1
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Singh PK, Stan RC. ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures. Database (Oxford) 2024; 2024:baae015. [PMID: 38502609 PMCID: PMC10950042 DOI: 10.1093/database/baae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
Progression of various cancers and autoimmune diseases is associated with changes in systemic or local tissue temperatures, which may impact current therapies. The role of fever and acute inflammation-range temperatures on the stability and activity of antibodies relevant for cancers and autoimmunity is unknown. To produce molecular dynamics (MD) trajectories of immune complexes at relevant temperatures, we used the Research Collaboratory for Structural Bioinformatics (RCSB) database to identify 50 antibody:antigen complexes of interest, in addition to single antibodies and antigens, and deployed Groningen Machine for Chemical Simulations (GROMACS) to prepare and run the structures at different temperatures for 100-500 ns, in single or multiple random seeds. MD trajectories are freely available. Processed data include Protein Data Bank outputs for all files obtained every 50 ns, and free binding energy calculations for some of the immune complexes. Protocols for using the data are also available. Individual datasets contain unique DOIs. We created a web interface, ThermoPCD, as a platform to explore the data. The outputs of ThermoPCD allow the users to relate thermally-dependent changes in epitopes:paratopes interfaces to their free binding energies, or against own experimentally derived binding affinities. ThermoPCD is a free to use database of immune complexes' trajectories at different temperatures that does not require registration and allows for all the data to be available for download. Database URL: https://sites.google.com/view/thermopcd/home.
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Affiliation(s)
- Puneet K Singh
- Department of Basic Medical Science, Chonnam National University, Hwasun 58128, Republic of Korea
| | - Razvan C Stan
- Department of Basic Medical Science, Chonnam National University, Hwasun 58128, Republic of Korea
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2
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Vander Meersche Y, Cretin G, Gheeraert A, Gelly JC, Galochkina T. ATLAS: protein flexibility description from atomistic molecular dynamics simulations. Nucleic Acids Res 2024; 52:D384-D392. [PMID: 37986215 PMCID: PMC10767941 DOI: 10.1093/nar/gkad1084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/15/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Dynamical behaviour is one of the most crucial protein characteristics. Despite the advances in the field of protein structure resolution and prediction, analysis and prediction of protein dynamic properties remains a major challenge, mostly due to the low accessibility of data and its diversity and heterogeneity. To address this issue, we present ATLAS, a database of standardised all-atom molecular dynamics simulations, accompanied by their analysis in the form of interactive diagrams and trajectory visualisation. ATLAS offers a large-scale view and valuable insights on protein dynamics for a large and representative set of proteins, by combining data obtained through molecular dynamics simulations with information extracted from experimental structures. Users can easily analyse dynamic properties of functional protein regions, such as domain limits (hinge positions) and residues involved in interaction with other biological molecules. Additionally, the database enables exploration of proteins with uncommon dynamic properties conditioned by their environment such as chameleon subsequences and Dual Personality Fragments. The ATLAS database is freely available at https://www.dsimb.inserm.fr/ATLAS.
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Affiliation(s)
- Yann Vander Meersche
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Gabriel Cretin
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Aria Gheeraert
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
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3
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Rahimi M, Taghdir M, Abasi Joozdani F. Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease. Sci Rep 2023; 13:14179. [PMID: 37648682 PMCID: PMC10469195 DOI: 10.1038/s41598-023-40818-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.
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Affiliation(s)
- Mohammad Rahimi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran.
| | - Farzane Abasi Joozdani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
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4
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Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein–Protein Interfaces, How and Why? Molecules 2022; 27:molecules27061841. [PMID: 35335203 PMCID: PMC8950966 DOI: 10.3390/molecules27061841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/07/2022] Open
Abstract
Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface.
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Affiliation(s)
- Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
- Correspondence:
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5
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Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants. PLoS Biol 2021; 19:e3001207. [PMID: 33909605 PMCID: PMC8110273 DOI: 10.1371/journal.pbio.3001207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 05/10/2021] [Accepted: 03/26/2021] [Indexed: 12/27/2022] Open
Abstract
Missense variants are present amongst the healthy population, but some of them are causative of human diseases. A classification of variants associated with “healthy” or “diseased” states is therefore not always straightforward. A deeper understanding of the nature of missense variants in health and disease, the cellular processes they may affect, and the general molecular principles which underlie these differences is essential to offer mechanistic explanations of the true impact of pathogenic variants. Here, we have formalised a statistical framework which enables robust probabilistic quantification of variant enrichment across full-length proteins, their domains, and 3D structure-defined regions. Using this framework, we validate and extend previously reported trends of variant enrichment in different protein structural regions (surface/core/interface). By examining the association of variant enrichment with available functional pathways and transcriptomic and proteomic (protein half-life, thermal stability, abundance) data, we have mined a rich set of molecular features which distinguish between pathogenic and population variants: Pathogenic variants mainly affect proteins involved in cell proliferation and nucleotide processing and are enriched in more abundant proteins. Additionally, rare population variants display features closer to common than pathogenic variants. We validate the association between these molecular features and variant pathogenicity by comparing against existing in silico variant impact annotations. This study provides molecular details into how different proteins exhibit resilience and/or sensitivity towards missense variants and provides the rationale to prioritise variant-enriched proteins and protein domains for therapeutic targeting and development. The ZoomVar database, which we created for this study, is available at fraternalilab.kcl.ac.uk/ZoomVar. It allows users to programmatically annotate missense variants with protein structural information and to calculate variant enrichment in different protein structural regions. How do can one improve the classification of genetic variants as harmful or harmless? This study uses a robust statistical analysis to exploit the interplay between protein structure, proteomic measurements and functional pathways to enable better discrimination between missense variants in health and disease.
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6
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Wheatley P, Gupta S, Pandini A, Chen Y, Petzold CJ, Ralston CY, Blair DF, Khan S. Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM. Biophys J 2020; 119:1108-1122. [PMID: 32891187 DOI: 10.1016/j.bpj.2020.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/22/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
Phosphorylation of Escherichia coli CheY protein transduces chemoreceptor stimulation to a highly cooperative flagellar motor response. CheY binds to the N-terminal peptide of the FliM motor protein (FliMN). Constitutively active D13K-Y106W CheY has been an important tool for motor physiology. The crystal structures of CheY and CheY ⋅ FliMN with and without D13K-Y106W have shown FliMN-bound CheY contains features of both active and inactive states. We used molecular dynamics (MD) simulations to characterize the CheY conformational landscape accessed by FliMN and D13K-Y106W. Mutual information measures identified the central features of the long-range CheY allosteric network between D57 phosphorylation site and the FliMN interface, namely the closure of the α4-β4 hinge and inward rotation of Y- or W106 with W58. We used hydroxy-radical foot printing with mass spectroscopy (XFMS) to track the solvent accessibility of these and other side chains. The solution XFMS oxidation rate correlated with the solvent-accessible area of the crystal structures. The protection of allosteric relay side chains reported by XFMS confirmed the intermediate conformation of the native CheY ⋅ FliMN complex, the inactive state of free D13K-Y106W CheY, and the MD-based network architecture. We extended the MD analysis to determine temporal coupling and energetics during activation. Coupled aromatic residue rotation was a graded rather than a binary switch, with Y- or W106 side-chain burial correlated with increased FliMN affinity. Activation entrained CheY fold stabilization to FliMN affinity. The CheY network could be partitioned into four dynamically coordinated sectors. Residue substitutions mapped to sectors around D57 or the FliMN interface according to phenotype. FliMN increased sector size and interactions. These sectors fused between the substituted K13-W106 residues to organize a tightly packed core and novel surfaces that may bind additional sites to explain the cooperative motor response. The community maps provide a more complete description of CheY priming than proposed thus far.
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Affiliation(s)
- Paige Wheatley
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Alessandro Pandini
- Department of Computer Science-Synthetic Biology Theme, Brunel University London, Uxbridge, United Kingdom; Computational Cell and Molecular Biology, the Francis Crick Institute, London, United Kingdom
| | - Yan Chen
- Biological Systems and Engineering, Lawrence, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Corie Y Ralston
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - David F Blair
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Shahid Khan
- Computational Cell and Molecular Biology, the Francis Crick Institute, London, United Kingdom; Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, California.
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7
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Ng JF, Fraternali F. Understanding the structural details of APOBEC3-DNA interactions using graph-based representations. Curr Res Struct Biol 2020; 2:130-143. [PMID: 34235473 PMCID: PMC8244423 DOI: 10.1016/j.crstbi.2020.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022] Open
Abstract
Human APOBEC3 (A3; apolipoprotein B mRNA editing catalytic polypeptide-like 3) is a family of seven enzymes involved in generating mutations in nascent reverse transcripts of many retroviruses, as well as the human genome in a range of cancer types. The structural details of the interaction between A3 proteins and DNA molecules are only available for a few family members. Here we use homology modelling techniques to address the difference in structural coverage of human A3 enzymes interacting with different DNA substrates. A3-DNA interfaces are represented as residue networks ("graphs"), based on which features at these interfaces are compared and quantified. We demonstrate that graph-based representations are effective in highlighting structural features of A3-DNA interfaces. By large-scale in silico mutagenesis of the bound DNA chain, we predicted the preference of substrate DNA sequence for multiple A3 domains. These data suggested that computational modelling approaches could contribute in the exploration of the structural basis for sequence specificity in A3 substrate selection, and demonstrated the utility of graph-based approaches in evaluating a large number of structural models generated in silico. APOBEC3(A3)-DNA structures have been resolved with modified deaminase domains. Structural modelling of interaction between wild-type A3 domains and DNA substrates. Graph-based representations reveal structural differences across A3-DNA interfaces. Using in silico mutagenesis we compared substrate preference of multiple A3 domains. Graph-based approaches can efficiently compare a large number of structural models.
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8
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Protein-Protein Interactions Mediated by Intrinsically Disordered Protein Regions Are Enriched in Missense Mutations. Biomolecules 2020; 10:biom10081097. [PMID: 32722039 PMCID: PMC7463635 DOI: 10.3390/biom10081097] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 12/27/2022] Open
Abstract
Because proteins are fundamental to most biological processes, many genetic diseases can be traced back to single nucleotide variants (SNVs) that cause changes in protein sequences. However, not all SNVs that result in amino acid substitutions cause disease as each residue is under different structural and functional constraints. Influential studies have shown that protein–protein interaction interfaces are enriched in disease-associated SNVs and depleted in SNVs that are common in the general population. These studies focus primarily on folded (globular) protein domains and overlook the prevalent class of protein interactions mediated by intrinsically disordered regions (IDRs). Therefore, we investigated the enrichment patterns of missense mutation-causing SNVs that are associated with disease and cancer, as well as those present in the healthy population, in structures of IDR-mediated interactions with comparisons to classical globular interactions. When comparing the different categories of interaction interfaces, division of the interface regions into solvent-exposed rim residues and buried core residues reveal distinctive enrichment patterns for the various types of missense mutations. Most notably, we demonstrate a strong enrichment at the interface core of interacting IDRs in disease mutations and its depletion in neutral ones, which supports the view that the disruption of IDR interactions is a mechanism underlying many diseases. Intriguingly, we also found an asymmetry across the IDR interaction interface in the enrichment of certain missense mutation types, which may hint at an increased variant tolerance and urges further investigations of IDR interactions.
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9
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Nichols C, Ng J, Keshu A, Kelly G, Conte MR, Marber MS, Fraternali F, De Nicola GF. Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1β-IL1R and p38α-TAB1 Complexes. J Med Chem 2020; 63:7559-7568. [PMID: 32543856 DOI: 10.1021/acs.jmedchem.0c00403] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nowadays, it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors. To prove it, we first performed a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cases where the crystal lattice of the target in the free form is such that large portions of the interacting surfaces are free from lattice contacts and therefore accessible to fragments during soaks. Among the tractable complexes identified, we then performed single fragment crystal screens on two particular interesting cases: the Il1β-ILR and p38α-TAB1 complexes. The result of the screens showed that fragments tend to bind in clusters, highlighting the small-molecule hotspots on the surface of the target protein. In most of the cases, the hotspots overlapped with the binding sites of the interacting proteins.
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Affiliation(s)
- Charlie Nichols
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Joseph Ng
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Annika Keshu
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Geoff Kelly
- NMR Facility, The Francis Crick Institute, London NW1 1AT, U.K
| | - Maria R Conte
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Michael S Marber
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K
| | - Franca Fraternali
- The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
| | - Gian F De Nicola
- British Heart Foundation Centre of Excellence, Department of Cardiology, The Rayne Institute, St Thomas' Hospital, King's College London, London SE1 7EH, U.K.,The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K
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10
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Portlock TJ, Tyson JY, Dantu SC, Rehman S, White RC, McIntire IE, Sewell L, Richardson K, Shaw R, Pandini A, Cianciotto NP, Garnett JA. Structure, Dynamics and Cellular Insight Into Novel Substrates of the Legionella pneumophila Type II Secretion System. Front Mol Biosci 2020; 7:112. [PMID: 32656228 PMCID: PMC7325957 DOI: 10.3389/fmolb.2020.00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Legionella pneumophila is a Gram-negative bacterium that is able to replicate within a broad range of aquatic protozoan hosts. L. pneumophila is also an opportunistic human pathogen that can infect macrophages and epithelia in the lung and lead to Legionnaires’ disease. The type II secretion system is a key virulence factor of L. pneumophila and is used to promote bacterial growth at low temperatures, regulate biofilm formation, modulate host responses to infection, facilitate bacterial penetration of mucin gels and is necessary for intracellular growth during the initial stages of infection. The L. pneumophila type II secretion system exports at least 25 substrates out of the bacterium and several of these, including NttA to NttG, contain unique amino acid sequences that are generally not observed outside of the Legionella genus. NttA, NttC, and NttD are required for infection of several amoebal species but it is unclear what influence other novel substrates have within their host. In this study, we show that NttE is required for optimal infection of Acanthamoeba castellanii and Vermamoeba vermiformis amoeba and is essential for the typical colony morphology of L. pneumophila. In addition, we report the atomic structures of NttA, NttC, and NttE and through a combined biophysical and biochemical hypothesis driven approach we propose novel functions for these substrates during infection. This work lays the foundation for future studies into the mechanistic understanding of novel type II substrate functions and how these relate to L. pneumophila ecology and disease.
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Affiliation(s)
- Theo J Portlock
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom.,Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Jessica Y Tyson
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Sarath C Dantu
- Department of Computer Science, Brunel University London, Uxbridge, United Kingdom
| | - Saima Rehman
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom
| | - Richard C White
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Ian E McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lee Sewell
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom
| | - Katherine Richardson
- Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Rosie Shaw
- Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Alessandro Pandini
- Department of Computer Science, Brunel University London, Uxbridge, United Kingdom
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom.,Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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11
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Macpherson JA, Theisen A, Masino L, Fets L, Driscoll PC, Encheva V, Snijders AP, Martin SR, Kleinjung J, Barran PE, Fraternali F, Anastasiou D. Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation. eLife 2019; 8:e45068. [PMID: 31264961 PMCID: PMC6636998 DOI: 10.7554/elife.45068] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
Several enzymes can simultaneously interact with multiple intracellular metabolites, however, how the allosteric effects of distinct ligands are integrated to coordinately control enzymatic activity remains poorly understood. We addressed this question using, as a model system, the glycolytic enzyme pyruvate kinase M2 (PKM2). We show that the PKM2 activator fructose 1,6-bisphosphate (FBP) alone promotes tetramerisation and increases PKM2 activity, but addition of the inhibitor L-phenylalanine (Phe) prevents maximal activation of FBP-bound PKM2 tetramers. We developed a method, AlloHubMat, that uses eigenvalue decomposition of mutual information derived from molecular dynamics trajectories to identify residues that mediate FBP-induced allostery. Experimental mutagenesis of these residues identified PKM2 variants in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings reveal residues involved in FBP-induced allostery that enable the integration of allosteric input from Phe and provide a paradigm for the coordinate regulation of enzymatic activity by simultaneous allosteric inputs.
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Affiliation(s)
- Jamie A Macpherson
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
| | - Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Laura Masino
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Louise Fets
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Paul C Driscoll
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Vesela Encheva
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Stephen R Martin
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Jens Kleinjung
- Computational Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Franca Fraternali
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
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12
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Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II. PLoS Comput Biol 2019; 15:e1006796. [PMID: 31150387 PMCID: PMC6576796 DOI: 10.1371/journal.pcbi.1006796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/17/2019] [Accepted: 03/28/2019] [Indexed: 12/16/2022] Open
Abstract
The calcium calmodulin-dependent protein kinase II (CaMKII) is a dodecameric holoenzyme important for encoding memory. Its activation, triggered by binding of calcium-calmodulin, persists autonomously after calmodulin dissociation. One (receiver) kinase captures and subsequently phosphorylates the regulatory domain peptide of a donor kinase forming a chained dimer as the first stage of autonomous activation. Protein dynamics simulations examined the conformational changes triggered by dimer formation and phosphorylation, aimed to provide a molecular rationale for human mutations that result in learning disabilities. Ensembles generated from X-ray crystal structures were characterized by network centrality and community analysis. Mutual information related collective motions to local fragment dynamics encoded with a structural alphabet. Implicit solvent tCONCOORD conformational ensembles revealed the dynamic architecture of inactive kinase domains was co-opted in the activated dimer but the network hub shifted from the nucleotide binding cleft to the captured peptide. Explicit solvent molecular dynamics (MD) showed nucleotide and substrate binding determinants formed coupled nodes in long-range signal relays between regulatory peptides in the dimer. Strain in the extended captured peptide was balanced by reduced flexibility of the receiver kinase C-lobe core. The relays were organized around a hydrophobic patch between the captured peptide and a key binding helix. The human mutations aligned along the relays. Thus, these mutations could disrupt the allosteric network alternatively, or in addition, to altered binding affinities. Non-binding protein sectors distant from the binding sites mediated the allosteric signalling; providing possible targets for inhibitor design. Phosphorylation of the peptide modulated the dielectric of its binding pocket to strengthen the patch, non-binding sectors, domain interface and temporal correlations between parallel relays. These results provide the molecular details underlying the reported positive kinase cooperativity to enrich the discussion on how autonomous activation by phosphorylation leads to long-term behavioural effects. Protein kinases play central roles in intracellular signalling. Auto-phosphorylation by bound nucleotide typically precedes phosphate transfer to multiple substrates. Protein conformational changes are central to kinase function, altering binding affinities to change cellular location and shunt from one signal pathway to another. In the brain, the multi-subunit kinase, CaMKII is activated by calcium-calmodulin upon calcium jumps produced by synaptic stimulation. Auto-transphosphorylation of a regulatory peptide enables the kinase to remain activated and mediate long-term behavioural effects after return to basal calcium levels. A database of mutated residues responsible for these effects is difficult to reconcile solely with impaired nucleotide or substrate binding. Therefore, we have computationally generated interaction networks to map the conformational plasticity of the kinase domains where most mutations localize. The network generated from the atomic structure of a phosphorylated dimer resolves protein sectors based on their collective motions. The sectors link nucleotide and substrate binding sites in self-reinforcing relays between regulatory peptides. The self-reinforcement is strengthened by phosphorylation consistent with the reported positive cooperativity of kinase activity with calcium-calmodulin concentration. The network gives a better match with the mutations and, in addition, reveals target sites for drug development.
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Kumar D, Kumar P. Integrated Mechanism of Lysine 351, PARK2, and STUB1 in AβPP Ubiquitination. J Alzheimers Dis 2019; 68:1125-1150. [DOI: 10.3233/jad-181219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dhiraj Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly DCE), Delhi, India
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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15
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Tiwari SP, Reuter N. Conservation of intrinsic dynamics in proteins — what have computational models taught us? Curr Opin Struct Biol 2018; 50:75-81. [DOI: 10.1016/j.sbi.2017.12.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/24/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
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16
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Motta S, Minici C, Corrada D, Bonati L, Pandini A. Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics. PLoS Comput Biol 2018; 14:e1006021. [PMID: 29489822 PMCID: PMC5847239 DOI: 10.1371/journal.pcbi.1006021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 03/12/2018] [Accepted: 02/01/2018] [Indexed: 11/18/2022] Open
Abstract
Hypoxia inducible factors (HIFs) are transcription factors belonging to the basic helix−loop−helix PER-ARNT-SIM (bHLH-PAS) protein family with a role in sensing oxygen levels in the cell. Under hypoxia, the HIF-α degradation pathway is blocked and dimerization with the aryl hydrocarbon receptor nuclear translocator (ARNT) makes HIF-α transcriptionally active. Due to the common hypoxic environment of tumors, inhibition of this mechanism by destabilization of HIF-α:ARNT dimerization has been proposed as a promising therapeutic strategy. Following the discovery of a druggable cavity within the PAS-B domain of HIF-2α, research efforts have been directed to identify artificial ligands that can impair heterodimerization. Although the crystallographic structures of the HIF-2α:ARNT complex have elucidated the dimer architecture and the 0X3-inhibitor placement within the HIF-2α PAS-B, unveiling the inhibition mechanism requires investigation of how ligand-induced perturbations could dynamically propagate through the structure and affect dimerization. To this end, we compared evolutionary features, intrinsic dynamics and energetic properties of the dimerization interfaces of HIF-2α:ARNT in both the apo and holo forms. Residue conservation analysis highlighted inter-domain connecting elements that have a role in dimerization. Analysis of domain contributions to the dimerization energy demonstrated the importance of bHLH and PAS-A of both partners and of HIF-2α PAS-B domain in dimer stabilization. Among quaternary structure oscillations revealed by Molecular Dynamics simulations, the hinge-bending motion of the ARNT PAS-B domain around the flexible PAS-A/PAS-B linker supports a general model for ARNT dimerization in different heterodimers. Comparison of the HIF-2α:ARNT dynamics in the apo and 0X3-bound forms indicated a model of inhibition where the HIF-2α-PAS-B interfaces are destabilised as a result of water-bridged ligand-protein interactions and these local effects allosterically propagate to perturb the correlated motions of the domains and inter-domain communication. These findings will guide the design of improved inhibitors to contrast cell survival in tumor masses. A low oxygen condition, called hypoxia, often occurs in tumor masses and generally correlates with worse prognosis. Cells in a tumor react to low oxygen levels with a metabolism modification induced by the activation of hypoxia inducible factors (HIFs) through dimerization with a partner protein and binding to a DNA target. Disrupting this protein-protein interaction could be a potential therapeutic strategy, but directly interfering with dimer formation can be troublesome because of the difficulty to design drugs that bind to protein interfaces. However, ligands that bind internal protein cavities can indirectly perturb the interfaces reducing dimers stability. Albeit protein crystallography had offered a detailed static picture of a HIF dimer bound to candidate inhibitors, it is not able to describe either the perturbation caused by binding or the molecular mechanism of dimer destabilization. Here we exploit molecular dynamics to identify the crucial interfaces in the HIF dimer stabilization and, by comparing the results obtained in the bound and unbound forms, we reveal the mechanism of ligand inhibition at atomic detail. All these findings will guide toward the design of improved dimerization inhibitors, to contrast cell survival in tumor masses.
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Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Claudia Minici
- Department of Immunology, Transplantation, and Infectious Diseases, DIBIT Fondazione San Raffaele, Milan, Italy
| | - Dario Corrada
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
- * E-mail: (AP); (LB)
| | - Alessandro Pandini
- Department of Computer Science–Synthetic Biology Theme, Brunel University London, Uxbridge, United Kingdom
- The Thomas Young Centre for Theory and Simulation of Materials, London, United Kingdom
- * E-mail: (AP); (LB)
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Laddach A, Ng JCF, Chung SS, Fraternali F. Genetic variants and protein-protein interactions: a multidimensional network-centric view. Curr Opin Struct Biol 2018; 50:82-90. [PMID: 29306755 DOI: 10.1016/j.sbi.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 01/18/2023]
Abstract
We review recent progress in the mapping of genetic variants to proteins, in the context of their interactions, as measured from experiments and/or computational predictions. Such variants can impact on the molecular mechanisms underlying an interaction and its stability. We highlight recent work which relies on the effective use of protein-protein interaction networks (PPINs), integrated with 3D structural information, for evaluating disease-associated variants. Furthermore, we discuss how the integration of multiple layers of biological information, in the context of PPINs, can improve the interpretation of genetic variants and inspire new therapeutic strategies.
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Affiliation(s)
- Anna Laddach
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Joseph Chi-Fung Ng
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Sun Sook Chung
- Randall Division of Cell and Molecular Biophysics, King's College London, UK; Department of Haematological Medicine, King's College London, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, UK.
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18
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Pappalardo M, Collu F, Macpherson J, Michaelis M, Fraternali F, Wass MN. Investigating Ebola virus pathogenicity using molecular dynamics. BMC Genomics 2017; 18:566. [PMID: 28812539 PMCID: PMC5558184 DOI: 10.1186/s12864-017-3912-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. RESULTS As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. CONCLUSION Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.
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Affiliation(s)
| | - Francesca Collu
- Randall Division of Cell and Molecular Biophysics King's College London, London, UK
| | - James Macpherson
- Randall Division of Cell and Molecular Biophysics King's College London, London, UK
| | | | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics King's College London, London, UK.
| | - Mark N Wass
- School of Biosciences, University of Kent, Kent, UK.
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Motta S, Bonati L. Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches. J Chem Inf Model 2017; 57:1563-1578. [DOI: 10.1021/acs.jcim.7b00125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental
Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Laura Bonati
- Department of Earth and Environmental
Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
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20
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Dey D, Nagaraja V, Ramakumar S. Structural and evolutionary analyses reveal determinants of DNA binding specificities of nucleoid-associated proteins HU and IHF. Mol Phylogenet Evol 2016; 107:356-366. [PMID: 27894997 DOI: 10.1016/j.ympev.2016.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 11/14/2016] [Accepted: 11/24/2016] [Indexed: 12/31/2022]
Abstract
Nucleoid-associated proteins (NAPs) are chromosome-organizing factors, which affect the transcriptional landscape of a bacterial cell. HU is an NAP, which binds to DNA with a broad specificity while homologous IHF (Integration Host Factor), binds DNA with moderately higher specificity. Specificity and differential binding affinity of HU/IHF proteins towards their target binding sites play a crucial role in their regulatory dynamics. Decades of biochemical and genomic studies have been carried out for HU and IHF like proteins. Yet, questions related to their DNA binding specificity, and differential ability to bend DNA thus affecting the binding site length remained unanswered. In addition, the problem has not been investigated from an evolutionary perspective. Our phylogenetic analysis revealed three major clades belonging to HU, IHFα and IHFβ like proteins with reference to E. coli. We carried out a comparative analysis of three-dimensional structures of HU/IHF proteins to gain insight into the structural basis of clade division. The present study revealed three major features which contribute to differential DNA binding specificity of HU/IHF proteins, (I) conformational restriction of DNA binding residues due to salt-bridge formation, (II) the enrichment of alanine in the DNA binding site increasing conformational space of flexible side chains in its vicinity and (III) nature of DNA binding residue (Arg to Lys bias in different clades) which interacts differentially to DNA bases. We observed an extended electropositive surface at the DNA draping site for IHF clade proteins compared to HU, which stabilizes the DNA bend. Differences in the dimer stabilization strategies between HU and IHF were also observed. Our analysis reveals a comprehensive evolutionary picture, which rationalizes the origin of multi-specificity of HU/IHF proteins using sequence and structure-based determinants, which could also be applied to understand differences in binding specificities of other nucleic acid binding proteins.
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Affiliation(s)
- Debayan Dey
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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21
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Laffy JMJ, Dodev T, Macpherson JA, Townsend C, Lu HC, Dunn-Walters D, Fraternali F. Promiscuous antibodies characterised by their physico-chemical properties: From sequence to structure and back. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 128:47-56. [PMID: 27639634 PMCID: PMC6167913 DOI: 10.1016/j.pbiomolbio.2016.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/25/2016] [Accepted: 09/05/2016] [Indexed: 12/26/2022]
Abstract
Human B cells produce antibodies, which bind to their cognate antigen based on distinct molecular properties of the antibody CDR loop. We have analysed a set of 10 antibodies showing a clear difference in their binding properties to a panel of antigens, resulting in two subsets of antibodies with a distinct binding phenotype. We call the observed binding multiplicity ‘promiscuous’ and selected physico-chemical CDRH3 characteristics and conformational preferences may characterise these promiscuous antibodies. To classify CDRH3 physico-chemical properties playing a role in their binding properties, we used statistical analyses of the sequences annotated by Kidera factors. To characterise structure-function requirements for antigen binding multiplicity we employed Molecular Modelling and Monte Carlo based coarse-grained simulations. The ability to predict the molecular causes of promiscuous, multi-binding behaviour would greatly improve the efficiency of the therapeutic antibody discovery process.
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Affiliation(s)
- Julie M J Laffy
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Tihomir Dodev
- Department of Immunobiology, King's College London, UK
| | - Jamie A Macpherson
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | | | - Hui Chun Lu
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Deborah Dunn-Walters
- Department of Immunobiology, King's College London, UK; Faculty of Health and Medical Sciences, University of Surrey, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, UK.
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22
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Corrada D, Soshilov AA, Denison MS, Bonati L. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation. PLoS Comput Biol 2016; 12:e1004981. [PMID: 27295348 PMCID: PMC4905635 DOI: 10.1371/journal.pcbi.1004981] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 05/12/2016] [Indexed: 01/15/2023] Open
Abstract
The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the functional activity of the AhR. Computational modeling combined with experimental validation may give insight into structural and functional properties of protein systems. The basic Helix-Loop-Helix PER-ARNT-SIM (bHLH-PAS) proteins show conserved functional domains despite the broad range of functions exerted by the different systems. Within this protein family, the Aryl hydrocarbon Receptor (AhR) is known to mediate the toxic effects of a number of environmental contaminants, including dioxins and dioxin-like chemicals, and it also exerts other biochemical and physiological effects. Despite the absence of experimentally determined structures, theoretical models of the AhR PAS domains developed on the basis of homologous systems have allowed understanding of some aspects of the molecular mechanisms underlying its function. In this work we present alternative structural models of the transcriptionally active complex of AhR with the AhR Nuclear Translocator (ARNT) protein. Computational characterization of the modeled protein-protein interaction interfaces guided the design of mutagenesis experiments, and evaluation of the DNA binding ability of the resulting AhR:ARNT dimer mutants allowed validation of the models and selection of the most reliable one. These findings open new research directions for understanding the molecular mechanisms underlying the functional activity of the AhR.
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Affiliation(s)
- Dario Corrada
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Anatoly A. Soshilov
- Department of Environmental Toxicology, University of California, Davis, Davis, California, United States of America
| | - Michael S. Denison
- Department of Environmental Toxicology, University of California, Davis, Davis, California, United States of America
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
- * E-mail:
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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Pandini A, Kleinjung J, Taylor WR, Junge W, Khan S. The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance. Biophys J 2016; 109:975-87. [PMID: 26331255 PMCID: PMC4564677 DOI: 10.1016/j.bpj.2015.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/20/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022] Open
Abstract
The proton-driven ATP synthase (FOF1) is comprised of two rotary, stepping motors (FO and F1) coupled by an elastic power transmission. The elastic compliance resides in the rotor module that includes the membrane-embedded FO c-ring. Proton transport by FO is firmly coupled to the rotation of the c-ring relative to other FO subunits (ab2). It drives ATP synthesis. We used a computational method to investigate the contribution of the c-ring to the total elastic compliance. We performed principal component analysis of conformational ensembles built using distance constraints from the bovine mitochondrial c-ring x-ray structure. Angular rotary twist, the dominant ring motion, was estimated to show that the c-ring accounted in part for the measured compliance. Ring rotation was entrained to rotation of the external helix within each hairpin-shaped c-subunit in the ring. Ensembles of monomer and dimers extracted from complete c-rings showed that the coupling between collective ring and the individual subunit motions was independent of the size of the c-ring, which varies between organisms. Molecular determinants were identified by covariance analysis of residue coevolution and structural-alphabet-based local dynamics correlations. The residue coevolution gave a readout of subunit architecture. The dynamic couplings revealed that the hinge for both ring and subunit helix rotations was constructed from the proton-binding site and the adjacent glycine motif (IB-GGGG) in the midmembrane plane. IB-GGGG motifs were linked by long-range couplings across the ring, while intrasubunit couplings connected the motif to the conserved cytoplasmic loop and adjacent segments. The correlation with principal collective motions shows that the couplings underlie both ring rotary and bending motions. Noncontact couplings between IB-GGGG motifs matched the coevolution signal as well as contact couplings. The residue coevolution reflects the physiological importance of the dynamics that may link proton transfer to ring compliance.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science and Synthetic Biology Theme, Brunel University London, Uxbridge, United Kingdom
| | - Jens Kleinjung
- Mathematical Biology, The Francis Crick Institute (formerly the National Institute for Medical Research), London, United Kingdom
| | - Willie R Taylor
- Mathematical Biology, The Francis Crick Institute (formerly the National Institute for Medical Research), London, United Kingdom
| | - Wolfgang Junge
- Department of Biophysics, University of Osnabrück, Osnabrück, Germany
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, California.
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Lu HC, Herrera Braga J, Fraternali F. PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. ACTA ACUST UNITED AC 2016; 32:2534-6. [PMID: 27153707 PMCID: PMC4978923 DOI: 10.1093/bioinformatics/btw153] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/15/2016] [Indexed: 12/24/2022]
Abstract
Summary: We present a practical computational pipeline to readily perform data analyses of protein–protein interaction networks by using genetic and functional information mapped onto protein structures. We provide a 3D representation of the available protein structure and its regions (surface, interface, core and disordered) for the selected genetic variants and/or SNPs, and a prediction of the mutants’ impact on the protein as measured by a range of methods. We have mapped in total 2587 genetic disorder-related SNPs from OMIM, 587 873 cancer-related variants from COSMIC, and 1 484 045 SNPs from dbSNP. All result data can be downloaded by the user together with an R-script to compute the enrichment of SNPs/variants in selected structural regions. Availability and Implementation: PinSnps is available as open-access service at http://fraternalilab.kcl.ac.uk/PinSnps/ Contact:franca.fraternali@kcl.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hui-Chun Lu
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Julián Herrera Braga
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
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Pandini A, Fornili A. Using Local States To Drive the Sampling of Global Conformations in Proteins. J Chem Theory Comput 2016; 12:1368-79. [PMID: 26808351 PMCID: PMC5356493 DOI: 10.1021/acs.jctc.5b00992] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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] [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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28
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Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci 2015; 2:20. [PMID: 26075209 PMCID: PMC4445325 DOI: 10.3389/fmolb.2015.00020] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 01/01/2023] Open
Abstract
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.
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Affiliation(s)
- Pierrick Craveur
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Agnel P Joseph
- Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK
| | - Jeremy Esque
- Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France
| | - Tarun J Narwani
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Floriane Noël
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Nicolas Shinada
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Matthieu Goguet
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Sylvain Leonard
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Pierre Poulain
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Ets Poulain Pointe-Noire, Congo
| | - Olivier Bertrand
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Guilhem Faure
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA
| | - Joseph Rebehmed
- Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie - MNHN - IRD - IUC Paris, France
| | | | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - Ramachandra M Bhaskara
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany
| | - Jonathan Barnoud
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France
| | - Stéphane Téletchéa
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France
| | - Vincent Jallu
- Platelet Unit, Institut National de la Transfusion Sanguine Paris, France
| | - Jiri Cerny
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Catherine Etchebest
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | | | - Jean-Christophe Gelly
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Alexandre G de Brevern
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
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29
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Pernigo S, Fukuzawa A, Pandini A, Holt M, Kleinjung J, Gautel M, Steiner RA. The Crystal Structure of the Human Titin:Obscurin Complex Reveals a Conserved yet Specific Muscle M-Band Zipper Module. J Mol Biol 2015; 427:718-736. [DOI: 10.1016/j.jmb.2014.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/15/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
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30
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Zou T, Risso VA, Gavira JA, Sanchez-Ruiz JM, Ozkan SB. Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme. Mol Biol Evol 2014; 32:132-43. [PMID: 25312912 DOI: 10.1093/molbev/msu281] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
β-Lactamases are produced by many modern bacteria as a mechanism of resistance toward β-lactam antibiotics, the most common antibiotics in use. β-Lactamases, however, are ancient enzymes that originated billions of years ago. Recently, proteins corresponding to 2- to 3-Gy-old Precambrian nodes in the evolution of Class A β-lactamases have been prepared and shown to be moderately efficient promiscuous catalysts, able to degrade a variety of antibiotics with catalytic efficiency levels similar to those of an average modern enzyme. Remarkably, there are few structural differences (in particular at the active-site regions) between the resurrected enzymes and a penicillin-specialist modern β-lactamase. Here, we propose that the ancestral promiscuity originates from conformational dynamics. We investigate the differences in conformational dynamics of the ancient and extant β-lactamases through MD simulations and quantify the contribution of each position to functionally related dynamics through Dynamic Flexibility Index. The modern TEM-1 lactamase shows a comparatively rigid active-site region, likely reflecting adaptation for efficient degradation of a specific substrate (penicillin), whereas enhanced deformability at the active-site neighborhood in the ancestral resurrected proteins likely accounts for the binding and subsequent degradation of antibiotic molecules of different size and shape. Clustering of the conformational dynamics on the basis of Principal Component Analysis is in agreement with the functional divergence, as the ancient β-lactamases cluster together, separated from their modern descendant. Finally, our analysis leads to testable predictions, as sites of potential relevance for the evolution of dynamics are identified and mutations at those sites are expected to alter substrate-specificity.
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Affiliation(s)
- Taisong Zou
- Center for Biological Physics, Department of Physics, Arizona State University
| | - Valeria A Risso
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Jose A Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-Universidad de Granada), Granada, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University
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