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Lombard V, Grudinin S, Laine E. Explaining Conformational Diversity in Protein Families through Molecular Motions. Sci Data 2024; 11:752. [PMID: 38987561 PMCID: PMC11237097 DOI: 10.1038/s41597-024-03524-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024] Open
Abstract
Proteins play a central role in biological processes, and understanding their conformational variability is crucial for unraveling their functional mechanisms. Recent advancements in high-throughput technologies have enhanced our knowledge of protein structures, yet predicting their multiple conformational states and motions remains challenging. This study introduces Dimensionality Analysis for protein Conformational Exploration (DANCE) for a systematic and comprehensive description of protein families conformational variability. DANCE accommodates both experimental and predicted structures. It is suitable for analysing anything from single proteins to superfamilies. Employing it, we clustered all experimentally resolved protein structures available in the Protein Data Bank into conformational collections and characterized them as sets of linear motions. The resource facilitates access and exploitation of the multiple states adopted by a protein and its homologs. Beyond descriptive analysis, we assessed classical dimensionality reduction techniques for sampling unseen states on a representative benchmark. This work improves our understanding of how proteins deform to perform their functions and opens ways to a standardised evaluation of methods designed to sample and generate protein conformations.
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Affiliation(s)
- Valentin Lombard
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France
| | - Sergei Grudinin
- Université Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000, Grenoble, France.
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005, Paris, France.
- Institut Universitaire de France (IUF), Paris, France.
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2
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Lam JH, Nakano A, Katritch V. Scalable computation of anisotropic vibrations for large macromolecular assemblies. Nat Commun 2024; 15:3479. [PMID: 38658556 PMCID: PMC11043083 DOI: 10.1038/s41467-024-47685-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
The Normal Mode Analysis (NMA) is a standard approach to elucidate the anisotropic vibrations of macromolecules at their folded states, where low-frequency collective motions can reveal rearrangements of domains and changes in the exposed surface of macromolecules. Recent advances in structural biology have enabled the resolution of megascale macromolecules with millions of atoms. However, the calculation of their vibrational modes remains elusive due to the prohibitive cost associated with constructing and diagonalizing the underlying eigenproblem and the current approaches to NMA are not readily adaptable for efficient parallel computing on graphic processing unit (GPU). Here, we present eigenproblem construction and diagonalization approach that implements level-structure bandwidth-reducing algorithms to transform the sparse computation in NMA to a globally-sparse-yet-locally-dense computation, allowing batched tensor products to be most efficiently executed on GPU. We map, optimize, and compare several low-complexity Krylov-subspace eigensolvers, supplemented by techniques such as Chebyshev filtering, sum decomposition, external explicit deflation and shift-and-inverse, to allow fast GPU-resident calculations. The method allows accurate calculation of the first 1000 vibrational modes of some largest structures in PDB ( > 2.4 million atoms) at least 250 times faster than existing methods.
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Affiliation(s)
- Jordy Homing Lam
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Bridge Institute and Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, University of Southern California, Los Angeles, CA, USA
| | - Aiichiro Nakano
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.
- Department of Computer Science, University of Southern California, Los Angeles, CA, USA.
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Bridge Institute and Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
- Center for New Technologies in Drug Discovery and Development, University of Southern California, Los Angeles, CA, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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3
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Luchniak A, Roy PS, Kumar A, Schneider IC, Gelfand VI, Jernigan RL, Gupta ML. Tubulin CFEOM mutations both inhibit or activate kinesin motor activity. Mol Biol Cell 2024; 35:ar32. [PMID: 38170592 PMCID: PMC10916880 DOI: 10.1091/mbc.e23-01-0020] [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: 01/23/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Kinesin-mediated transport along microtubules is critical for axon development and health. Mutations in the kinesin Kif21a, or the microtubule subunit β-tubulin, inhibit axon growth and/or maintenance resulting in the eye-movement disorder congenital fibrosis of the extraocular muscles (CFEOM). While most examined CFEOM-causing β-tubulin mutations inhibit kinesin-microtubule interactions, Kif21a mutations activate the motor protein. These contrasting observations have led to opposed models of inhibited or hyperactive Kif21a in CFEOM. We show that, contrary to other CFEOM-causing β-tubulin mutations, R380C enhances kinesin activity. Expression of β-tubulin-R380C increases kinesin-mediated peroxisome transport in S2 cells. The binding frequency, percent motile engagements, run length and plus-end dwell time of Kif21a are also elevated on β-tubulin-R380C compared with wildtype microtubules in vitro. This conserved effect persists across tubulins from multiple species and kinesins from different families. The enhanced activity is independent of tail-mediated kinesin autoinhibition and thus utilizes a mechanism distinct from CFEOM-causing Kif21a mutations. Using molecular dynamics, we visualize how β-tubulin-R380C allosterically alters critical structural elements within the kinesin motor domain, suggesting a basis for the enhanced motility. These findings resolve the disparate models and confirm that inhibited or increased kinesin activity can both contribute to CFEOM. They also demonstrate the microtubule's role in regulating kinesins and highlight the importance of balanced transport for cellular and organismal health.
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Affiliation(s)
- Anna Luchniak
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011
| | - Pallavi Sinha Roy
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011
| | - Ambuj Kumar
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Ian C. Schneider
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011
| | - Vladimir I. Gelfand
- Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611
| | - Robert L. Jernigan
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Mohan L. Gupta
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011
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4
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Yánez Arcos DL, Thirumuruganandham SP. Structural and pKa Estimation of the Amphipathic HR1 in SARS-CoV-2: Insights from Constant pH MD, Linear vs. Nonlinear Normal Mode Analysis. Int J Mol Sci 2023; 24:16190. [PMID: 38003380 PMCID: PMC10671649 DOI: 10.3390/ijms242216190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
A comprehensive understanding of molecular interactions and functions is imperative for unraveling the intricacies of viral protein behavior and conformational dynamics during cellular entry. Focusing on the SARS-CoV-2 spike protein (SARS-CoV-2 sp), a Principal Component Analysis (PCA) on a subset comprising 131 A-chain structures in presence of various inhibitors was conducted. Our analyses unveiled a compelling correlation between PCA modes and Anisotropic Network Model (ANM) modes, underscoring the reliability and functional significance of low-frequency modes in adapting to diverse inhibitor binding scenarios. The role of HR1 in viral processing, both linear Normal Mode Analysis (NMA) and Nonlinear NMA were implemented. Linear NMA exhibited substantial inter-structure variability, as evident from a higher Root Mean Square Deviation (RMSD) range (7.30 Å), nonlinear NMA show stability throughout the simulations (RMSD 4.85 Å). Frequency analysis further emphasized that the energy requirements for conformational changes in nonlinear modes are notably lower compared to their linear counterparts. Using simulations of molecular dynamics at constant pH (cpH-MD), we successfully predicted the pKa order of the interconnected residues within the HR1 mutations at lower pH values, suggesting a transition to a post-fusion structure. The pKa determination study illustrates the profound effects of pH variations on protein structure. Key results include pKa values of 9.5179 for lys-921 in the D936H mutant, 9.50 for the D950N mutant, and a slightly higher value of 10.49 for the D936Y variant. To further understand the behavior and physicochemical characteristics of the protein in a biologically relevant setting, we also examine hydrophobic regions in the prefused states of the HR1 protein mutants D950N, D936Y, and D936H in our study. This analysis was conducted to ascertain the hydrophobic moment of the protein within a lipid environment, shedding light on its behavior and physicochemical properties in a biologically relevant context.
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5
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Sabei A, Caldas Baia TG, Saffar R, Martin J, Frezza E. Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. J Chem Inf Model 2023; 63:2554-2572. [PMID: 36972178 DOI: 10.1021/acs.jcim.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
We investigated the capability of internal normal modes to reproduce RNA flexibility and predict observed RNA conformational changes and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified representation of the RNA structure and its potential energy. Three data sets were also created to investigate different aspects. Despite all the approximations, our study shows that iNMA is a suitable method to take into account RNA flexibility and describe its conformational changes opening the route to its applicability in any integrative approach where these properties are crucial.
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Golub M, Moldenhauer M, Matsarskaia O, Martel A, Grudinin S, Soloviov D, Kuklin A, Maksimov EG, Friedrich T, Pieper J. Stages of OCP-FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 2: Small-Angle Neutron Scattering with Partial Deuteration. J Phys Chem B 2023; 127:1901-1913. [PMID: 36815674 DOI: 10.1021/acs.jpcb.2c07182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We used small-angle neutron scattering partially coupled with size-exclusion chromatography to unravel the solution structures of two variants of the Orange Carotenoid Protein (OCP) lacking the N-terminal extension (OCP-ΔNTE) and its complex formation with the Fluorescence Recovery Protein (FRP). The dark-adapted, orange form OCP-ΔNTEO is fully photoswitchable and preferentially binds the pigment echinenone. Its complex with FRP consists of a monomeric OCP component, which closely resembles the compact structure expected for the OCP ground state, OCPO. In contrast, the pink form OCP-ΔNTEP, preferentially binding the pigment canthaxanthin, is mostly nonswitchable. The pink OCP form appears to occur as a dimer and is characterized by a separation of the N- and C-terminal domains, with the canthaxanthin embedded only into the N-terminal domain. Therefore, OCP-ΔNTEP can be viewed as a prototypical model system for the active, spectrally red-shifted state of OCP, OCPR. The dimeric structure of OCP-ΔNTEP is retained in its complex with FRP. Small-angle neutron scattering using partially deuterated OCP-FRP complexes reveals that FRP undergoes significant structural changes upon complex formation with OCP. The observed structures are assigned to individual intermediates of the OCP photocycle in the presence of FRP.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
| | - Marcus Moldenhauer
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Olga Matsarskaia
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, Avenue des Martyrs 71, 38042 Cedex 9 Grenoble, France
| | - Sergei Grudinin
- Université Grenoble Alpes, CNRS, Grenoble INP, LJK, 38000 Grenoble, France
| | - Dmytro Soloviov
- Faculty of Physics, Adam Mickiewicz University, ul. Wieniawskiego 1, 61-712 Poznan, Poland.,Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kirova 36a, 07270 Chornobyl, Ukraine
| | - Alexander Kuklin
- Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980 Dubna, Russia.,Moscow Institute of Physics and Technology, Institutskiy per. 9, 141701 Dolgoprudny, Russia
| | - Eugene G Maksimov
- Department of Biophysics, M. V. Lomonosov Moscow State University, Vorob'jovy Gory 1-12, 119899 Moscow, Russia
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, 50411 Tartu, Estonia
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7
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Tordai H, Suhajda E, Sillitoe I, Nair S, Varadi M, Hegedus T. Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology. Int J Mol Sci 2022; 23:ijms23168877. [PMID: 36012140 PMCID: PMC9408558 DOI: 10.3390/ijms23168877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 02/06/2023] Open
Abstract
The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
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Affiliation(s)
- Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
| | - Erzsebet Suhajda
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, 1111 Budapest, Hungary
- Wigner Research Centre for Physics, 1121 Budapest, Hungary
| | - Ian Sillitoe
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Sreenath Nair
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Mihaly Varadi
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Tamas Hegedus
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, 1052 Budapest, Hungary
- Correspondence:
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8
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van Keulen SC, Martin J, Colizzi F, Frezza E, Trpevski D, Diaz NC, Vidossich P, Rothlisberger U, Hellgren Kotaleski J, Wade RC, Carloni P. Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Siri C. van Keulen
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science – Chemistry Utrecht University Utrecht The Netherlands
| | - Juliette Martin
- CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry University of Lyon Lyon France
| | - Francesco Colizzi
- Molecular Ocean Laboratory, Department of Marine Biology and Oceanography Institute of Marine Sciences, ICM‐CSIC Barcelona Spain
| | - Elisa Frezza
- Université Paris Cité, CiTCoM, CNRS Paris France
| | - Daniel Trpevski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science KTH Royal Institute of Technology Stockholm
| | - Nuria Cirauqui Diaz
- CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry University of Lyon Lyon France
| | - Pietro Vidossich
- Molecular Modeling and Drug Discovery Lab Istituto Italiano di Tecnologia Genoa Italy
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry Ecole Polytechnique Fédérale de Lausanne (EPFL) Lausanne
| | - Jeanette Hellgren Kotaleski
- Science for Life Laboratory, School of Electrical Engineering and Computer Science KTH Royal Institute of Technology Stockholm
- Department of Neuroscience Karolinska Institute Stockholm
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group Heidelberg Institute for Theoretical Studies (HITS) Heidelberg Germany
- Center for Molecular Biology (ZMBH), DKFZ‐ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University Heidelberg Germany
| | - Paolo Carloni
- Institute for Neuroscience and Medicine (INM‐9) and Institute for Advanced Simulations (IAS‐5) “Computational biomedicine” Forschungszentrum Jülich Jülich Germany
- INM‐11 JARA‐Institute: Molecular Neuroscience and Neuroimaging Forschungszentrum Jülich Jülich Germany
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9
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Molza AE, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost C. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Front Mol Biosci 2022; 9:826136. [PMID: 35480882 PMCID: PMC9035671 DOI: 10.3389/fmolb.2022.826136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/21/2022] [Indexed: 01/25/2023] Open
Abstract
Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.
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Affiliation(s)
- Anne-Elisabeth Molza
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Yvonne Westermaier
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | - Pierre Ducrot
- Biophysics and Modelling Department/In Vitro Pharmacology Unit–IDRS (Servier Research Institute), Croissy-sur-Seine, France
| | | | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA, United States
| | - Charles H. Robert
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Chantal Prévost
- CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
- *Correspondence: Chantal Prévost ,
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10
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Structural insights into the catalytic cycle of a bacterial multidrug ABC efflux pump. J Mol Biol 2022; 434:167541. [DOI: 10.1016/j.jmb.2022.167541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
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11
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Johansen NT, Bonaccorsi M, Bengtsen T, Larsen AH, Tidemand FG, Pedersen MC, Huda P, Berndtsson J, Darwish T, Yepuri NR, Martel A, Pomorski TG, Bertarello A, Sansom MS, Rapp M, Crehuet R, Schubeis T, Lindorff-Larsen K, Pintacuda G, Arleth L. Mg 2+-dependent conformational equilibria in CorA and an integrated view on transport regulation. eLife 2022; 11:71887. [PMID: 35129435 PMCID: PMC8865849 DOI: 10.7554/elife.71887] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
The CorA family of proteins regulates the homeostasis of divalent metal ions in many bacteria, archaea, and eukaryotic mitochondria, making it an important target in the investigation of the mechanisms of transport and its functional regulation. Although numerous structures of open and closed channels are now available for the CorA family, the mechanism of the transport regulation remains elusive. Here, we investigated the conformational distribution and associated dynamic behaviour of the pentameric Mg2+ channel CorA at room temperature using small-angle neutron scattering (SANS) in combination with molecular dynamics (MD) simulations and solid-state nuclear magnetic resonance spectroscopy (NMR). We find that neither the Mg2+-bound closed structure nor the Mg2+-free open forms are sufficient to explain the average conformation of CorA. Our data support the presence of conformational equilibria between multiple states, and we further find a variation in the behaviour of the backbone dynamics with and without Mg2+. We propose that CorA must be in a dynamic equilibrium between different non-conducting states, both symmetric and asymmetric, regardless of bound Mg2+ but that conducting states become more populated in Mg2+-free conditions. These properties are regulated by backbone dynamics and are key to understanding the functional regulation of CorA.
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Affiliation(s)
| | - Marta Bonaccorsi
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Tone Bengtsen
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Andreas Haahr Larsen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen E, Denmark
| | | | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen E, Denmark
| | - Pie Huda
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Australia
| | - Jens Berndtsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Tamim Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, Australia
| | - Nageshewar Rao Yepuri
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, Australia
| | | | - Thomas Günther Pomorski
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Andrea Bertarello
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Mark Sp Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mikaela Rapp
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ramon Crehuet
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Tobias Schubeis
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | | | - Guido Pintacuda
- Centre de RMN à Très hauts Champs de Lyon, UMR 5280, CNRS, University of Lyon, Villeurbanne, France
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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12
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Sanejouand YH. Normal-mode driven exploration of protein domain motions. J Comput Chem 2021; 42:2250-2257. [PMID: 34599620 DOI: 10.1002/jcc.26755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/02/2021] [Accepted: 09/05/2021] [Indexed: 12/27/2022]
Abstract
Domain motions involved in the function of proteins can often be well described as a combination of motions along a handfull of low-frequency modes, that is, with the values of a few normal coordinates. This means that, when the functional motion of a protein is unknown, it should prove possible to predict it, since it amounts to guess a few values. However, without the help of additional experimental data, using normal coordinates for generating accurate conformers far away from the initial one is not so straightforward. To do so, a new approach is proposed: instead of building conformers directly with the values of a subset of normal coordinates, they are built in two steps, the conformer built with normal coordinates being just used for defining a set of distance constraints, the final conformer being built so as to match them. Note that this approach amounts to transform the problem of generating accurate protein conformers using normal coordinates into a better known one: the distance-geometry problem, which is herein solved with the help of the ROSETTA software. In the present study, this approach allowed to rebuild accurately six large amplitude conformational changes, using at most six low-frequency normal coordinates. As a consequence of the low-dimensionality of the corresponding subspace, random exploration also proved enough for generating low-energy conformers close to the known end-point of the conformational change of the LAO binding protein, lysozyme T4 and adenylate kinase.
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13
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Hassan A, Byju S, Whitford PC. The energetics of subunit rotation in the ribosome. Biophys Rev 2021; 13:1029-1037. [PMID: 35059025 PMCID: PMC8724491 DOI: 10.1007/s12551-021-00877-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis in the cell is controlled by an elaborate sequence of conformational rearrangements in the ribosome. The composition of a ribosome varies by species, though they typically contain ∼ 50-100 RNA and protein molecules. While advances in structural techniques have revolutionized our understanding of long-lived conformational states, a vast range of transiently visited configurations can not be directly observed. In these cases, computational/simulation methods can be used to understand the mechanical properties of the ribosome. Insights from these approaches can then help guide next-generation experimental measurements. In this short review, we discuss theoretical strategies that have been deployed to quantitatively describe the energetics of collective rearrangements in the ribosome. We focus on efforts to probe large-scale subunit rotation events, which involve the coordinated displacement of large numbers of atoms (tens of thousands). These investigations are revealing how the molecular structure of the ribosome encodes the mechanical properties that control large-scale dynamics.
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Affiliation(s)
- Asem Hassan
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
| | - Sandra Byju
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
| | - Paul C. Whitford
- Center for Theoretical Biological Physics, 360 Huntington Ave, Boston, 02115 MA USA
- Physics Department, Northeastern University, 360 Huntington Ave, Boston, 02115 MA USA
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14
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Khade PM, Scaramozzino D, Kumar A, Lacidogna G, Carpinteri A, Jernigan RL. hdANM: a new comprehensive dynamics model for protein hinges. Biophys J 2021; 120:4955-4965. [PMID: 34687719 PMCID: PMC8633836 DOI: 10.1016/j.bpj.2021.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
Hinge motions are essential for many protein functions, and their dynamics are important to understand underlying biological mechanisms. The ways that these motions are represented by various computational methods differ significantly. By focusing on a specific class of motion, we have developed a new hinge-domain anisotropic network model (hdANM) that is based on the prior identification of flexible hinges and rigid domains in the protein structure and the subsequent generation of global hinge motions. This yields a set of motions in which the relative translations and rotations of the rigid domains are modulated and controlled by the deformation of the flexible hinges, leading to a more restricted, specific view of these motions. hdANM is the first model, to our knowledge, that combines information about protein hinges and domains to model the characteristic hinge motions of a protein. The motions predicted with this new elastic network model provide important conceptual advantages for understanding the underlying biological mechanisms. As a matter of fact, the generated hinge movements are found to resemble the expected mechanisms required for the biological functions of diverse proteins. Another advantage of this model is that the domain-level coarse graining makes it significantly more computationally efficient, enabling the generation of hinge motions within even the largest molecular assemblies, such as those from cryo-electron microscopy. hdANM is also comprehensive as it can perform in the same way as the well-known protein dynamics models (anisotropic network model, rotations-translations of blocks, and nonlinear rigid block normal mode analysis), depending on the definition of flexible and rigid parts in the protein structure and on whether the motions are extrapolated in a linear or nonlinear fashion. Furthermore, our results indicate that hdANM produces more realistic motions as compared to the anisotropic network model. hdANM is an open-source software, freely available, and hosted on a user-friendly website.
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Affiliation(s)
- Pranav M Khade
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa
| | - Domenico Scaramozzino
- Department of Structural, Geotechnical, and Building Engineering, Politecnico di Torino, Torino, Italy
| | - Ambuj Kumar
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa
| | - Giuseppe Lacidogna
- Department of Structural, Geotechnical, and Building Engineering, Politecnico di Torino, Torino, Italy
| | - Alberto Carpinteri
- Department of Structural, Geotechnical, and Building Engineering, Politecnico di Torino, Torino, Italy
| | - Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa.
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15
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Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes. Int J Mol Sci 2021; 22:ijms221910501. [PMID: 34638837 PMCID: PMC8508695 DOI: 10.3390/ijms221910501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/18/2021] [Accepted: 09/26/2021] [Indexed: 02/01/2023] Open
Abstract
Protein dynamics has been investigated since almost half a century, as it is believed to constitute the fundamental connection between structure and function. Elastic network models (ENMs) have been widely used to predict protein dynamics, flexibility and the biological mechanism, from which remarkable results have been found regarding the prediction of protein conformational changes. Starting from the knowledge of the reference structure only, these conformational changes have been usually predicted either by looking at the individual mode shapes of vibrations (i.e., by considering the free vibrations of the ENM) or by applying static perturbations to the protein network (i.e., by considering a linear response theory). In this paper, we put together the two previous approaches and evaluate the complete protein response under the application of dynamic perturbations. Harmonic forces with random directions are applied to the protein ENM, which are meant to simulate the single frequency-dependent components of the collisions of the surrounding particles, and the protein response is computed by solving the dynamic equations in the underdamped regime, where mass, viscous damping and elastic stiffness contributions are explicitly taken into account. The obtained motion is investigated both in the coordinate space and in the sub-space of principal components (PCs). The results show that the application of perturbations in the low-frequency range is able to drive the protein conformational change, leading to remarkably high values of direction similarity. Eventually, this suggests that protein conformational change might be triggered by external collisions and favored by the inherent low-frequency dynamics of the protein structure.
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16
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Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD. Nat Commun 2021; 12:5004. [PMID: 34408154 PMCID: PMC8373988 DOI: 10.1038/s41467-021-25076-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/15/2021] [Indexed: 12/22/2022] Open
Abstract
The endoplasmic reticulum (ER) Hsp70 chaperone BiP is regulated by AMPylation, a reversible inactivating post-translational modification. Both BiP AMPylation and deAMPylation are catalysed by a single ER-localised enzyme, FICD. Here we present crystallographic and solution structures of a deAMPylation Michaelis complex formed between mammalian AMPylated BiP and FICD. The latter, via its tetratricopeptide repeat domain, binds a surface that is specific to ATP-state Hsp70 chaperones, explaining the exquisite selectivity of FICD for BiP’s ATP-bound conformation both when AMPylating and deAMPylating Thr518. The eukaryotic deAMPylation mechanism thus revealed, rationalises the role of the conserved Fic domain Glu234 as a gatekeeper residue that both inhibits AMPylation and facilitates hydrolytic deAMPylation catalysed by dimeric FICD. These findings point to a monomerisation-induced increase in Glu234 flexibility as the basis of an oligomeric state-dependent switch between FICD’s antagonistic activities, despite a similar mode of engagement of its two substrates — unmodified and AMPylated BiP. The ER chaperone BiP is regulated by FICD-mediated AMPylation and deAMPylation. Here, the authors characterise the structure of mammalian AMPylated BiP bound to FICD, by X-ray crystallography and neutron scattering, providing insights into the mechanism of BiP AMPylation and deAMPylation.
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17
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Igashov I, Pavlichenko N, Grudinin S. Spherical convolutions on molecular graphs for protein model quality assessment. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abf856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Abstract
Processing information on three-dimensional (3D) objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using rotation-equivariant operations. However, contrary to images, graphs generally have irregular topology. This makes it challenging to define a rotation-equivariant convolution operation on these structures. In this work, we propose spherical graph convolutional network that processes 3D models of proteins represented as molecular graphs. In a protein molecule, individual amino acids have common topological elements. This allows us to unambiguously associate each amino acid with a local coordinate system and construct rotation-equivariant spherical filters that operate on angular information between graph nodes. Within the framework of the protein model quality assessment problem, we demonstrate that the proposed spherical convolution method significantly improves the quality of model assessment compared to the standard message-passing approach. It is also comparable to state-of-the-art methods, as we demonstrate on critical assessment of structure prediction benchmarks. The proposed technique operates only on geometric features of protein 3D models. This makes it universal and applicable to any other geometric-learning task where the graph structure allows constructing local coordinate systems. The method is available at https://team.inria.fr/nano-d/software/s-gcn/.
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18
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Laine E, Grudinin S. HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps. J Phys Chem B 2021; 125:2577-2588. [PMID: 33687221 DOI: 10.1021/acs.jpcb.0c11633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In light of the recent very rapid progress in protein structure prediction, accessing the multitude of functional protein states is becoming more central than ever before. Indeed, proteins are flexible macromolecules, and they often perform their function by switching between different conformations. However, high-resolution experimental techniques such as X-ray crystallography and cryogenic electron microscopy can catch relatively few protein functional states. Many others are only accessible under physiological conditions in solution. Therefore, there is a pressing need to fill this gap with computational approaches. We present HOPMA, a novel method to predict protein functional states and transitions by using a modified elastic network model. The method exploits patterns in a protein contact map, taking its 3D structure as input, and excludes some disconnected patches from the elastic network. Combined with nonlinear normal mode analysis, this strategy boosts the protein conformational space exploration, especially when the input structure is highly constrained, as we demonstrate on a set of more than 400 transitions. Our results let us envision the discovery of new functional conformations, which were unreachable previously, starting from the experimentally known protein structures. The method is computationally efficient and available at https://github.com/elolaine/HOPMA and https://team.inria.fr/nano-d/software/nolb-normal-modes.
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Affiliation(s)
- Elodie Laine
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005 Paris, France
| | - Sergei Grudinin
- CNRS, Inria, Grenoble INP, LJK, Univ. Grenoble Alpes, 38000 Grenoble, France
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19
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Igashov I, Olechnovič L, Kadukova M, Venclovas Č, Grudinin S. VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures. Bioinformatics 2021; 37:2332-2339. [PMID: 33620450 DOI: 10.1093/bioinformatics/btab118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 01/08/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Effective use of evolutionary information has recently led to tremendous progress in computational prediction of three-dimensional (3D) structures of proteins and their complexes. Despite the progress, the accuracy of predicted structures tends to vary considerably from case to case. Since the utility of computational models depends on their accuracy, reliable estimates of deviation between predicted and native structures are of utmost importance. RESULTS For the first time, we present a deep convolutional neural network (CNN) constructed on a Voronoi tessellation of 3D molecular structures. Despite the irregular data domain, our data representation allows us to efficiently introduce both convolution and pooling operations and train the network in an end-to-end fashion without precomputed descriptors. The resultant model, VoroCNN, predicts local qualities of 3D protein folds. The prediction results are competitive to state of the art and superior to the previous 3D CNN architectures built for the same task. We also discuss practical applications of VoroCNN, for example, in recognition of protein binding interfaces. AVAILABILITY The model, data, and evaluation tests are available at https://team.inria.fr/nano-d/software/vorocnn/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ilia Igashov
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, 38000 Grenoble, France.,Moscow Institute of Physics and Technology, 141701 Dolgoprudniy, Russia
| | - Liment Olechnovič
- Institute of Biotechnology Life Sciences Center Vilnius University, Saulėtekio 7, Vilnius, LT 10257, Lithuania
| | - Maria Kadukova
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, 38000 Grenoble, France.,Moscow Institute of Physics and Technology, 141701 Dolgoprudniy, Russia
| | - Česlovas Venclovas
- Institute of Biotechnology Life Sciences Center Vilnius University, Saulėtekio 7, Vilnius, LT 10257, Lithuania
| | - Sergei Grudinin
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, 38000 Grenoble, France
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20
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Modal Analysis of the Lysozyme Protein Considering All-Atom and Coarse-Grained Finite Element Models. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Proteins are the fundamental entities of several organic activities. They are essential for a broad range of tasks in a way that their shapes and folding processes are crucial to achieving proper biological functions. Low-frequency modes, generally associated with collective movements at terahertz (THz) and sub-terahertz frequencies, have been appointed as critical for the conformational processes of many proteins. Dynamic simulations, such as molecular dynamics, are vastly applied by biochemical researchers in this field. However, in the last years, proposals that define the protein as a simplified elastic macrostructure have shown appealing results when dealing with this type of problem. In this context, modal analysis based on different modelization techniques, i.e., considering both an all-atom (AA) and coarse-grained (CG) representation, is proposed to analyze the hen egg-white lysozyme. This work presents new considerations and conclusions compared to previous analyses. Experimental values for the B-factor, considering all the heavy atoms or only one representative point per amino acid, are used to evaluate the validity of the numerical solutions. In general terms, this comparison allows the assessment of the regional flexibility of the protein. Besides, the low computational requirements make this approach a quick method to extract the protein’s dynamic properties under scrutiny.
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21
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Gurusaran M, Davies OR. A molecular mechanism for LINC complex branching by structurally diverse SUN-KASH 6:6 assemblies. eLife 2021; 10:60175. [PMID: 33393904 PMCID: PMC7800377 DOI: 10.7554/elife.60175] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/03/2021] [Indexed: 12/11/2022] Open
Abstract
The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex mechanically couples cytoskeletal and nuclear components across the nuclear envelope to fulfil a myriad of cellular functions, including nuclear shape and positioning, hearing, and meiotic chromosome movements. The canonical model is that 3:3 interactions between SUN and KASH proteins underlie the nucleocytoskeletal linkages provided by the LINC complex. Here, we provide crystallographic and biophysical evidence that SUN-KASH is a constitutive 6:6 complex in which two constituent 3:3 complexes interact head-to-head. A common SUN-KASH topology is achieved through structurally diverse 6:6 interaction mechanisms by distinct KASH proteins, including zinc-coordination by Nesprin-4. The SUN-KASH 6:6 interface provides a molecular mechanism for the establishment of integrative and distributive connections between 3:3 structures within a branched LINC complex network. In this model, SUN-KASH 6:6 complexes act as nodes for force distribution and integration between adjacent SUN and KASH molecules, enabling the coordinated transduction of large forces across the nuclear envelope.
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Affiliation(s)
- Manickam Gurusaran
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Owen Richard Davies
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
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22
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Cirauqui Diaz N, Frezza E, Martin J. Using normal mode analysis on protein structural models. How far can we go on our predictions? Proteins 2020; 89:531-543. [PMID: 33349977 DOI: 10.1002/prot.26037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/12/2020] [Indexed: 01/01/2023]
Abstract
Normal mode analysis (NMA) is a fast and inexpensive approach that is largely used to gain insight into functional protein motions, and more recently to create conformations for further computational studies. However, when the protein structure is unknown, the use of computational models is necessary. Here, we analyze the capacity of NMA in internal coordinate space to predict protein motion, its intrinsic flexibility, and atomic displacements, using protein models instead of native structures, and the possibility to use it for model refinement. Our results show that NMA is quite insensitive to modeling errors, but that calculations are strictly reliable only for very accurate models. Our study also suggests that internal NMA is a more suitable tool for the improvement of structural models, and for integrating them with experimental data or in other computational techniques, such as protein docking or more refined molecular dynamics simulations.
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Affiliation(s)
- Nuria Cirauqui Diaz
- CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, Université de Lyon, Lyon, France
| | - Elisa Frezza
- CiTCoM, CNRS, Université de Paris, Paris, France
| | - Juliette Martin
- CNRS, UMR 5086 Molecular Microbiology and Structural Biochemistry, Université de Lyon, Lyon, France
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23
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Marcaida MJ, Kauzlaric A, Duperrex A, Sülzle J, Moncrieffe MC, Adebajo D, Manley S, Trono D, Dal Peraro M. The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity. iScience 2020; 23:101811. [PMID: 33313488 PMCID: PMC7721647 DOI: 10.1016/j.isci.2020.101811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Members of the DEAD-box helicase family are involved in all fundamental processes of RNA metabolism, and as such, their malfunction is associated with various diseases. Currently, whether and how oligomerization impacts their biochemical and biological functions is not well understood. In this work, we show that DDX21, a human DEAD-box helicase with RNA G-quadruplex resolving activity, is dimeric and that its oligomerization state influences its helicase activity. Solution small-angle X-ray scattering (SAXS) analysis uncovers a flexible multi-domain protein with a central dimerization domain. While the Arg/Gly rich C termini, rather than dimerization, are key to maintaining high affinity for RNA substrates, in vitro helicase assays indicate that an intact dimer is essential for both DDX21 ATP-dependent double-stranded RNA unwinding and ATP-independent G-quadruplex remodeling activities. Our results suggest that oligomerization plays a key role in regulating RNA DEAD-box helicase activity. The human RNA DEAD-box helicase DDX21 is dimeric DDX21 dimerization is mediated by a hydrophobic central core domain SAXS-based modeling reveals that DDX21 is intrinsically flexible Dimerization and C-terminal domains mediate G-quadruplex and dsRNA unwinding
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Affiliation(s)
- Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Annamaria Kauzlaric
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Alice Duperrex
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Jenny Sülzle
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Martin C Moncrieffe
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Damilola Adebajo
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Suliana Manley
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
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24
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Bueno JGR, Borelli G, Corrêa TLR, Fiamenghi MB, José J, de Carvalho M, de Oliveira LC, Pereira GAG, dos Santos LV. Novel xylose transporter Cs4130 expands the sugar uptake repertoire in recombinant Saccharomyces cerevisiae strains at high xylose concentrations. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:145. [PMID: 32818042 PMCID: PMC7427733 DOI: 10.1186/s13068-020-01782-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/04/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND The need to restructure the world's energy matrix based on fossil fuels and mitigate greenhouse gas emissions stimulated the development of new biobased technologies for renewable energy. One promising and cleaner alternative is the use of second-generation (2G) fuels, produced from lignocellulosic biomass sugars. A major challenge on 2G technologies establishment is the inefficient assimilation of the five-carbon sugar xylose by engineered Saccharomyces cerevisiae strains, increasing fermentation time. The uptake of xylose across the plasma membrane is a critical limiting step and the budding yeast S. cerevisiae is not designed with a broad transport system and regulatory mechanisms to assimilate xylose in a wide range of concentrations present in 2G processes. RESULTS Assessing diverse microbiomes such as the digestive tract of plague insects and several decayed lignocellulosic biomasses, we isolated several yeast species capable of using xylose. Comparative fermentations selected the yeast Candida sojae as a potential source of high-affinity transporters. Comparative genomic analysis elects four potential xylose transporters whose properties were evaluated in the transporter null EBY.VW4000 strain carrying the xylose-utilizing pathway integrated into the genome. While the traditional xylose transporter Gxf1 allows an improved growth at lower concentrations (10 g/L), strains containing Cs3894 and Cs4130 show opposite responses with superior xylose uptake at higher concentrations (up to 50 g/L). Docking and normal mode analysis of Cs4130 and Gxf1 variants pointed out important residues related to xylose transport, identifying key differences regarding substrate translocation comparing both transporters. CONCLUSIONS Considering that xylose concentrations in second-generation hydrolysates can reach high values in several designed processes, Cs4130 is a promising novel candidate for xylose uptake. Here, we demonstrate a novel eukaryotic molecular transporter protein that improves growth at high xylose concentrations and can be used as a promising target towards engineering efficient pentose utilization in yeast.
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Affiliation(s)
- João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Guilherme Borelli
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
| | - Mateus Bernabe Fiamenghi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Juliana José
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Murilo de Carvalho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics-Institute of Biosciences, Humanities and Exact Sciences, UNESP, São Paulo State University, São José do Rio Preto, São Paulo 15054-000 Brazil
| | - Gonçalo A. G. Pereira
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo 13083-100 Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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25
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Torchala M, Gerguri T, Chaleil RAG, Gordon P, Russell F, Keshani M, Bates PA. Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock. Proteins 2020; 88:962-972. [PMID: 31697436 PMCID: PMC7496321 DOI: 10.1002/prot.25851] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/02/2019] [Accepted: 11/03/2019] [Indexed: 12/12/2022]
Abstract
The formation of specific protein-protein interactions is often a key to a protein's function. During complex formation, each protein component will undergo a change in the conformational state, for some these changes are relatively small and reside primarily at the sidechain level; however, others may display notable backbone adjustments. One of the classic problems in the protein-docking field is to be able to a priori predict the extent of such conformational changes. In this work, we investigated three protocols to find the most suitable input structure conformations for cross-docking, including a robust sampling approach in normal mode space. Counterintuitively, knowledge of the theoretically best combination of normal modes for unbound-bound transitions does not always lead to the best results. We used a novel spatial partitioning library, Aether Engine (see Supplementary Materials), to efficiently search the conformational states of 56 receptor/ligand pairs, including a recent CAPRI target, in a systematic manner and selected diverse conformations as input to our automated docking server, SwarmDock, a server that allows moderate conformational adjustments during the docking process. In essence, here we present a dynamic cross-docking protocol, which when benchmarked against the simpler approach of just docking the unbound components shows a 10% uplift in the quality of the top docking pose.
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Affiliation(s)
- Mieczyslaw Torchala
- Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK
- Hadean Supercomputing LtdLondonUK
| | - Tereza Gerguri
- Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK
| | | | | | | | | | - Paul A. Bates
- Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK
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26
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Scaramozzino D, Khade PM, Jernigan RL, Lacidogna G, Carpinteri A. Structural compliance: A new metric for protein flexibility. Proteins 2020; 88:1482-1492. [PMID: 32548853 DOI: 10.1002/prot.25968] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/29/2020] [Accepted: 06/06/2020] [Indexed: 12/17/2022]
Abstract
Proteins are the active players in performing essential molecular activities throughout biology, and their dynamics has been broadly demonstrated to relate to their mechanisms. The intrinsic fluctuations have often been used to represent their dynamics and then compared to the experimental B-factors. However, proteins do not move in a vacuum and their motions are modulated by solvent that can impose forces on the structure. In this paper, we introduce a new structural concept, which has been called the structural compliance, for the evaluation of the global and local deformability of the protein structure in response to intramolecular and solvent forces. Based on the application of pairwise pulling forces to a protein elastic network, this structural quantity has been computed and sometimes is even found to yield an improved correlation with the experimental B-factors, meaning that it may serve as a better metric for protein flexibility. The inverse of structural compliance, namely the structural stiffness, has also been defined, which shows a clear anticorrelation with the experimental data. Although the present applications are made to proteins, this approach can also be applied to other biomolecular structures such as RNA. This present study considers only elastic network models, but the approach could be applied further to conventional atomic molecular dynamics. Compliance is found to have a slightly better agreement with the experimental B-factors, perhaps reflecting its bias toward the effects of local perturbations, in contrast to mean square fluctuations. The code for calculating protein compliance and stiffness is freely accessible at https://jerniganlab.github.io/Software/PACKMAN/Tutorials/compliance.
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Affiliation(s)
- Domenico Scaramozzino
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
| | - Pranav M Khade
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Giuseppe Lacidogna
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
| | - Alberto Carpinteri
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
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27
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Karasikov M, Pagès G, Grudinin S. Smooth orientation-dependent scoring function for coarse-grained protein quality assessment. Bioinformatics 2020; 35:2801-2808. [PMID: 30590384 DOI: 10.1093/bioinformatics/bty1037] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/29/2018] [Accepted: 12/19/2018] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION Protein quality assessment (QA) is a crucial element of protein structure prediction, a fundamental and yet open problem in structural bioinformatics. QA aims at ranking predicted protein models to select the best candidates. The assessment can be performed based either on a single model or on a consensus derived from an ensemble of models. The latter strategy can yield very high performance but substantially depends on the pool of available candidate models, which limits its applicability. Hence, single-model QA methods remain an important research target, also because they can assist the sampling of candidate models. RESULTS We present a novel single-model QA method called SBROD. The SBROD (Smooth Backbone-Reliant Orientation-Dependent) method uses only the backbone protein conformation, and hence it can be applied to scoring coarse-grained protein models. The proposed method deduces its scoring function from a training set of protein models. The SBROD scoring function is composed of four terms related to different structural features: residue-residue orientations, contacts between backbone atoms, hydrogen bonding and solvent-solute interactions. It is smooth with respect to atomic coordinates and thus is potentially applicable to continuous gradient-based optimization of protein conformations. Furthermore, it can also be used for coarse-grained protein modeling and computational protein design. SBROD proved to achieve similar performance to state-of-the-art single-model QA methods on diverse datasets (CASP11, CASP12 and MOULDER). AVAILABILITY AND IMPLEMENTATION The standalone application implemented in C++ and Python is freely available at https://gitlab.inria.fr/grudinin/sbrod and supported on Linux, MacOS and Windows. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mikhail Karasikov
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France.,Center for Energy Systems, Skolkovo Institute of Science and Technology, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Guillaume Pagès
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
| | - Sergei Grudinin
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
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28
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Shape-preserving elastic solid models of macromolecules. PLoS Comput Biol 2020; 16:e1007855. [PMID: 32407309 PMCID: PMC7297265 DOI: 10.1371/journal.pcbi.1007855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 06/09/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mass-spring models have been a standard approach in molecular modeling for the last few decades, such as elastic network models (ENMs) that are widely used for normal mode analysis. In this work, we present a vastly different elastic solid model (ESM) of macromolecules that shares the same simplicity and efficiency as ENMs in producing the equilibrium dynamics and moreover, offers some significant new features that may greatly benefit the research community. ESM is different from ENM in that it treats macromolecules as elastic solids. Our particular version of ESM presented in this work, named αESM, captures the shape of a given biomolecule most economically using alpha shape, a well-established technique from the computational geometry community. Consequently, it can produce most economical coarse-grained models while faithfully preserving the shape and thus makes normal mode computations and visualization of extremely large complexes more manageable. Secondly, as a solid model, ESM’s close link to finite element analysis renders it ideally suited for studying mechanical responses of macromolecules under external force. Lastly, we show that ESM can be applied also to structures without atomic coordinates such as those from cryo-electron microscopy. The complete MATLAB code of αESM is provided. Mass-spring models have been a standard approach in classical molecular modeling where atoms are modeled as spheres with a mass and their interactions modeled as springs. The models have been extremely successful. Thinking ahead, however, as molecular systems of our interest grow more quickly in size or dimension than what our computation resources can keep up with, some adjustments in methodology are timely. This work presents a vastly different elastic solid model (ESM) of macromolecules that shares the same simplicity and efficiency as mass-spring models in producing the equilibrium dynamics and moreover, offers some unique features that make it suitable for much larger systems. ESM is different from ENMs in that it treats macromolecules as elastic solids. Our particular version of ESM model presented in this work, named αESM, captures the shape of a given biomolecule most economically using alpha shape, a well-established technique from the computational geometry community. Consequently, it can produce most economical coarse-grained models while faithfully preserving the shape. ESM can be applied also to structures without atomic coordinates such as those from cryo-electron microscopy.
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29
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Grudinin S, Laine E, Hoffmann A. Predicting Protein Functional Motions: an Old Recipe with a New Twist. Biophys J 2020; 118:2513-2525. [PMID: 32330413 DOI: 10.1016/j.bpj.2020.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/09/2020] [Accepted: 03/18/2020] [Indexed: 01/21/2023] Open
Abstract
Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. Some of them can be seen experimentally, for example with x-ray crystallography or cryo-electron microscopy. This structural heterogeneity is not occasional and is frequently linked with specific biological function. Thus, the accurate description of macromolecular conformational transitions is crucial for understanding fundamental mechanisms of life's machinery. We report on a real-time method to predict such transitions by extrapolating from instantaneous eigen motions, computed using the normal mode analysis, to a series of twists. We demonstrate the applicability of our approach to the prediction of a wide range of motions, including large collective opening-closing transitions and conformational changes induced by partner binding. We also highlight particularly difficult cases of very small transitions between crystal and solution structures. Our method guarantees preservation of the protein structure during the transition and allows accessing conformations that are unreachable with classical normal mode analysis. We provide practical solutions to describe localized motions with a few low-frequency modes and to relax some geometrical constraints along the predicted transitions. This work opens the way to the systematic description of protein motions, whatever their degree of collectivity. Our method is freely available as a part of the NOn-Linear rigid Block (NOLB) package.
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Affiliation(s)
- Sergei Grudinin
- University Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Alexandre Hoffmann
- University Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France
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30
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Glashagen G, de Vries S, Uciechowska-Kaczmarzyk U, Samsonov SA, Murail S, Tuffery P, Zacharias M. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins 2019; 88:1018-1028. [PMID: 31785163 DOI: 10.1002/prot.25860] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 01/17/2023]
Abstract
The ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI rounds 38-45. For 11 out of 16 targets acceptable or better quality solutions have been submitted (~70%). It includes also several cases of peptide-protein docking and the successful prediction of the geometry of carbohydrate-protein interactions. The option of combining rigid body minimization and simultaneous optimization in collective degrees of freedom based on elastic network modes was employed and systematically evaluated. Application to a large benchmark set indicates a modest improvement in docking performance compared to rigid docking. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.
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Affiliation(s)
- Glenn Glashagen
- Physik-Department T38, Technische Universität München, Garching, Germany
| | - Sjoerd de Vries
- Université de Paris, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | | | | | - Samuel Murail
- Université de Paris, CNRS UMR 8251, INSERM ERL U1133, Paris, France
| | - Pierre Tuffery
- Université de Paris, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, Garching, Germany
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31
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Fajardo JE, Shrestha R, Gil N, Belsom A, Crivelli SN, Czaplewski C, Fidelis K, Grudinin S, Karasikov M, Karczyńska AS, Kryshtafovych A, Leitner A, Liwo A, Lubecka EA, Monastyrskyy B, Pagès G, Rappsilber J, Sieradzan AK, Sikorska C, Trabjerg E, Fiser A. Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins 2019; 87:1283-1297. [PMID: 31569265 PMCID: PMC6851497 DOI: 10.1002/prot.25816] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/08/2019] [Accepted: 09/13/2019] [Indexed: 12/22/2022]
Abstract
With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.
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Affiliation(s)
- J. Eduardo Fajardo
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Rojan Shrestha
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Nelson Gil
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Adam Belsom
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Silvia N. Crivelli
- Department of Computer Science, UC Davis, One Shields Ave., Davis, CA 95616
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Krzysztof Fidelis
- Genome Center, University of California, Davis, 451 Health Sciences Dr., Davis CA 95616-8816, USA
| | - Sergei Grudinin
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP LJK, 38000 Grenoble, France
| | - Mikhail Karasikov
- Center for Energy Systems, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
- Moscow Institute of Physics and Technology, Moscow, 141701, Russia
- Department of Computer Science, ETH Zurich, Zurich, 8092, Switzerland
| | | | - Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Dr., Davis CA 95616-8816, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Emilia A. Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Wita Stwosza 57, 80-308 Gdańsk, Poland
| | - Bohdan Monastyrskyy
- Genome Center, University of California, Davis, 451 Health Sciences Dr., Davis CA 95616-8816, USA
| | - Guillaume Pagès
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP LJK, 38000 Grenoble, France
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Celina Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Esben Trabjerg
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Andras Fiser
- Department of Systems and Computational Biology, and Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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32
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Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE. Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences. Proteins 2019; 87:1298-1314. [PMID: 31589784 DOI: 10.1002/prot.25827] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 12/14/2022]
Abstract
Small angle X-ray scattering (SAXS) measures comprehensive distance information on a protein's structure, which can constrain and guide computational structure prediction algorithms. Here, we evaluate structure predictions of 11 monomeric and oligomeric proteins for which SAXS data were collected and provided to predictors in the 13th round of the Critical Assessment of protein Structure Prediction (CASP13). The category for SAXS-assisted predictions made gains in certain areas for CASP13 compared to CASP12. Improvements included higher quality data with size exclusion chromatography-SAXS (SEC-SAXS) and better selection of targets and communication of results by CASP organizers. In several cases, we can track improvements in model accuracy with use of SAXS data. For hard multimeric targets where regular folding algorithms were unsuccessful, SAXS data helped predictors to build models better resembling the global shape of the target. For most models, however, no significant improvement in model accuracy at the domain level was registered from use of SAXS data, when rigorously comparing SAXS-assisted models to the best regular server predictions. To promote future progress in this category, we identify successes, challenges, and opportunities for improved strategies in prediction, assessment, and communication of SAXS data to predictors. An important observation is that, for many targets, SAXS data were inconsistent with crystal structures, suggesting that these proteins adopt different conformation(s) in solution. This CASP13 result, if representative of PDB structures and future CASP targets, may have substantive implications for the structure training databases used for machine learning, CASP, and use of prediction models for biology.
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Affiliation(s)
- Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California
| | - Curtis D Hodge
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Daniel Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Dmytro Guzenko
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California
| | - Jose M Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California
| | - Bohdan Monastyrskyy
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California
| | - Sergei Grudinin
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, 38000, Grenoble, France
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California
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33
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Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions. Biomolecules 2019; 9:biom9100549. [PMID: 31575003 PMCID: PMC6843209 DOI: 10.3390/biom9100549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 01/26/2023] Open
Abstract
Simple protein elastic networks which neglect amino-acid information often yield reasonable predictions of conformational dynamics and are broadly used. Recently, model variants which incorporate sequence-specific and distance-dependent interactions of residue pairs have been constructed and demonstrated to improve agreement with experimental data. We have applied the new variants in a systematic study of protein fluctuation properties and compared their predictions with those of conventional anisotropic network models. We find that the quality of predictions is frequently linked to poor estimations in highly flexible protein regions. An analysis of a large set of protein structures shows that fluctuations of very weakly connected network residues are intrinsically prone to be significantly overestimated by all models. This problem persists in the new models and is not resolved by taking into account sequence information. The effect becomes even enhanced in the model variant which takes into account very soft long-ranged residue interactions. Beyond these shortcomings, we find that model predictions are largely insensitive to the integration of chemical information, at least regarding the fluctuation properties of individual residues. One can furthermore conclude that the inherent drawbacks may present a serious hindrance when improvement of elastic network models are attempted.
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34
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Neveu E, Popov P, Hoffmann A, Migliosi A, Besseron X, Danoy G, Bouvry P, Grudinin S. RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules. Bioinformatics 2019; 34:2757-2765. [PMID: 29554205 DOI: 10.1093/bioinformatics/bty160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/13/2018] [Indexed: 12/27/2022] Open
Abstract
Motivation The root mean square deviation (RMSD) is one of the most used similarity criteria in structural biology and bioinformatics. Standard computation of the RMSD has a linear complexity with respect to the number of atoms in a molecule, making RMSD calculations time-consuming for the large-scale modeling applications, such as assessment of molecular docking predictions or clustering of spatially proximate molecular conformations. Previously, we introduced the RigidRMSD algorithm to compute the RMSD corresponding to the rigid-body motion of a molecule. In this study, we go beyond the limits of the rigid-body approximation by taking into account conformational flexibility of the molecule. We model the flexibility with a reduced set of collective motions computed with e.g. normal modes or principal component analysis. Results The initialization of our algorithm is linear in the number of atoms and all the subsequent evaluations of RMSD values between flexible molecular conformations depend only on the number of collective motions that are selected to model the flexibility. Therefore, our algorithm is much faster compared to the standard RMSD computation for large-scale modeling applications. We demonstrate the efficiency of our method on several clustering examples, including clustering of flexible docking results and molecular dynamics (MD) trajectories. We also demonstrate how to use the presented formalism to generate pseudo-random constant-RMSD structural molecular ensembles and how to use these in cross-docking. Availability and implementation We provide the algorithm written in C++ as the open-source RapidRMSD library governed by the BSD-compatible license, which is available at http://team.inria.fr/nano-d/software/RapidRMSD/. The constant-RMSD structural ensemble application and clustering of MD trajectories is available at http://team.inria.fr/nano-d/software/nolb-normal-modes/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emilie Neveu
- Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France.,Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Petr Popov
- Inria/Univ. Grenoble Alpes/LJK-CNRS, Grenoble, France.,Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | | | - Angelo Migliosi
- Faculté des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg
| | - Xavier Besseron
- Faculté des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg
| | - Grégoire Danoy
- Faculté des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg
| | - Pascal Bouvry
- Faculté des Sciences, de la Technologie et de la Communication, University of Luxembourg, Luxembourg, Luxembourg
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35
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Fonti G, Marcaida MJ, Bryan LC, Träger S, Kalantzi AS, Helleboid PYJ, Demurtas D, Tully MD, Grudinin S, Trono D, Fierz B, Dal Peraro M. KAP1 is an antiparallel dimer with a functional asymmetry. Life Sci Alliance 2019; 2:2/4/e201900349. [PMID: 31427381 PMCID: PMC6701479 DOI: 10.26508/lsa.201900349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 01/10/2023] Open
Abstract
This study reveals the architecture of human KAP1 by integrating molecular modeling with small-angle X-ray scattering and single-molecule experiments. KAP1 dimers feature a structural asymmetry at the C-terminal domains that has functional implications for recruitment of HP1. KAP1 (KRAB domain–associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 small ubiquitin modifier ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering data, integrative modeling, and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with an asymmetry at the C-terminal domains. This conformation is consistent with the finding that the Really Interesting New Gene (RING) domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.
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Affiliation(s)
- Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Louise C Bryan
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra S Kalantzi
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pierre-Yves Jl Helleboid
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Davide Demurtas
- Interdisciplinary Centre for Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mark D Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Sergei Grudinin
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Inria, Grenoble Institut Polytechnique de Grenoble, Laboratoire Jean Kuntzmann, Grenoble, France
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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36
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Bloyet LM, Schramm A, Lazert C, Raynal B, Hologne M, Walker O, Longhi S, Gerlier D. Regulation of measles virus gene expression by P protein coiled-coil properties. SCIENCE ADVANCES 2019; 5:eaaw3702. [PMID: 31086822 PMCID: PMC6506246 DOI: 10.1126/sciadv.aaw3702] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 05/18/2023]
Abstract
The polymerase of negative-stranded RNA viruses consists of the large protein (L) and the phosphoprotein (P), the latter serving both as a chaperon and a cofactor for L. We mapped within measles virus (MeV) P the regions responsible for binding and stabilizing L and showed that the coiled-coil multimerization domain (MD) of P is required for gene expression. MeV MD is kinked as a result of the presence of a stammer. Both restoration of the heptad regularity and displacement of the stammer strongly decrease or abrogate activity in a minigenome assay. By contrast, P activity is rather tolerant of substitutions within the stammer. Single substitutions at the "a" or "d" hydrophobic anchor positions with residues of variable hydrophobicity revealed that P functionality requires a narrow range of cohesiveness of its MD. Results collectively indicate that, beyond merely ensuring P oligomerization, the MD finely tunes viral gene expression through its cohesiveness.
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Affiliation(s)
- Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Antoine Schramm
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Carine Lazert
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique Moléculaire, Paris, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon 1, Lyon France
| | - Sonia Longhi
- Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
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37
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Sorzano COS, Jiménez A, Mota J, Vilas JL, Maluenda D, Martínez M, Ramírez-Aportela E, Majtner T, Segura J, Sánchez-García R, Rancel Y, del Caño L, Conesa P, Melero R, Jonic S, Vargas J, Cazals F, Freyberg Z, Krieger J, Bahar I, Marabini R, Carazo JM. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallogr F Struct Biol Commun 2019; 75:19-32. [PMID: 30605122 PMCID: PMC6317454 DOI: 10.1107/s2053230x18015108] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/26/2018] [Indexed: 11/10/2022] Open
Abstract
Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.
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Affiliation(s)
| | - A. Jiménez
- National Center of Biotechnology (CSIC), Spain
| | - J. Mota
- National Center of Biotechnology (CSIC), Spain
| | - J. L. Vilas
- National Center of Biotechnology (CSIC), Spain
| | - D. Maluenda
- National Center of Biotechnology (CSIC), Spain
| | - M. Martínez
- National Center of Biotechnology (CSIC), Spain
| | | | - T. Majtner
- National Center of Biotechnology (CSIC), Spain
| | - J. Segura
- National Center of Biotechnology (CSIC), Spain
| | | | - Y. Rancel
- National Center of Biotechnology (CSIC), Spain
| | - L. del Caño
- National Center of Biotechnology (CSIC), Spain
| | - P. Conesa
- National Center of Biotechnology (CSIC), Spain
| | - R. Melero
- National Center of Biotechnology (CSIC), Spain
| | - S. Jonic
- Sorbonne Université, UMR CNRS 7590, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | | | - F. Cazals
- Inria Sophia Antipolis – Méditerranée, France
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38
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Nazarenko VV, Remeeva A, Yudenko A, Kovalev K, Dubenko A, Goncharov IM, Kuzmichev P, Rogachev AV, Buslaev P, Borshchevskiy V, Mishin A, Dhoke GV, Schwaneberg U, Davari MD, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies. Photochem Photobiol Sci 2019; 18:1793-1805. [DOI: 10.1039/c9pp00067d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new thermostable fluorescent protein is shown to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.
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39
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Nguyen MK, Jaillet L, Redon S. Generating conformational transition paths with low potential-energy barriers for proteins. J Comput Aided Mol Des 2018; 32:853-867. [PMID: 30069648 DOI: 10.1007/s10822-018-0137-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.
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Affiliation(s)
- Minh Khoa Nguyen
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
| | - Léonard Jaillet
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France.
| | - Stéphane Redon
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
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40
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Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation. Proc Natl Acad Sci U S A 2018; 115:E3959-E3968. [PMID: 29632192 DOI: 10.1073/pnas.1717700115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) constitute a widespread class of ion channels, present in archaea, bacteria, and eukaryotes. Upon binding of their agonists in the extracellular domain, the transmembrane pore opens, allowing ions to go through, via a gating mechanism that can be modulated by a number of drugs. Even though high-resolution structural information on pLGICs has increased in a spectacular way in recent years, both in bacterial and in eukaryotic systems, the structure of the open channel conformation of some intensively studied receptors whose structures are known in a nonactive (closed) form, such as Erwinia chrysanthemi pLGIC (ELIC), is still lacking. Here we describe a gammaproteobacterial pLGIC from an endo-symbiont of Tevnia jerichonana (sTeLIC), whose sequence is closely related to the pLGIC from ELIC with 28% identity. We provide an X-ray crystallographic structure at 2.3 Å in an active conformation, where the pore is found to be more open than any current conformation found for pLGICs. In addition, two charged restriction rings are present in the vestibule. Functional characterization shows sTeLIC to be a cationic channel activated at alkaline pH. It is inhibited by divalent cations, but not by quaternary ammonium ions, such as tetramethylammonium. Additionally, we found that sTeLIC is allosterically potentiated by aromatic amino acids Phe and Trp, as well as their derivatives, such as 4-bromo-cinnamate, whose cocrystal structure reveals a vestibular binding site equivalent to, but more deeply buried than, the one already described for benzodiazepines in ELIC.
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41
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Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A, Buslaev P, Bourenkov G, Grudinin S, Round E, Balandin T, Borshchevskiy V, Willbold D, Leonard G, Büldt G, Popov A, Gordeliy V. Mechanism of transmembrane signaling by sensor histidine kinases. Science 2017; 356:science.aah6345. [PMID: 28522691 DOI: 10.1126/science.aah6345] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 05/08/2017] [Indexed: 11/02/2022]
Abstract
One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. We present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor histidine kinase NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces rearrangements and pistonlike shifts of TM helices. The HAMP domain protomers undergo leverlike motions and convert these pistonlike motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCSs.
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Affiliation(s)
- Ivan Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany. .,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Igor Melnikov
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Andrii Ishchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), 52056 Aachen, Germany
| | - Anastasia Yuzhakova
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Outstation, 22607 Hamburg, Germany
| | - Sergei Grudinin
- Université Grenoble Alpes, LJK, F-38000 Grenoble, France.,CNRS, LJK, F-38000 Grenoble, France.,Inria, F-38000 Grenoble, France
| | - Ekaterina Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Dieter Willbold
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Gordon Leonard
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Georg Büldt
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Alexander Popov
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany. .,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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