1
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Nayak SS, Krishna R. Phosphorylation at the D56 residue of MtrA in Mycobacterium tuberculosis enhances its DNA binding affinity by modulating inter-domain interaction. Comput Biol Chem 2024; 113:108222. [PMID: 39366081 DOI: 10.1016/j.compbiolchem.2024.108222] [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: 07/22/2024] [Revised: 09/15/2024] [Accepted: 09/20/2024] [Indexed: 10/06/2024]
Abstract
The response regulator, MtrA, plays a major role in adaptation to the host environment, cell division, replication, and dormancy activation of Mycobacterium tuberculosis (Mtb). The phosphorylation of the response regulator MtrA alters the downstream activity, typically involving changes in DNA binding activity. However, there is a substantial knowledge gap in understanding the phosphorylation-mediated structural changes in MtrA. Additionally, the active conformation of the protein has yet to be determined. Therefore, in this study, we have investigated the phosphorylation-induced conformational changes of MtrA using all-atom molecular dynamics simulations under various phosphorylation conditions. The results from this study demonstrate that the phosphorylation at D56 (pD56-MtrA) increases the compactness of the MtrA protein by stabilizing the inter-domain interaction between the regulatory domain and DNA binding domain. Notably, the higher occupancy H-bond (over 95 %) between Arg200-Asn100 in case of the pD56-MtrA condition, which is otherwise absent in the non-phosphorylated (uMtrA) condition, suggests the importance of this interaction in the active conformation of the protein. The dynamic cross-correlation analysis reveals that phosphorylation (especially pD56-MtrA) reduces the anti-correlated motions and increases correlated motions between different domains. Moreover, the higher DNA binding affinity of pD56-MtrA compared to uMtrA supported by molecular docking and MD simulation followed by MMPBSA analysis suggests that pD56-MtrA is the possible active conformation of the MtrA protein. Overall, this investigation elucidates the key structural changes in MtrA under different phosphorylated conditions, which might help in designing novel therapeutics against tuberculosis.
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Affiliation(s)
| | - Ramadas Krishna
- Department of Bioinformatics, Pondicherry University, Pondicherry 605014, India.
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2
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Omwansu W, Musembi R, Derese S. Graph-based analysis of H-bond networks and unsupervised learning reveal conformational coupling in prion peptide segments. Phys Chem Chem Phys 2024. [PMID: 39291469 DOI: 10.1039/d4cp02123a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
In this study, we employed a comprehensive computational approach to investigate the physical chemistry of the water networks surrounding hydrated peptide segments, as derived from molecular dynamics simulations. Our analysis uncovers a complex interplay of direct and water-mediated hydrogen bonds that intricately weave through the peptides. We demonstrate that these hydrogen bond networks encode critical information about the peptides' conformational behavior, with the dimensionality of these networks showing sensitivity to the peptides' conformations. Additionally, we estimated the free-energy landscape of the peptides across various conformations, revealing that their structures are predominantly characterized by unfolded, partially folded, and folded configurations, resulting in broad and rugged free-energy surfaces due to the numerous degrees of freedom contributed by the surrounding solvent. Importantly, the structured nature of this free-energy landscape becomes obscured when conventional collective variables, such as the number of hydrogen bonds, are used. Our findings provide new insights into the molecular mechanisms that couple protein and solvent degrees of freedom, highlighting their significance in the functioning of biological systems.
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Affiliation(s)
- Wycliffe Omwansu
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Robinson Musembi
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
| | - Solomon Derese
- Department of Chemistry, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
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3
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Bondar AN. Graphs of Hydrogen-Bond Networks to Dissect Protein Conformational Dynamics. J Phys Chem B 2022; 126:3973-3984. [PMID: 35639610 DOI: 10.1021/acs.jpcb.2c00200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dynamic hydrogen bonds and hydrogen-bond networks are ubiquitous in proteins and protein complexes. Functional roles that have been assigned to hydrogen-bond networks include structural plasticity for protein function, allosteric conformational coupling, long-distance proton transfers, and transient storage of protons. Advances in structural biology provide invaluable insights into architectures of large proteins and protein complexes of direct interest to human physiology and disease, including G Protein Coupled Receptors (GPCRs) and the SARS-Covid-19 spike protein S, and give rise to the challenge of how to identify those interactions that are more likely to govern protein dynamics. This Perspective discusses applications of graph-based algorithms to dissect dynamical hydrogen-bond networks of protein complexes, with illustrations for GPCRs and spike protein S. H-bond graphs provide an overview of sites in GPCR structures where hydrogen-bond dynamics would be required to assemble longer-distance networks between functionally important motifs. In the case of spike protein S, graphs identify regions of the protein where hydrogen bonds rearrange during the reaction cycle and where local hydrogen-bond networks likely change in a virus variant of concern.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, 077125 Bucharest-Măgurele, Romania.,Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany
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4
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Lazaratos M, Siemers M, Brown LS, Bondar AN. Conserved hydrogen-bond motifs of membrane transporters and receptors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183896. [PMID: 35217000 DOI: 10.1016/j.bbamem.2022.183896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]
Abstract
Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins. Here we apply graph-theory approaches to identify hydrogen-bond motifs of carboxylate and histidine sidechains in a large data set of static membrane protein structures. We find that carboxylate-hydroxyl hydrogen bonds are present in numerous structures of the dataset, and can be part of more extended H-bond clusters that could be relevant to conformational coupling. Carboxylate-carboxyamide and imidazole-imidazole hydrogen bonds are represented in comparably fewer protein structures of the dataset. Atomistic simulations on two membrane transporters in lipid membranes suggest that many of the hydrogen bond motifs present in static protein structures tend to be robust, and can be part of larger hydrogen-bond clusters that recruit additional hydrogen bonds.
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Affiliation(s)
- Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S Brown
- University of Guelph, Department of Physics, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany.
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5
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Karathanou K, Bondar AN. Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183859. [PMID: 34999081 DOI: 10.1016/j.bbamem.2022.183859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.
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Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.
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6
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Krishnamurthy S, Sardis MF, Eleftheriadis N, Chatzi KE, Smit JH, Karathanou K, Gouridis G, Portaliou AG, Bondar AN, Karamanou S, Economou A. Preproteins couple the intrinsic dynamics of SecA to its ATPase cycle to translocate via a catch and release mechanism. Cell Rep 2022; 38:110346. [PMID: 35139375 DOI: 10.1016/j.celrep.2022.110346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/22/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Protein machines undergo conformational motions to interact with and manipulate polymeric substrates. The Sec translocase promiscuously recognizes, becomes activated, and secretes >500 non-folded preprotein clients across bacterial cytoplasmic membranes. Here, we reveal that the intrinsic dynamics of the translocase ATPase, SecA, and of preproteins combine to achieve translocation. SecA possesses an intrinsically dynamic preprotein clamp attached to an equally dynamic ATPase motor. Alternating motor conformations are finely controlled by the γ-phosphate of ATP, while ADP causes motor stalling, independently of clamp motions. Functional preproteins physically bridge these independent dynamics. Their signal peptides promote clamp closing; their mature domain overcomes the rate-limiting ADP release. While repeated ATP cycles shift the motor between unique states, multiple conformationally frustrated prongs in the clamp repeatedly "catch and release" trapped preprotein segments until translocation completion. This universal mechanism allows any preprotein to promiscuously recognize the translocase, usurp its intrinsic dynamics, and become secreted.
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Affiliation(s)
- Srinath Krishnamurthy
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Marios-Frantzeskos Sardis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Nikolaos Eleftheriadis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Katerina E Chatzi
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Jochem H Smit
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany
| | - Giorgos Gouridis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands; Structural Biology Division, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Nikolaou Plastira 100, Heraklion, Crete, Greece
| | - Athina G Portaliou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, 077125 Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, IAS-5/INM-9, Wilhelm-Johnen Straße, 5428 Jülich, Germany
| | - Spyridoula Karamanou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium.
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7
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Shang C, Wang L, Cao Y, Yu X, Li Y, Sun C, Cui J. Is it possible to switch ESIPT-channel of hydroxyanthraquinones with the strategy of modifying electronic groups? J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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Bondar AN. Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:199-239. [PMID: 35034719 DOI: 10.1016/bs.apcsb.2021.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Membrane transporters that use proton binding and proton transfer for function couple local protonation change with changes in protein conformation and water dynamics. Changes of protein conformation might be required to allow transient formation of hydrogen-bond networks that bridge proton donor and acceptor pairs separated by long distances. Inter-helical hydrogen-bond networks adjust rapidly to protonation change, and ensure rapid response of the protein structure and dynamics. Membrane transporters with known three-dimensional structures and proton-binding groups inform on general principles of protonation-coupled protein conformational dynamics. Inter-helical hydrogen bond motifs between proton-binding carboxylate groups and a polar sidechain are observed in unrelated membrane transporters, suggesting common principles of coupling protonation change with protein conformational dynamics.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany.
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9
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Pal S, Chattopadhyay A. Hydration Dynamics in Biological Membranes: Emerging Applications of Terahertz Spectroscopy. J Phys Chem Lett 2021; 12:9697-9709. [PMID: 34590862 DOI: 10.1021/acs.jpclett.1c02576] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Water drives the spontaneous self-assembly of lipids and proteins into quasi two-dimensional biological membranes that act as catalytic scaffolds for numerous processes central to life. However, the functional relevance of hydration in membrane biology is only beginning to be addressed, predominantly because of challenges associated with direct measurements of hydration microstructure and dynamics in a biological milieu. Our recent work on the novel interplay of membrane electrostatics and crowding in shaping membrane hydration dynamics utilizing terahertz (THz) spectroscopy represents an important step in this context. In this Perspective, we provide a glimpse into the ever-broadening functional landscape of hydration dynamics in biological membranes in the backdrop of the unique physical chemistry of water molecules. We further highlight the immense (and largely untapped) potential of the THz toolbox in addressing contemporary problems in membrane biology, while emphasizing the adaptability of the analytical framework reported recently by us to such studies.
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Affiliation(s)
- Sreetama Pal
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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10
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Siemers M, Bondar AN. Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S. J Chem Inf Model 2021; 61:2998-3014. [PMID: 34133162 DOI: 10.1021/acs.jcim.1c00306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamic hydrogen-bond networks are key determinants of protein conformational dynamics. In the case of macromolecular protein complexes, which can have a large number of hydrogen bonds giving rise to extensive hydrogen-bond networks, efficient algorithms are required to analyze interactions that could be important for the dynamics and biological function of the complex. We present here a highly efficient, standalone interface designed for analyses of dynamical hydrogen-bond networks of biomolecules and macromolecular complexes. To facilitate a comprehensive description of protein dynamics, the interface includes analyses of hydrophobic interactions. We illustrate the usefulness and workflow of the interface by dissecting the dynamics of the ectodomain of SARS-CoV-2 protein S in its closed conformation. We find that protein S contains numerous local clusters of dynamic hydrogen bonds and identify hydrogen bonds that are sampled persistently. The receptor binding domain of the spike protein hosts only a handful of persistent hydrogen-bond clusters, suggesting structural plasticity. Our data analysis interface is released here for open use.
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Affiliation(s)
- Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
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11
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A nexus of intrinsic dynamics underlies translocase priming. Structure 2021; 29:846-858.e7. [PMID: 33852897 DOI: 10.1016/j.str.2021.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/06/2021] [Accepted: 03/25/2021] [Indexed: 11/22/2022]
Abstract
The cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel assemble to form the Sec translocase. How this interaction primes and catalytically activates the translocase remains unclear. We show that priming exploits a nexus of intrinsic dynamics in SecA. Using atomistic simulations, smFRET, and HDX-MS, we reveal multiple dynamic islands that cross-talk with domain and quaternary motions. These dynamic elements are functionally important and conserved. Central to the nexus is a slender stem through which rotation of the preprotein clamp of SecA is biased by ATPase domain motions between open and closed clamping states. An H-bonded framework covering most of SecA enables multi-tier dynamics and conformational alterations with minimal energy input. As a result, cognate ligands select preexisting conformations and alter local dynamics to regulate catalytic activity and clamp motions. These events prime the translocase for high-affinity reception of non-folded preprotein clients. Dynamics nexuses are likely universal and essential in multi-liganded proteins.
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12
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Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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13
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Bertalan É, Lešnik S, Bren U, Bondar AN. Protein-water hydrogen-bond networks of G protein-coupled receptors: Graph-based analyses of static structures and molecular dynamics. J Struct Biol 2020; 212:107634. [DOI: 10.1016/j.jsb.2020.107634] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/06/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022]
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14
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Karathanou K, Lazaratos M, Bertalan É, Siemers M, Buzar K, Schertler GFX, Del Val C, Bondar AN. A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2. J Struct Biol 2020; 212:107617. [PMID: 32919067 PMCID: PMC7481144 DOI: 10.1016/j.jsb.2020.107617] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023]
Abstract
Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, and contribute symmetrically to a relatively large H-bond cluster at the receptor binding domain, and to a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding.
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Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Éva Bertalan
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Krzysztof Buzar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Gebhard F X Schertler
- Paul Scherrer Institut, Department of Biology and Chemistry, Laboratory of Biomolecular Research, CH-5303 Villigen-PSI, Switzerland; ETH Zürich, Department of Biology, 8093 Zürich, Switzerland
| | - Coral Del Val
- University of Granada, Department of Computer Science and Artificial Intelligence, E-18071 Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany.
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15
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Lazaratos M, Karathanou K, Bondar AN. Graphs of dynamic H-bond networks: from model proteins to protein complexes in cell signaling. Curr Opin Struct Biol 2020; 64:79-87. [DOI: 10.1016/j.sbi.2020.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/28/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
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16
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Harris A, Lazaratos M, Siemers M, Watt E, Hoang A, Tomida S, Schubert L, Saita M, Heberle J, Furutani Y, Kandori H, Bondar AN, Brown LS. Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin. J Phys Chem B 2020; 124:4851-4872. [DOI: 10.1021/acs.jpcb.0c02767] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrew Harris
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Michalis Lazaratos
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Malte Siemers
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Ethan Watt
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Anh Hoang
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Luiz Schubert
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Mattia Saita
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Leonid S. Brown
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
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17
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Siemers M, Lazaratos M, Karathanou K, Guerra F, Brown LS, Bondar AN. Bridge: A Graph-Based Algorithm to Analyze Dynamic H-Bond Networks in Membrane Proteins. J Chem Theory Comput 2019; 15:6781-6798. [DOI: 10.1021/acs.jctc.9b00697] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Malte Siemers
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Federico Guerra
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
| | - Leonid S. Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D14195 Berlin, Germany
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18
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Wahab HA, Amaro RE, Cournia Z. A Celebration of Women in Computational Chemistry. J Chem Inf Model 2019; 59:1683-1692. [DOI: 10.1021/acs.jcim.9b00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall, #0340, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
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19
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Kemmler L, Ibrahim M, Dobbek H, Zouni A, Bondar AN. Dynamic water bridging and proton transfer at a surface carboxylate cluster of photosystem II. Phys Chem Chem Phys 2019; 21:25449-25466. [DOI: 10.1039/c9cp03926k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A hydrogen-bond cluster at a negatively-charged protein interface with a bound protein and long-lived waters might be a proton storage site.
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Affiliation(s)
- Lukas Kemmler
- Freie Universität Berlin
- Department of Physics
- Theoretical Molecular Biophysics Group
- D-14195 Berlin
- Germany
| | - Mohamed Ibrahim
- Humboldt Universtät zu Berlin
- Institute for Biology, Structural Biology and Biochemistry
- Berlin
- Germany
| | - Holger Dobbek
- Humboldt Universtät zu Berlin
- Institute for Biology, Structural Biology and Biochemistry
- Berlin
- Germany
| | - Athina Zouni
- Humboldt Universtät zu Berlin
- Institute for Biology, Biophysics of Photosynthesis
- Berlin
- Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin
- Department of Physics
- Theoretical Molecular Biophysics Group
- D-14195 Berlin
- Germany
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