follow the evolution of the OM binding site during the recovery stroke transition of human β-cardiac myosin. We found that steering two internal coordinates of the motor domain can recapture the main features of the transition and in particular the rearrangements of the binding site, which shows significant changes in size, shape and composition. Possible intermediate conformations were also identified, in remarkable agreement with experimental findings. The differences in the binding site properties observed along the transition can be exploited for the future development of conformation-selective myosin modulators.
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Affiliation(s)
- Fariha Akter
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Julien Ochala
- Department of Biomedical Sciences, University of Copenhagen, København N, Denmark
- Centre of Human and Applied Physiological Sciences, King's College London, London, United Kingdom
| | - Arianna Fornili
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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5
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Katarina Antonovic A, Ochala J, Fornili A. A rational approach to selective targeting of skeletal myosin. Biophys J 2023; 122:117a. [PMID: 36782512 DOI: 10.1016/j.bpj.2022.11.806] [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: 02/12/2023] Open
Affiliation(s)
- Anna Katarina Antonovic
- School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Julien Ochala
- Department of Biomedical Sciences, University of Copenhagen, Denmark, Denmark; Centre of Human and Applied Physiological Sciences, King's College London, London, United Kingdom
| | - Arianna Fornili
- School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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6
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Antonovic AK, Ochala J, Fornili A. Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin. Biophys J 2023; 122:54-62. [PMID: 36451546 PMCID: PMC9822794 DOI: 10.1016/j.bpj.2022.11.2942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/11/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
The development of small molecule myosin modulators has seen an increased effort in recent years due to their possible use in the treatment of cardiac and skeletal myopathies. Omecamtiv mecarbil (OM) is the first-in-class cardiac myotrope and the first to enter clinical trials. Its selectivity toward slow/beta-cardiac myosin lies at the heart of its function; however, little is known about the underlying reasons for selectivity to this isoform as opposed to other closely related ones such as fast-type skeletal myosins. In this work, we compared the structure and dynamics of the OM binding site in cardiac and in fasttype IIa skeletal myosin to identify possible reasons for OM selectivity. We found that the different shape, size, and composition of the binding pocket in skeletal myosin directly affects the binding mode and related affinity of OM, which is potentially a result of weaker interactions and less optimal molecular recognition. Moreover, we identified a side pocket adjacent to the OM binding site that shows increased accessibility in skeletal myosin compared with the cardiac isoform. These findings could pave the way to the development of skeletal-selective compounds that can target this region of the protein and potentially be used to treat congenital myopathies where muscle weakness is related to myosin loss of function.
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Affiliation(s)
- Anna Katarina Antonovic
- School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Julien Ochala
- Department of Biomedical Sciences, University of Copenhagen, København N 2200, Denmark; Centre of Human and Applied Physiological Sciences, King's College London, London SE1 9RT, United Kingdom
| | - Arianna Fornili
- School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
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7
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Motta S, Pandini A, Fornili A, Bonati L. Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks. J Chem Theory Comput 2021; 17:2080-2089. [PMID: 33780250 PMCID: PMC8047803 DOI: 10.1021/acs.jctc.0c01308] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Indexed: 12/03/2022]
Abstract
![]()
Several experimental
studies indicated that large conformational
changes, including partial domain unfolding, have a role in the functional
mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription
factors. Recently, single-molecule atomic force microscopy (AFM) revealed
two distinct pathways for the mechanical unfolding of the ARNT PAS-B.
In this work we used steered molecular dynamics simulations to gain
new insights into this process at an atomistic level. To reconstruct
and classify pathways sampled in multiple simulations, we designed
an original approach based on the use of self-organizing maps (SOMs).
This led us to identify two types of unfolding pathways for the ARNT
PAS-B, which are in good agreement with the AFM findings. Analysis
of average forces mapped on the SOM revealed a stable conformation
of the PAS-B along one pathway, which represents a possible structural
model for the intermediate state detected by AFM. The approach here
proposed will facilitate the study of other signal transmission mechanisms
involving the folding/unfolding of PAS domains.
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Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Alessandro Pandini
- Department of Computer Science, Brunel University London, Uxbridge UB8 3PH, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
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8
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Hashem S, Davies WG, Fornili A. Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin. J Chem Inf Model 2020; 60:6438-6446. [PMID: 33283509 DOI: 10.1021/acs.jcim.0c00953] [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: 11/29/2022]
Abstract
Omecamtiv mecarbil (OM), currently investigated for the treatment of heart failure, is the first example of a new class of drugs (cardiac myotropes) that can modify muscle contractility by directly targeting sarcomeric proteins. Using atomistic molecular dynamics simulations, we show that the binding of OM to the pre-power stroke state of cardiac myosin inhibits the functional motions of the protein and potentially affects Pi release from the nucleotide binding site. We also show that the changes in myosin ATPase activity induced by a set of OM analogues can be predicted from their relative affinity to the pre-power stroke state compared to the near rigor one, indicating that conformational selectivity plays an important role in determining the activity of these compounds.
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Affiliation(s)
- Shaima Hashem
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - William George Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London WC1E 6BN, United Kingdom
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9
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Rehman S, Grigoryeva LS, Richardson KH, Corsini P, White RC, Shaw R, Portlock TJ, Dorgan B, Zanjani ZS, Fornili A, Cianciotto NP, Garnett JA. Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation. PLoS Pathog 2020; 16:e1008342. [PMID: 32365117 PMCID: PMC7224574 DOI: 10.1371/journal.ppat.1008342] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 07/16/2019] [Revised: 05/14/2020] [Accepted: 01/22/2020] [Indexed: 12/18/2022] Open
Abstract
Chitinases are important enzymes that contribute to the generation of carbon and nitrogen from chitin, a long chain polymer of N-acetylglucosamine that is abundant in insects, fungi, invertebrates and fish. Although mammals do not produce chitin, chitinases have been identified in bacteria that are key virulence factors in severe respiratory, gastrointestinal and urinary diseases. However, it is unclear how these enzymes are able to carry out this dual function. Legionella pneumophila is the causative agent of Legionnaires' disease, an often-fatal pneumonia and its chitinase ChiA is essential for the survival of L. pneumophila in the lung. Here we report the first atomic resolution insight into the pathogenic mechanism of a bacterial chitinase. We derive an experimental model of intact ChiA and show how its N-terminal region targets ChiA to the bacterial surface after its secretion. We provide the first evidence that L. pneumophila can bind mucins on its surface, but this is not dependent on ChiA. This demonstrates that additional peripheral mucin binding proteins are also expressed in L. pneumophila. We also show that the ChiA C-terminal chitinase domain has novel Zn2+-dependent peptidase activity against mammalian mucin-like proteins, namely MUC5AC and the C1-esterase inhibitor, and that ChiA promotes bacterial penetration of mucin gels. Our findings suggest that ChiA can facilitate passage of L. pneumophila through the alveolar mucosa, can modulate the host complement system and that ChiA may be a promising target for vaccine development.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
| | - Lubov S. Grigoryeva
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Katherine H. Richardson
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Paula Corsini
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Richard C. White
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Rosie Shaw
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Theo J. Portlock
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Benjamin Dorgan
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Zeinab S. Zanjani
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arianna Fornili
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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10
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Motta S, Pandini A, Fornili A, Bonati L. Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding Conformations. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1681] [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: 10/25/2022] Open
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11
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Abstract
We report the first observation of a pocket that opens as a result of a mechanical force applied to an Ig-like domain from the cardiac muscle. This previously unseen mechanism of pocket formation is revealed by molecular dynamics simulations under force. Preliminary investigations show that this "mechano-pocket" is potentially druggable and could be found in other domains from the same fold family, suggesting the existence of a general mechanism of pocket formation under mechanical stress.
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Affiliation(s)
- Matteo Tiberti
- School of Biological and Chemical Sciences , Queen Mary University of London , London E1 4NS , United Kingdom
| | - Bob-Dan Lechner
- School of Biological and Chemical Sciences , Queen Mary University of London , London E1 4NS , United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences , Queen Mary University of London , London E1 4NS , United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials , London , United Kingdom
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12
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Hashem S, Tiberti M, Fornili A. Allosteric Modulation of Cardiac Myosin Dynamics by Omecamtiv Mecarbil. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.251] [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: 10/18/2022] Open
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13
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Tiberti M, Pandini A, Fraternali F, Fornili A. In Silico Identification of Rescue Sites by Double Force Scanning. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.285] [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: 10/18/2022] Open
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14
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Tiberti M, Lechner BD, Fornili A. Binding Pockets Under Mechanical Stress. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.218] [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: 11/30/2022] Open
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15
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Tiberti M, Pandini A, Fraternali F, Fornili A. In silico identification of rescue sites by double force scanning. Bioinformatics 2018; 34:207-214. [PMID: 28961796 PMCID: PMC5860198 DOI: 10.1093/bioinformatics/btx515] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/23/2017] [Accepted: 08/10/2017] [Indexed: 01/03/2023] Open
Abstract
Motivation A deleterious amino acid change in a protein can be compensated by a second-site rescue mutation. These compensatory mechanisms can be mimicked by drugs. In particular, the location of rescue mutations can be used to identify protein regions that can be targeted by small molecules to reactivate a damaged mutant. Results We present the first general computational method to detect rescue sites. By mimicking the effect of mutations through the application of forces, the double force scanning (DFS) method identifies the second-site residues that make the protein structure most resilient to the effect of pathogenic mutations. We tested DFS predictions against two datasets containing experimentally validated and putative evolutionary-related rescue sites. A remarkably good agreement was found between predictions and experimental data. Indeed, almost half of the rescue sites in p53 was correctly predicted by DFS, with 65% of remaining sites in contact with DFS predictions. Similar results were found for other proteins in the evolutionary dataset. Availability and implementation The DFS code is available under GPL at https://fornililab.github.io/dfs/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matteo Tiberti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Alessandro Pandini
- Department of Computer Science, College of Engineering, Design and Physical Sciences and Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, London, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King‘s College London, London, UK
- The Francis Crick Institute, London, UK
- The Thomas Young Centre for Theory and Simulation of Materials, London, UK
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- The Thomas Young Centre for Theory and Simulation of Materials, London, UK
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Hashem S, Tiberti M, Fornili A. Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil. PLoS Comput Biol 2017; 13:e1005826. [PMID: 29108014 PMCID: PMC5690683 DOI: 10.1371/journal.pcbi.1005826] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 05/22/2017] [Revised: 11/16/2017] [Accepted: 10/16/2017] [Indexed: 01/10/2023] Open
Abstract
New promising avenues for the pharmacological treatment of skeletal and heart muscle diseases rely on direct sarcomeric modulators, which are molecules that can directly bind to sarcomeric proteins and either inhibit or enhance their activity. A recent breakthrough has been the discovery of the myosin activator omecamtiv mecarbil (OM), which has been shown to increase the power output of the cardiac muscle and is currently in clinical trials for the treatment of heart failure. While the overall effect of OM on the mechano-chemical cycle of myosin is to increase the fraction of myosin molecules in the sarcomere that are strongly bound to actin, the molecular basis of its action is still not completely clear. We present here a Molecular Dynamics study of the motor domain of human cardiac myosin bound to OM, where the effects of the drug on the dynamical properties of the protein are investigated for the first time with atomistic resolution. We found that OM has a double effect on myosin dynamics, inducing a) an increased coupling of the motions of the converter and lever arm subdomains to the rest of the protein and b) a rewiring of the network of dynamic correlations, which produces preferential communication pathways between the OM binding site and distant functional regions. The location of the residues responsible for these effects suggests possible strategies for the future development of improved drugs and the targeting of specific cardiomyopathy-related mutations.
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Affiliation(s)
- Shaima Hashem
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Matteo Tiberti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- The Thomas Young Centre for Theory and Simulation of Materials, London, United Kingdom
- * E-mail:
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17
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Abstract
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Conformational
changes associated with protein function often occur
beyond the time scale currently accessible to unbiased molecular dynamics
(MD) simulations, so that different approaches have been developed
to accelerate their sampling. Here we investigate how the knowledge
of backbone conformations preferentially adopted by protein fragments,
as contained in precalculated libraries known as structural alphabets
(SA), can be used to explore the landscape of protein conformations
in MD simulations. We find that (a) enhancing the sampling of native
local states in both metadynamics and steered MD simulations allows
the recovery of global folded states in small proteins; (b) folded
states can still be recovered when the amount of information on the
native local states is reduced by using a low-resolution version of
the SA, where states are clustered into macrostates; and (c) sequences
of SA states derived from collections of structural motifs can be
used to sample alternative conformations of preselected protein regions.
The present findings have potential impact on several applications,
ranging from protein model refinement to protein folding and design.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science, College of Engineering, Design and Physical Sciences and Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London , Uxbridge UB8 3PH, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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18
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Fornili A, Rostkova E, Fraternali F, Pfuhl M. Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1600] [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: 10/22/2022] Open
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19
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Carluccio C, Fraternali F, Salvatore F, Fornili A, Zagari A. Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. J Biomol Struct Dyn 2015; 34:497-507. [PMID: 26479306 DOI: 10.1080/07391102.2015.1052016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 10/22/2022]
Abstract
The enzyme phenylalanine hydroxylase (PAH) is defective in the inherited disorder phenylketonuria. PAH, a tetrameric enzyme, is highly regulated and displays positive cooperativity for its substrate, Phe. Whether Phe binds to an allosteric site is a matter of debate, despite several studies worldwide. To address this issue, we generated a dimeric model for Phe-PAH interactions, by performing molecular docking combined with molecular dynamics simulations on human and rat wild-type sequences and also on a human G46S mutant. Our results suggest that the allosteric Phe-binding site lies at the dimeric interface between the regulatory and the catalytic domains of two adjacent subunits. The structural and dynamical features of the site were characterized in depth and described. Interestingly, our findings provide evidence for lower allosteric Phe-binding ability of the G46S mutant than the human wild-type enzyme. This also explains the disease-causing nature of this mutant.
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Affiliation(s)
- Carla Carluccio
- a CEINGE-Biotecnologie Avanzate , S.c. a r.l., Napoli , Italy
| | - Franca Fraternali
- b Randall Division of Cell and Molecular Biophysics , King's College London , London , UK
| | - Francesco Salvatore
- a CEINGE-Biotecnologie Avanzate , S.c. a r.l., Napoli , Italy.,c SDN-Istituto di Ricerca Diagnostica e Nucleare , Napoli , Italy
| | - Arianna Fornili
- b Randall Division of Cell and Molecular Biophysics , King's College London , London , UK
| | - Adriana Zagari
- a CEINGE-Biotecnologie Avanzate , S.c. a r.l., Napoli , Italy
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20
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Lu HC, Chung SS, Fornili A, Fraternali F. Anatomy of protein disorder, flexibility and disease-related mutations. Front Mol Biosci 2015; 2:47. [PMID: 26322316 PMCID: PMC4532925 DOI: 10.3389/fmolb.2015.00047] [Citation(s) in RCA: 15] [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: 05/31/2015] [Accepted: 07/29/2015] [Indexed: 01/23/2023] Open
Abstract
Integration of protein structural information with human genetic variation and pathogenic mutations is essential to understand molecular mechanisms associated with the effects of polymorphisms on protein interactions and cellular processes. We investigate occurrences of non-synonymous SNPs in ordered and disordered protein regions by systematic mapping of common variants and disease-related SNPs onto these regions. We show that common variants accumulate in disordered regions; conversely pathogenic variants are significantly depleted in disordered regions. These different occurrences of pathogenic and common SNPs can be attributed to a negative selection on random mutations in structurally highly constrained regions. New approaches in the study of quantitative effects of pathogenic-related mutations should effectively account for all the possible contexts and relative functional constraints in which the sequence variation occurs.
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Affiliation(s)
- Hui-Chun Lu
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK
| | - Sun Sook Chung
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK ; Department of Haematological Medicine, King's College London London, UK
| | - Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK ; School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London London, UK
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21
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Abstract
Protein-protein interaction networks (PPINs) are a powerful tool to study biological processes in living cells. In this review, we present the progress of PPIN studies from abstract to more detailed representations. We will focus on 3D interactome networks, which offer detailed information at the atomic level. This information can be exploited in understanding not only the underlying cellular mechanisms, but also how human variants and disease-causing mutations affect protein functions and complexes' stability. Recent studies have used structural information on PPINs to also understand the molecular mechanisms of binding partner selection. We will address the challenges in generating 3D PPINs due to the restricted number of solved protein structures. Finally, some of the current use of 3D PPINs will be discussed, highlighting their contribution to the studies in genotype-phenotype relationships and in the optimization of targeted studies to design novel chemical compounds for medical treatments.
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Affiliation(s)
- Hui-Chun Lu
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London SE1 1UL, UK
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22
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Pandini A, Fornili A, Fraternali F, Kleinjung J. Gsatools: Analysis of Allosteric Communication and Functional Local Motions using a Structural Alphabet. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3586] [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: 10/23/2022] Open
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23
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Fornili A, Pandini A, Lu HC, Fraternali F. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. J Chem Theory Comput 2013; 9:5127-5147. [PMID: 24250278 PMCID: PMC3827836 DOI: 10.1021/ct400486p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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: 06/09/2013] [Indexed: 12/13/2022]
Abstract
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The
ability to interact with different partners is one of the most
important features in proteins. Proteins that bind a large number
of partners (hubs) have been often associated with intrinsic disorder.
However, many examples exist of hubs with an ordered structure, and
evidence of a general mechanism promoting promiscuity in ordered proteins
is still elusive. An intriguing hypothesis is that promiscuous binding
sites have specific dynamical properties, distinct from the rest of
the interface and pre-existing in the protein isolated state. Here,
we present the first comprehensive study of the intrinsic dynamics
of promiscuous residues in a large protein data set. Different computational
methods, from coarse-grained elastic models to geometry-based sampling
methods and to full-atom Molecular Dynamics simulations, were used
to generate conformational ensembles for the isolated proteins. The
flexibility and dynamic correlations of interface residues with a
different degree of binding promiscuity were calculated and compared
considering side chain and backbone motions, the latter both on a
local and on a global scale. The study revealed that (a) promiscuous
residues tend to be more flexible than nonpromiscuous ones, (b) this
additional flexibility has a higher degree of organization, and (c)
evolutionary conservation and binding promiscuity have opposite effects
on intrinsic dynamics. Findings on simulated ensembles were also validated
on ensembles of experimental structures extracted from the Protein
Data Bank (PDB). Additionally, the low occurrence of single nucleotide
polymorphisms observed for promiscuous residues indicated a tendency
to preserve binding diversity at these positions. A case study on
two ubiquitin-like proteins exemplifies how binding promiscuity in
evolutionary related proteins can be modulated by the fine-tuning
of the interface dynamics. The interplay between promiscuity and flexibility
highlighted here can inspire new directions in protein–protein
interaction prediction and design methods.
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Affiliation(s)
- Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, King's College London , New Hunt's House, London SE1 1UL, United Kingdom
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24
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Pandini A, Fornili A, Fraternali F, Kleinjung J. GSATools: analysis of allosteric communication and functional local motions using a structural alphabet. ACTA ACUST UNITED AC 2013; 29:2053-5. [PMID: 23740748 PMCID: PMC3722520 DOI: 10.1093/bioinformatics/btt326] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [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: 11/14/2022]
Abstract
Motivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact:alessandro.pandini@kcl.ac.uk or jkleinj@nimr.mrc.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alessandro Pandini
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
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25
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Chakroun N, Fornili A, Prigent S, Kleinjung J, Dreiss CA, Rezaei H, Fraternali F. Decrypting Prion Protein Conversion into a β-Rich Conformer by Molecular Dynamics. J Chem Theory Comput 2013; 9:2455-2465. [PMID: 23700393 PMCID: PMC3656828 DOI: 10.1021/ct301118j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 12/21/2012] [Indexed: 01/08/2023]
Abstract
Prion diseases are fatal neurodegenerative diseases characterized by the formation of β-rich oligomers and the accumulation of amyloid fibrillar deposits in the central nervous system. Understanding the conversion of the cellular prion protein into its β-rich polymeric conformers is fundamental to tackling the early stages of the development of prion diseases. In this paper, we have identified unfolding and refolding steps critical to the conversion into a β-rich conformer for different constructs of the ovine prion protein by molecular dynamics simulations. By combining our results with in vitro experiments, we show that the folded C-terminus of the ovine prion protein is able to recurrently undergo a drastic conformational change by displacement of the H1 helix, uncovering of the H2H3 domain, and formation of persistent β-sheets between H2 and H3 residues. The observed β-sheets refold toward the C-terminus exposing what we call a "bending region" comprising residues 204-214. This is strikingly coincident with the region harboring mutations determining the fate of the prion oligomerization process. The β-rich intermediate is used here for the construction of a putative model for the assembly into an oligomeric aggregate. The results presented here confirm the importance of the H2H3 domain for prion oligomer formation and therefore its potential use as molecular target in the design of novel prion inhibitors.
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Affiliation(s)
- Nesrine Chakroun
- Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London, SE1 9NH, United Kingdom ; Randall Division of Cell and Molecular Biophysics, King's College London, Guy's Campus, London, SE1 1UL, United Kingdom
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26
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Abstract
Allostery offers a highly specific way to modulate protein function. Therefore, understanding this mechanism is of increasing interest for protein science and drug discovery. However, allosteric signal transmission is difficult to detect experimentally and to model because it is often mediated by local structural changes propagating along multiple pathways. To address this, we developed a method to identify communication pathways by an information-theoretical analysis of molecular dynamics simulations. Signal propagation was described as information exchange through a network of correlated local motions, modeled as transitions between canonical states of protein fragments. The method was used to describe allostery in two-component regulatory systems. In particular, the transmission from the allosteric site to the signaling surface of the receiver domain NtrC was shown to be mediated by a layer of hub residues. The location of hubs preferentially connected to the allosteric site was found in close agreement with key residues experimentally identified as involved in the signal transmission. The comparison with the networks of the homologues CheY and FixJ highlighted similarities in their dynamics. In particular, we showed that a preorganized network of fragment connections between the allosteric and functional sites exists already in the inactive state of all three proteins.
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Affiliation(s)
- Alessandro Pandini
- Division of Mathematical Biology, Medical Research Council National Institute for Medical Research, London, UK; ,Randall Division of Cell and Molecular Biophysics, King's College London, London, UK; and , Correspondence: Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA London, UK. E-mail: A.P., ; J.K.,
| | - Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK; and
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK; and ,The Thomas Young Centre for Theory and Simulation of Materials, London, UK
| | - Jens Kleinjung
- Division of Mathematical Biology, Medical Research Council National Institute for Medical Research, London, UK; , Correspondence: Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA London, UK. E-mail: A.P., ; J.K.,
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27
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Fornili A, Pfuhl M, Fraternali F. Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle Contraction. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2472] [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: 11/25/2022] Open
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28
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Autore F, Pagano B, Fornili A, Rittinger K, Fraternali F. In silico phosphorylation of the autoinhibited form of p47(phox): insights into the mechanism of activation. Biophys J 2010; 99:3716-25. [PMID: 21112296 PMCID: PMC2998635 DOI: 10.1016/j.bpj.2010.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 08/26/2010] [Accepted: 09/07/2010] [Indexed: 11/19/2022] Open
Abstract
Activation of the multicomponent enzyme NADPH oxidase requires the interaction between the tandem SH3 domain of the cytosolic subunit p47(phox) and the cytoplasmic tail of membrane-bound p22(phox). In the resting state, p47(phox) exists in an autoinhibited conformation stabilized by intramolecular contacts between the SH3 domains and an adjacent polybasic region. Phosphorylation of three serine residues, Ser(303), Ser(304), and Ser(328) within this polybasic region has been shown to be sufficient for the disruption of the intramolecular interactions thereby inducing an active state of p47(phox). This active conformation is accessible to the cytoplasmic tail of p22(phox) and initiates the formation of the membrane-bound functional enzyme complex. Molecular dynamics simulations reveal insights in the mechanism of activation of the autoinhibited form of p47(phox) by in silico phosphorylation, of the three serine residues, Ser(303), Ser(304), and Ser(328). The simulations highlight the major collective coordinates generating the opening and the closing of the two SH3 domains and the residues that cause the unmasking of the p22(phox) binding site.
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Affiliation(s)
- Flavia Autore
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
| | - Bruno Pagano
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, Fisciano, Italy
| | - Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
| | - Katrin Rittinger
- Division of Molecular Structure, MRC-National Institute for Medical Research, London, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
- KCL Centre for Bioinformatics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
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Fornili A, Giabbai B, Garau G, Degano M. Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures. J Am Chem Soc 2010; 132:17570-7. [DOI: 10.1021/ja107640u] [Citation(s) in RCA: 15] [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: 11/30/2022]
Affiliation(s)
- Arianna Fornili
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Barbara Giabbai
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Gianpiero Garau
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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30
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Pandini A, Fornili A, Kleinjung J. Structural alphabets derived from attractors in conformational space. BMC Bioinformatics 2010; 11:97. [PMID: 20170534 PMCID: PMC2838871 DOI: 10.1186/1471-2105-11-97] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [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: 08/24/2009] [Accepted: 02/20/2010] [Indexed: 11/20/2022] Open
Abstract
Background The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis. Results A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness. Conclusions The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics.
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Affiliation(s)
- Alessandro Pandini
- Division of Mathematical Biology, MRC National Institute for Medical Research, London, UK
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31
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Fornili A, Pandini A, Fraternali F. Interface Dynamics In Hub Proteins. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1294] [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: 11/27/2022] Open
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32
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Iovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F, Degano M. Structural Basis for Substrate Specificity in Group I Nucleoside Hydrolases,. Biochemistry 2008; 47:4418-26. [DOI: 10.1021/bi702448s] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [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)
- Elena Iovane
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Barbara Giabbai
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Laura Muzzolini
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Vittoria Matafora
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Arianna Fornili
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Claudia Minici
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Francesca Giannese
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
| | - Massimo Degano
- Biocrystallography Unit and Mass Spectrometry Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy
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Fornili A, Sironi M, Degano M. Accurate description of nitrogenous base flexibility in classical molecular dynamics simulations of nucleotides bound to proteins. J Phys Chem B 2007; 111:6297-302. [PMID: 17508739 DOI: 10.1021/jp0713357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Proteins can induce significant distortions in planar cyclic compounds upon binding, in particular in nucleotide-enzyme complexes. An accurate representation of the ring flexibility is thus desirable when modeling these systems through classical force fields, especially when deformations are supposed to be involved in the catalytic mechanism. In this study, we use a newly developed general procedure to determine sets of dihedral parameters for planar cycles that accurately reproduce their out-of-plane normal modes as determined at the quantum mechanical (QM) level. The optimization allows the deviation from reference data to be reduced for the pyrimidine bases to values comparable to the accuracy of the QM data. Furthermore, the influence of the description of ring flexibility in protein-ligand interactions is assessed through molecular dynamics simulations of the complex between uridine and the pyrimidine-specific nucleoside hydrolase YeiK using the AMBER force field. The differences in ligand-protein interactions emerging from different parameter sets are also discussed with respect to existing biochemical data.
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Abstract
In the QM/MM method we have developed (LSCF/MM), the QM and the MM parts are held together by means of strictly localized bonding orbitals (SLBOs). Generally these SLBOs are derived from localized bond orbitals (LBOs) that undergo tails deletion, resulting in a nonpredictable change of their properties. An alternative set of SLBOs is provided by the extremely localized molecular orbitals (ELMOs) approach, where the orbitals are rigorously localized on some prefixed atoms without tails on the other atoms of the molecule. A comparative study of SLBOs arising from various localization schemes and ELMOs is presented to test the reliability and the transferability of these functions within the Local Self-Consistent Field (LSCF) framework. Two types of chemical bonds were considered: C--C and C--O single bonds. The localized functions are obtained on the ethane and the methanol molecules, and are tested on beta-alanine and diethyl ether molecules. Moreover, the various protonation forms of beta-alanine have been investigated to illustrate how well the polarity variation of the chemical bond can be handled throughout a chemical process. At last, rotation energy profiles around C--C and C--O bonds are reproduced for butane and fluoromethanol. Energetic, geometric, as well as electronic factors all indicate that ELMO functions are much more transferable from one molecule to another, leading to results closer to the usual SCF reference than any other calculations involving any other localized orbitals. When the shape of the orbital is the most important factor then ELMO functions will perform as well as any other localized orbital.
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Affiliation(s)
- Arianna Fornili
- Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Milan, Italy
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Genoni A, Fornili A, Sironi M. Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals. J Comput Chem 2005; 26:827-35. [PMID: 15812780 DOI: 10.1002/jcc.20213] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Extremely localized molecular orbitals (ELMOs), namely orbitals strictly localized on molecular fragments, are easily transferable from one molecule to another one. Hence, they provide a natural way to set up the electronic structure of large molecules using a data base of orbitals obtained from model molecules. However, this procedure obviously increases the energy with respect to a traditional MO calculation. To gain accuracy, it is important to introduce a partial electron delocalization. This can be carried out by defining proper optimal virtual orbitals that supply an efficient set for nonorthogonal configurations to be employed in VB-like expansions.
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Affiliation(s)
- Alessandro Genoni
- Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
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Morelli CF, Fornili A, Sironi M, Durì L, Speranza G, Manitto P. Evidence for a nucleophilic anti-attack on the cleaved C(2)–oxygen bond in Cl2AlH-catalyzed ring-opening of 2-substituted 1,3-dioxolanes. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.01.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fornili A, Sironi M, Raimondi M. Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00296-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Fornili A, Civera M, Sironi M, Fornili SL. Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcohol. Phys Chem Chem Phys 2003. [DOI: 10.1039/b308248b] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Morelli CF, Fornili A, Sironi M, Durı̀ L, Speranza G, Manitto P. Regio- and diastereoselectivity in TiCl4-promoted reduction of 2-aryl-substituted cis-4-methyl-5-trifluoromethyl-1,3-dioxolanes. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0957-4166(02)00687-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Sironi M, Fornili A, Fornili SL. Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation. Phys Chem Chem Phys 2001. [DOI: 10.1039/b009779i] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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