1
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Mailhot O, Frappier V, Major F, Najmanovich RJ. Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation. PLoS Comput Biol 2022; 18:e1010777. [PMID: 36516216 PMCID: PMC9797095 DOI: 10.1371/journal.pcbi.1010777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/28/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
The Elastic Network Contact Model (ENCoM) is a coarse-grained normal mode analysis (NMA) model unique in its all-atom sensitivity to the sequence of the studied macromolecule and thus to the effect of mutations. We adapted ENCoM to simulate the dynamics of ribonucleic acid (RNA) molecules, benchmarked its performance against other popular NMA models and used it to study the 3D structural dynamics of human microRNA miR-125a, leveraging high-throughput experimental maturation efficiency data of over 26 000 sequence variants. We also introduce a novel way of using dynamical information from NMA to train multivariate linear regression models, with the purpose of highlighting the most salient contributions of dynamics to function. ENCoM has a similar performance profile on RNA than on proteins when compared to the Anisotropic Network Model (ANM), the most widely used coarse-grained NMA model; it has the advantage on predicting large-scale motions while ANM performs better on B-factors prediction. A stringent benchmark from the miR-125a maturation dataset, in which the training set contains no sequence information in common with the testing set, reveals that ENCoM is the only tested model able to capture signal beyond the sequence. This ability translates to better predictive power on a second benchmark in which sequence features are shared between the train and test sets. When training the linear regression model using all available data, the dynamical features identified as necessary for miR-125a maturation point to known patterns but also offer new insights into the biogenesis of microRNAs. Our novel approach combining NMA with multivariate linear regression is generalizable to any macromolecule for which relatively high-throughput mutational data is available.
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Affiliation(s)
- Olivier Mailhot
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montreal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Vincent Frappier
- Generate Biomedicines, Cambridge, Massachusetts, United States of America
| | - François Major
- Department of Computer Science and Operations Research, Université de Montréal, Montreal, QC, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
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2
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Kaynak BT, Krieger JM, Dudas B, Dahmani ZL, Costa MGS, Balog E, Scott AL, Doruker P, Perahia D, Bahar I. Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods. Front Mol Biosci 2022; 9:832847. [PMID: 35187088 PMCID: PMC8855042 DOI: 10.3389/fmolb.2022.832847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022] Open
Abstract
Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomic molecular dynamics (MD) simulations with the goal of rapidly sampling large and cooperative conformational changes at full atomic resolution. We present here a systematic comparison of the utility and limits of four such hybrid methods that have been introduced in recent years: MD with excited normal modes (MDeNM), collective modes-driven MD (CoMD), and elastic network model (ENM)-based generation, clustering, and relaxation of conformations (ClustENM) as well as its updated version integrated with MD simulations (ClustENMD). We analyzed the predicted conformational spaces using each of these four hybrid methods, applied to four well-studied proteins, triosephosphate isomerase (TIM), 3-phosphoglycerate kinase (PGK), HIV-1 protease (PR) and HIV-1 reverse transcriptase (RT), which provide extensive ensembles of experimental structures for benchmarking and comparing the methods. We show that a rigorous multi-faceted comparison and multiple metrics are necessary to properly assess the differences between conformational ensembles and provide an optimal protocol for achieving good agreement with experimental data. While all four hybrid methods perform well in general, being especially useful as computationally efficient methods that retain atomic resolution, the systematic analysis of the same systems by these four hybrid methods highlights the strengths and limitations of the methods and provides guidance for parameters and protocols to be adopted in future studies.
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Affiliation(s)
- Burak T. Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - James M. Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Balint Dudas
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zakaria L. Dahmani
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mauricio G. S. Costa
- Programa de Computação Científica, Vice-Presiden̂cia de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ana Ligia Scott
- Laboratory of Bioinformatics and Computational Biology, Center of Mathematics, Computation and Cognition, Federal University of ABC-UFABC, Santo André, Brazil
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Ivet Bahar, ; David Perahia, ; Pemra Doruker,
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
- *Correspondence: Ivet Bahar, ; David Perahia, ; Pemra Doruker,
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Ivet Bahar, ; David Perahia, ; Pemra Doruker,
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3
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Bose Majumdar A, Kim IJ, Na H. Effect of solvent on protein structure and dynamics. Phys Biol 2020; 17:036006. [DOI: 10.1088/1478-3975/ab74b3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Kulkarni YS, Amyes TL, Richard JP, Kamerlin SCL. Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase. J Am Chem Soc 2019; 141:16139-16150. [PMID: 31508957 PMCID: PMC7032883 DOI: 10.1021/jacs.9b08713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We report results of detailed empirical valence bond simulations that model the effect of several amino acid substitutions on the thermodynamic (ΔG°) and kinetic activation (ΔG⧧) barriers to deprotonation of dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) bound to wild-type triosephosphate isomerase (TIM), as well as to the K12G, E97A, E97D, E97Q, K12G/E97A, I170A, L230A, I170A/L230A, and P166A variants of this enzyme. The EVB simulations model the observed effect of the P166A mutation on protein structure. The E97A, E97Q, and E97D mutations of the conserved E97 side chain result in ≤1.0 kcal mol-1 decreases in the activation barrier for substrate deprotonation. The agreement between experimental and computed activation barriers is within ±1 kcal mol-1, with a strong linear correlation between ΔG⧧ and ΔG° for all 11 variants, with slopes β = 0.73 (R2 = 0.994) and β = 0.74 (R2 = 0.995) for the deprotonation of DHAP and GAP, respectively. These Brønsted-type correlations show that the amino acid side chains examined in this study function to reduce the standard-state Gibbs free energy of reaction for deprotonation of the weak α-carbonyl carbon acid substrate to form the enediolate phosphate reaction intermediate. TIM utilizes the cationic side chain of K12 to provide direct electrostatic stabilization of the enolate oxyanion, and the nonpolar side chains of P166, I170, and L230 are utilized for the construction of an active-site cavity that provides optimal stabilization of the enediolate phosphate intermediate relative to the carbon acid substrate.
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Affiliation(s)
- Yashraj S Kulkarni
- Science for Life Laboratory, Department of Chemistry - BMC , Uppsala University, BMC , Box 576, S-751 23 Uppsala , Sweden
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Chemistry - BMC , Uppsala University, BMC , Box 576, S-751 23 Uppsala , Sweden
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5
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Frezza E, Lavery R. Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions. J Phys Chem B 2019; 123:1294-1301. [DOI: 10.1021/acs.jpcb.8b11913] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elisa Frezza
- MMSB, UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Richard Lavery
- MMSB, UMR 5086 CNRS/Univ. Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
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6
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Anand DV, Meng Z, Xia K. A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes. Phys Chem Chem Phys 2019; 21:4359-4366. [DOI: 10.1039/c8cp07442a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CMVP-ENM for virus normal mode analysis. With a special ratio parameter, CMVP-ENM can characterize the multi-material properties of biomolecular complexes and systematically enhance or suppress the modes for different components.
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Affiliation(s)
- D. Vijay Anand
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - Zhenyu Meng
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Kelin Xia
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
- School of Biological Sciences
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7
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Song G. Symmetry in normal modes and its strong dependence on symmetry in structure. J Mol Graph Model 2017; 75:32-41. [DOI: 10.1016/j.jmgm.2017.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 10/19/2022]
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8
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Mishra SK, Sankar K, Jernigan RL. Altered dynamics upon oligomerization corresponds to key functional sites. Proteins 2017; 85:1422-1434. [PMID: 28383162 DOI: 10.1002/prot.25302] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 12/18/2022]
Abstract
It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse-grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with ¼ of the residues increasing in their mobilities and ¼ having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures. Proteins 2017; 85:1422-1434. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sambit Kumar Mishra
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Kannan Sankar
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
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9
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Kurkcuoglu Z, Bahar I, Doruker P. ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution. J Chem Theory Comput 2016; 12:4549-62. [PMID: 27494296 DOI: 10.1021/acs.jctc.6b00319] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Accurate sampling of conformational space and, in particular, the transitions between functional substates has been a challenge in molecular dynamic (MD) simulations of large biomolecular systems. We developed an Elastic Network Model (ENM)-based computational method, ClustENM, for sampling large conformational changes of biomolecules with various sizes and oligomerization states. ClustENM is an iterative method that combines ENM with energy minimization and clustering steps. It is an unbiased technique, which requires only an initial structure as input, and no information about the target conformation. To test the performance of ClustENM, we applied it to six biomolecular systems: adenylate kinase (AK), calmodulin, p38 MAP kinase, HIV-1 reverse transcriptase (RT), triosephosphate isomerase (TIM), and the 70S ribosomal complex. The generated ensembles of conformers determined at atomic resolution show good agreement with experimental data (979 structures resolved by X-ray and/or NMR) and encompass the subspaces covered in independent MD simulations for TIM, p38, and RT. ClustENM emerges as a computationally efficient tool for characterizing the conformational space of large systems at atomic detail, in addition to generating a representative ensemble of conformers that can be advantageously used in simulating substrate/ligand-binding events.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University , Bebek 34342, Istanbul, Turkey
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University , Bebek 34342, Istanbul, Turkey
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10
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Tiwari SP, Reuter N. Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes. PLoS Comput Biol 2016; 12:e1004834. [PMID: 27015412 PMCID: PMC4807811 DOI: 10.1371/journal.pcbi.1004834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/25/2016] [Indexed: 11/19/2022] Open
Abstract
The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence, structure and functional conservation. We characterise the conservation of such dynamics in a case where the structure is conserved but function differs greatly. The triosephosphate isomerase barrel fold (TBF), renowned for its 8 β-strand-α-helix repeats that close to form a barrel, is one of the most diverse and abundant folds found in known protein structures. Proteins with this fold have diverse enzymatic functions spanning five of six Enzyme Commission classes, and we have picked five different superfamily candidates for our analysis using elastic network models. We find that the overall shape is a large determinant in the similarity of the intrinsic dynamics, regardless of function. In particular, the β-barrel core is highly rigid, while the α-helices that flank the β-strands have greater relative mobility, allowing for the many possibilities for placement of catalytic residues. We find that these elements correlate with each other via the loops that link them, as opposed to being directly correlated. We are also able to analyse the types of motions encoded by the normal mode vectors of the α-helices. We suggest that the global conservation of the intrinsic dynamics in the TBF contributes greatly to its success as an enzymatic scaffold both through evolution and enzyme design.
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Affiliation(s)
- Sandhya P. Tiwari
- Department of Molecular Biology, University of Bergen, Pb. 7803, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, Bergen, Norway
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Pb. 7803, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Pb. 7803, Bergen, Norway
- * E-mail:
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11
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Zhao ZW, Xie XS, Ge H. Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J Phys Chem B 2016; 120:2869-77. [PMID: 26918464 DOI: 10.1021/acs.jpcb.5b11002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleotide-induced conformational closing of the finger domain of DNA polymerase is crucial for its catalytic action during DNA replication. Such large-amplitude molecular motion is often not fully accessible to either direct experimental monitoring or molecular dynamics simulations. However, a coarse-grained model can offer an informative alternative, especially for probing the relationship between conformational dynamics and catalysis. Here we investigate the dynamics of T7 DNA polymerase catalysis using a Langevin-type elastic network model incorporating detailed structural information on the open conformation without the substrate bound. Such a single-parameter model remarkably captures the induced conformational dynamics of DNA polymerase upon dNTP binding, and reveals its close coupling to the advancement toward transition state along the coordinate of the target reaction, which contributes to significant lowering of the activation energy barrier. Furthermore, analysis of stochastic catalytic rates suggests that when the activation energy barrier has already been significantly lowered and nonequilibrium relaxation toward the closed form dominates the catalytic rate, one must appeal to a picture of two-dimensional free energy surface in order to account for the full spectrum of catalytic modes. Our semiquantitative study illustrates the general role of conformational dynamics in achieving transition-state stabilization, and suggests that such an elastic network model, albeit simplified, possesses the potential to furnish significant mechanistic insights into the functioning of a variety of enzymatic systems.
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Affiliation(s)
- Ziqing W Zhao
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.,Graduate Program in Biophysics, Harvard University , Cambridge, Massachusetts 02138, United States
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.,Graduate Program in Biophysics, Harvard University , Cambridge, Massachusetts 02138, United States.,Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, P. R. China
| | - Hao Ge
- Biodynamic Optical Imaging Center (BIOPIC), Peking University , Beijing 100871, P. R. China.,Beijing International Center for Mathematical Research (BICMR), Peking University , Beijing 100871, P. R. China
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12
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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13
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Na H, Jernigan RL, Song G. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models. PLoS Comput Biol 2015; 11:e1004542. [PMID: 26473491 PMCID: PMC4608564 DOI: 10.1371/journal.pcbi.1004542] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/08/2015] [Indexed: 11/24/2022] Open
Abstract
Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. Proteins and other biomolecules are not static but are constantly in motion. Moreover, they possess intrinsic collective motion patterns that are tightly linked to their functions. Thus, an accurate and detailed description of their motions can provide deep insights into their functional mechanisms. For large protein complexes with hundreds of thousands of atoms or more, an atomic level description of the motions can be computationally prohibitive, and so coarse-grained models with fewer structural details are often used instead. However, there can be a big gap between the quality of motions derived from atomic models and those from coarse-grained models. In this work, we solve an important problem in protein dynamics studies: how to preserve the atomic-level accuracy in describing molecular motions while using coarse-grained models? We accomplish this by developing a novel iterative matrix projection method that dramatically speeds up the computations. This method is significant since it promises accurate descriptions of protein motions approaching an all-atom level even for the largest biomolecular complexes. Results shown here for a large molecular chaperonin demonstrate how this can provide new insights into its functional process.
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Affiliation(s)
- Hyuntae Na
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
| | - Robert L. Jernigan
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- Program of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Guang Song
- Department of Computer Science, Iowa State University, Ames, Iowa, United States of America
- Program of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, United States of America
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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14
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Frezza E, Lavery R. Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility. J Chem Theory Comput 2015; 11:5503-12. [DOI: 10.1021/acs.jctc.5b00724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elisa Frezza
- BMSSI, UMR 5086 CNRS/Univ.
Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Richard Lavery
- BMSSI, UMR 5086 CNRS/Univ.
Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
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15
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Kurkcuoglu Z, Findik D, Akten ED, Doruker P. How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophys J 2015; 109:1169-78. [PMID: 26190635 DOI: 10.1016/j.bpj.2015.06.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/18/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022] Open
Abstract
The tunnel region at triosephosphate isomerase (TIM)'s dimer interface, distant from its catalytic site, is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi, the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor, named bt10. Within the time frame of our MD simulations, we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10, which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54,000 MD snapshots. Using this computationally efficient technique, we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly, we observed allosteric changes in the catalytic loop's dynamics, flexibility, and correlations, as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Doga Findik
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali, Istanbul, Turkey
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
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16
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The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors. Proteins 2015; 83:1273-83. [DOI: 10.1002/prot.24819] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/10/2015] [Accepted: 04/17/2015] [Indexed: 11/07/2022]
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17
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Sim J, Sim J, Park E, Lee J. Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration. Proteins 2015; 83:1054-67. [DOI: 10.1002/prot.24799] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/28/2015] [Accepted: 03/10/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Jaehyun Sim
- Department of Oral Microbiology and Immunology; School of Dentistry, Seoul National University; Seoul 110-749 Korea
| | - Jun Sim
- Department of Bioinformatics and Life Science; Soongsil University; Seoul 156-743 Korea
| | - Eunsung Park
- Administrative Service Division, Apsun Dental Hospital; Seoul 135-590 Korea
| | - Julian Lee
- Department of Oral Microbiology and Immunology; School of Dentistry, Seoul National University; Seoul 110-749 Korea
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18
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Na H, Song G. Conventional NMA as a better standard for evaluating elastic network models. Proteins 2014; 83:259-67. [DOI: 10.1002/prot.24735] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/14/2014] [Accepted: 11/26/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Hyuntae Na
- Department of Computer Science; Iowa State University; Ames Iowa 50011
| | - Guang Song
- Department of Computer Science; Iowa State University; Ames Iowa 50011
- Program of Bioinformatics and Computational Biology, Iowa State University; Ames Iowa 50011
- L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University; Ames Iowaa 50011
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19
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Na H, Song G. Bridging between normal mode analysis and elastic network models. Proteins 2014; 82:2157-68. [DOI: 10.1002/prot.24571] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/06/2014] [Accepted: 03/21/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Hyuntae Na
- Department of Computer Science; Iowa State University; Ames Iowa 50011
| | - Guang Song
- Department of Computer Science; Iowa State University; Ames Iowa 50011
- Program of Bioinformatics and Computational Biology; Iowa State University; Ames Iowa 50011
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University; Ames Iowa 50011
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20
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Frappier V, Najmanovich RJ. A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PLoS Comput Biol 2014; 10:e1003569. [PMID: 24762569 PMCID: PMC3998880 DOI: 10.1371/journal.pcbi.1003569] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/25/2014] [Indexed: 11/18/2022] Open
Abstract
Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.
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Affiliation(s)
- Vincent Frappier
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Rafael J Najmanovich
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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21
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Katebi AR, Jernigan RL. The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality. Protein Sci 2013; 23:213-28. [PMID: 24318986 DOI: 10.1002/pro.2407] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/01/2013] [Accepted: 12/03/2013] [Indexed: 11/11/2022]
Abstract
Triosephosphate isomerase (TIM) catalyzes the reaction to convert dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and vice versa. In most organisms, its functional oligomeric state is a homodimer; however, tetramer formation in hyperthermophiles is required for functional activity. The tetrameric TIM structure also provides added stability to the structure, enabling it to function at more extreme temperatures. We apply Principal Component Analysis to find that the TIM structure space is clearly divided into two groups--the open and the closed TIM structures. The distribution of the structures in the open set is much sparser than that in the closed set, showing a greater conformational diversity of the open structures. We also apply the Elastic Network Model to four different TIM structures--an engineered monomeric structure, a dimeric structure from a mesophile--Trypanosoma brucei, and two tetrameric structures from hyperthermophiles Thermotoga maritima and Pyrococcus woesei. We find that dimerization not only stabilizes the structures, it also enhances their functional dynamics. Moreover, tetramerization of the hyperthermophilic structures increases their functional loop dynamics, enabling them to function in the destabilizing environment of extreme temperatures. Computations also show that the functional loop motions, especially loops 6 and 7, are highly coordinated. In summary, our computations reveal the underlying mechanism of the allosteric regulation of the functional loops of the TIM structures, and show that tetramerization of the structure as found in the hyperthermophilic organisms is required to maintain the coordination of the functional loops at a level similar to that in the dimeric mesophilic structure.
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Affiliation(s)
- Ataur R Katebi
- Department of Biochemistry, Biophysics and Molecular Biology, LH Baker Center for Bioinformatics and Biological Statistics, Interdepartmental Program for Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, 50011-3020
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22
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Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase. ENTROPY 2013. [DOI: 10.3390/e15031085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Micheletti C. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys Life Rev 2012. [PMID: 23199577 DOI: 10.1016/j.plrev.2012.10.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship.
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Affiliation(s)
- Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, Italy.
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24
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Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P. Coupling between catalytic loop motions and enzyme global dynamics. PLoS Comput Biol 2012; 8:e1002705. [PMID: 23028297 PMCID: PMC3459879 DOI: 10.1371/journal.pcbi.1002705] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 08/02/2012] [Indexed: 11/18/2022] Open
Abstract
Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions. We performed an extensive study on a set of enzymes to assess whether the collective/global dynamics, as predicted by elastic network models (ENMs), facilitates or even defines the local motions undergone by functional loops. Our dataset includes a total of 117 crystal structures for ten enzymes of different sizes and oligomerization states. Each enzyme contains a specific functional/catalytic loop (10–21 residues long) that closes over the active site during catalysis. Principal component analysis (PCA) of the available crystal structures (including apo and ligand-bound forms) for each enzyme revealed the dominant conformational changes taking place in these loops upon substrate binding. These experimentally observed loop reconfigurations are shown to be predominantly driven by energetically favored modes of motion intrinsically accessible to the enzyme in the absence of its substrate. The analysis suggests that robust global modes cooperatively defined by the overall enzyme architecture also entail local components that assist in suitable opening/closure of the catalytic loop over the active site. Protein loops have critical roles in ligand binding and catalysis. An unresolved issue in this context is the extent to which the intrinsic dynamics of proteins predispose loops to perform their molecular function. In this work, we (i) critically examine the structural changes undergone by functional/catalytic loops based on a set of enzyme crystal structures in the presence/absence of a ligand, and (ii) examine to what extent those motions are correlated with, or driven by, the global modes that are predictable using simplified, physics-based models. Using a dataset of 117 structures for ten enzymes of different sizes and oligomerization states, we show that the collective modes defined by the protein topology favor loop rearrangements in reasonable agreement with those experimentally observed upon activation. These results suggest that simple but robust motions encoded by the entire architecture, not the local binding site only, assist in binding of the ligand, positioning of the catalytic loop, and/or sequestration of the catalytic site, which in turn, enable efficient catalysis.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Ahmet Bakan
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Duygu Kocaman
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Ivet Bahar
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (IB); (PD)
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
- * E-mail: (IB); (PD)
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25
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Skliros A, Zimmermann MT, Chakraborty D, Saraswathi S, Katebi AR, Leelananda SP, Kloczkowski A, Jernigan RL. The importance of slow motions for protein functional loops. Phys Biol 2012; 9:014001. [PMID: 22314977 DOI: 10.1088/1478-3975/9/1/014001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Loops in proteins that connect secondary structures such as alpha-helix and beta-sheet, are often on the surface and may play a critical role in some functions of a protein. The mobility of loops is central for the motional freedom and flexibility requirements of active-site loops and may play a critical role for some functions. The structures and behaviors of loops have not been studied much in the context of the whole structure and its overall motions, especially how these might be coupled. Here we investigate loop motions by using coarse-grained structures (C(α) atoms only) to solve the motions of the system by applying Lagrange equations with elastic network models to learn about which loops move in an independent fashion and which move in coordination with domain motions, faster and slower, respectively. The normal modes of the system are calculated using eigen-decomposition of the stiffness matrix. The contribution of individual modes and groups of modes is investigated for their effects on all residues in each loop by using Fourier analyses. Our results indicate overall that the motions of functional sets of loops behave in similar ways as the whole structure. But overall only a relatively few loops move in coordination with the dominant slow modes of motion, and these are often closely related to function.
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Affiliation(s)
- Aris Skliros
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA. Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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26
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Uyar A, Kurkcuoglu O, Nilsson L, Doruker P. The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases. Phys Biol 2011; 8:056001. [PMID: 21791727 DOI: 10.1088/1478-3975/8/5/056001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The vibrational dynamics of various type II restriction endonucleases, in complex with cognate/non-cognate DNA and in the apo form, are investigated with the elastic network model in order to reveal common functional mechanisms in this enzyme family. Scissor-like and tong-like motions observed in the slowest modes of all enzymes and their complexes point to common DNA recognition and cleavage mechanisms. Normal mode analysis further points out that the scissor-like motion has an important role in differentiating between cognate and non-cognate sequences at the recognition site, thus implying its catalytic relevance. Flexible regions observed around the DNA-binding site of the enzyme usually concentrate on the highly conserved β-strands, especially after DNA binding. These β-strands may have a structurally stabilizing role in functional dynamics for target site recognition and cleavage. In addition, hot spot residues based on high-frequency modes reveal possible communication pathways between the two distant cleavage sites in the enzyme family. Some of these hot spots also exist on the shortest path between the catalytic sites and are highly conserved.
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Affiliation(s)
- A Uyar
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342 Bebek, Istanbul, Turkey
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27
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Ahmed A, Rippmann F, Barnickel G, Gohlke H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model 2011; 51:1604-22. [PMID: 21639141 DOI: 10.1021/ci100461k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 Å) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.
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Affiliation(s)
- Aqeel Ahmed
- Department of Biological Sciences, Molecular Bioinformatics Group, Goethe University, Frankfurt, Germany
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28
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Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: a molecular dynamics and normal mode analysis study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:630-7. [PMID: 21440684 DOI: 10.1016/j.bbapap.2011.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 02/19/2011] [Accepted: 03/18/2011] [Indexed: 01/28/2023]
Abstract
Enzymes from thermophiles are poorly active at temperatures at which their mesophilic homologs exhibit high activity and attain corresponding active states at high temperatures. In this study, comparative molecular dynamics (MD) simulations, supplemented by normal mode analysis, have been performed on an enzyme Adenylosuccinate synthetase (AdSS) from E. coli (mesophilic) and P. horikoshii (thermophilic) systems to understand the effects of loop dynamics on thermal stability of AdSS. In mesophilic AdSS, both ligand binding and catalysis are facilitated through the coordinated movement of five loops on the protein. The simulation results suggest that thermophilic P. horikoshii preserves structure and catalytic function at high temperatures by using the movement of only a subset of loops (two out of five) for ligand binding and catalysis unlike its mesophilic counterpart in E. coli. The pre-arrangement of the catalytic residues in P. horikoshii is well-preserved and salt bridges remain stable at high temperature (363K). The simulations suggest a general mechanism (including pre-arrangement of catalytic residues, increased polar residue content, stable salt bridges, increased rigidity, and fewer loop movements) used by thermophilic enzymes to preserve structure and be catalytically active at elevated temperatures.
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29
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Markwick PRL, McCammon JA. Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys 2011; 13:20053-65. [DOI: 10.1039/c1cp22100k] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Moal IH, Bates PA. SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci 2010; 11:3623-48. [PMID: 21152290 PMCID: PMC2996808 DOI: 10.3390/ijms11103623] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 07/29/2010] [Accepted: 09/16/2010] [Indexed: 11/17/2022] Open
Abstract
Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.
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Affiliation(s)
- Iain H. Moal
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY, UK
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY, UK
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31
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Ozer N, Schiffer CA, Haliloglu T. Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophys J 2010; 99:1650-9. [PMID: 20816079 PMCID: PMC2931728 DOI: 10.1016/j.bpj.2010.06.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 06/25/2010] [Accepted: 06/28/2010] [Indexed: 11/29/2022] Open
Abstract
The structural fluctuations of HIV-1 protease in interaction with its substrates versus inhibitors were analyzed using the anisotropic network model. The directions of fluctuations in the most cooperative functional modes differ mainly around the dynamically key regions, i.e., the hinge axes, which appear to be more flexible in substrate complexes. The flexibility of HIV-1 protease is likely optimized for the substrates' turnover, resulting in substrate complexes being dynamic. In contrast, in an inhibitor complex, the inhibitor should bind and lock down to inactivate the active site. Protease and ligands are not independent. Substrates are also more flexible than inhibitors and have the potential to meet the dynamic distributions that are inherent in the protease. This may suggest a rationale and guidelines for designing inhibitors that can better fit the ensemble of binding sites that are dynamically accessible to the protease.
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Affiliation(s)
- Nevra Ozer
- Polymer Research Center, Bogazici University, Istanbul, Turkey
- Chemical Engineering Department, Bogazici University, Istanbul, Turkey
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Turkan Haliloglu
- Polymer Research Center, Bogazici University, Istanbul, Turkey
- Chemical Engineering Department, Bogazici University, Istanbul, Turkey
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32
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33
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Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010; 110:1463-97. [PMID: 19785456 PMCID: PMC2836427 DOI: 10.1021/cr900095e] [Citation(s) in RCA: 393] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.
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34
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Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophys J 2009; 97:1178-87. [PMID: 19686666 DOI: 10.1016/j.bpj.2009.06.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 05/12/2009] [Accepted: 06/01/2009] [Indexed: 01/03/2023] Open
Abstract
The mixed-resolution elastic network model was introduced previously for computing the motions of a structure, which is described at different levels of detail in different parts, for example, with atomistic and residue-level regions. This method has proved to be an efficient tool to explore the collective dynamics of proteins with some atomistic details, which would be difficult to obtain with either conventional full-atom approaches or fully coarse-grained models. Understanding function often requires atomic detail, but not necessarily for the entire structure. In this study, the calculation of the interaction forces between different resolution regions for the hierarchical levels of coarse-graining is further elaborated on in the new approach by considering explicitly the atomic contacts in the crystal structure. The collective dynamics of the enzyme triosephosphate isomerase and its active site together with loop 6 motions are considered in detail. The supramolecular assemblage ribosome and local atomic motions in its "interesting" functional part-the decoding center-are investigated for the low frequency range of the spectrum with high computational efficiency. This new atom-based mixed coarse-graining approach can be effectively used to generate realistic high-resolution conformations of extremely large protein-DNA or RNA complexes by performing energy minimization on structures deformed along the normal modes of the elastic network model. The new model permits focusing on specific functional parts that move in coordination and response to the remainder of the entire structure.
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Affiliation(s)
- Ozge Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, 34342, Bebek, Istanbul, Turkey
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35
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Abstract
Elastic network models (ENMs) are entropic models that have demonstrated in many previous studies their abilities to capture overall the important internal motions, with comparisons having been made against crystallographic B-factors and NMR conformational variabilities. ENMs have become an increasingly important tool and have been widely used to comprehend protein dynamics, function, and even conformational changes. However, reliance upon an arbitrary cutoff distance to delimit the range of interactions has presented a drawback for these models, because the optimal cutoff values can differ somewhat from protein to protein and can lead to quirks such as some shuffling in the order of the normal modes when applied to structures that differ only slightly. Here, we have replaced the requirement for a cutoff distance and introduced the more physical concept of inverse power dependence for the interactions, with a set of elastic network models that are parameter-free, with the distance cutoff removed. For small fluctuations about the native forms, the power dependence is the inverse square, but for larger deformations, the power dependence may become inverse 6th or 7th power. These models maintain and enhance the simplicity and generality of the original ENMs, and at the same time yield better predictions of crystallographic B-factors (both isotropic and anisotropic) and of the directions of conformational transitions. Thus, these parameter-free ENMs can be models of choice whenever elastic network models are used.
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36
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Ho BK, Agard DA. Probing the flexibility of large conformational changes in protein structures through local perturbations. PLoS Comput Biol 2009; 5:e1000343. [PMID: 19343225 PMCID: PMC2660149 DOI: 10.1371/journal.pcbi.1000343] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 02/27/2009] [Indexed: 11/19/2022] Open
Abstract
Protein conformational changes and dynamic behavior are fundamental for such processes as catalysis, regulation, and substrate recognition. Although protein dynamics have been successfully explored in computer simulation, there is an intermediate-scale of motions that has proven difficult to simulate—the motion of individual segments or domains that move independently of the body the protein. Here, we introduce a molecular-dynamics perturbation method, the Rotamerically Induced Perturbation (RIP), which can generate large, coherent motions of structural elements in picoseconds by applying large torsional perturbations to individual sidechains. Despite the large-scale motions, secondary structure elements remain intact without the need for applying backbone positional restraints. Owing to its computational efficiency, RIP can be applied to every residue in a protein, producing a global map of deformability. This map is remarkably sparse, with the dominant sites of deformation generally found on the protein surface. The global map can be used to identify loops and helices that are less tightly bound to the protein and thus are likely sites of dynamic modulation that may have important functional consequences. Additionally, they identify individual residues that have the potential to drive large-scale coherent conformational change. Applying RIP to two well-studied proteins, Dihdydrofolate Reductase and Triosephosphate Isomerase, which possess functionally-relevant mobile loops that fluctuate on the microsecond/millisecond timescale, the RIP deformation map identifies and recapitulates the flexibility of these elements. In contrast, the RIP deformation map of α-lytic protease, a kinetically stable protein, results in a map with no significant deformations. In the N-terminal domain of HSP90, the RIP deformation map clearly identifies the ligand-binding lid as a highly flexible region capable of large conformational changes. In the Estrogen Receptor ligand-binding domain, the RIP deformation map is quite sparse except for one large conformational change involving Helix-12, which is the structural element that allosterically links ligand binding to receptor activation. RIP analysis has the potential to discover sites of functional conformational changes and the linchpin residues critical in determining these conformational states. Many proteins undergo large motions to carry out their biological functions. The exact nature of these motions is typically inferred from the crystal structures of the protein trapped in different states, which normally constitutes a difficult series of experiments. As molecular dynamics is generally accepted to accurately model the motion of proteins, the promise is that a long enough simulation will generate all the motions of a given protein structure. Unfortunately, current systems run too slowly to simulate all but the smallest motions. To overcome this computational limit, we have developed a molecular-dynamics perturbation method that induces large changes in a protein structure in very short simulation times. The changes correspond to large motions of specific structural elements on the surface of the protein that corroborate well with the canonical motions of several well-characterized proteins. This bodes well for our method to identify, for any given protein structure, structural elements on the surface that might bind drugs, regulate signals, undergo chemical modifications, or become unstructured.
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Affiliation(s)
- Bosco K Ho
- Howard Hughes Medical Institute and the Department of Biochemistry, University of California San Francisco, San Francisco, California, United States of America.
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37
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Delarue M. Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2007; 64:40-8. [PMID: 18094466 PMCID: PMC2394787 DOI: 10.1107/s0907444907053516] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 10/26/2007] [Indexed: 01/08/2023]
Abstract
Normal-mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular-replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimental data (X-ray or cryo-EM), generalizing rigid-body refinement methods by adding just a few additional degrees of freedom that sample collective and large-amplitude movements. It is also argued that the situation where several (conformations of) models are present simultaneously in the crystal can be studied with adjustable occupancies using techniques derived from statistical thermodynamics and already used in molecular modelling.
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Affiliation(s)
- Marc Delarue
- Unité de Dynamique Structurale des Macromolecules, Departement de Biologie Structurale et Chimie, URA 2185 du CNRS, Institut Pasteur, 25 Rue du Dr Roux, 75015 Paris, France.
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38
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Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol 2007; 17:633-40. [PMID: 18024008 DOI: 10.1016/j.sbi.2007.09.011] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 08/21/2007] [Accepted: 09/28/2007] [Indexed: 11/23/2022]
Abstract
In recent years, there has been a surge in the number of studies exploring the relationship between proteins' equilibrium dynamics and structural changes involved in function. An emerging concept, supported by both theory and experiments, is that under native state conditions proteins have an intrinsic ability to sample conformations that meet functional requirements. A typical example is the ability of enzymes to sample open and closed forms, irrespective of substrate, succeeded by the stabilization of one form (usually closed) upon substrate binding. This ability is structure-encoded, and plays a key role in facilitating allosteric regulation, which suggests complementing the sequence-encodes-structure paradigm of protein science by structure-encodes-dynamics-encodes-function. The emerging connection implies an evolutionary role in selecting/conserving structures based on their ability to achieve functional dynamics, and in turn, selecting sequences that fold into such 'apt' structures.
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Olivares-Illana V, Rodríguez-Romero A, Becker I, Berzunza M, García J, Pérez-Montfort R, Cabrera N, López-Calahorra F, de Gómez-Puyou MT, Gómez-Puyou A. Perturbation of the dimer interface of triosephosphate isomerase and its effect on Trypanosoma cruzi. PLoS Negl Trop Dis 2007; 1:e1. [PMID: 17989778 PMCID: PMC2041813 DOI: 10.1371/journal.pntd.0000001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 06/07/2007] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Chagas disease affects around 18 million people in the American continent. Unfortunately, there is no satisfactory treatment for the disease. The drugs currently used are not specific and exert serious toxic effects. Thus, there is an urgent need for drugs that are effective. Looking for molecules to eliminate the parasite, we have targeted a central enzyme of the glycolytic pathway: triosephosphate isomerase (TIM). The homodimeric enzyme is catalytically active only as a dimer. Because there are significant differences in the interface of the enzymes from the parasite and humans, we searched for small molecules that specifically disrupt contact between the two subunits of the enzyme from Trypanosoma cruzi but not those of TIM from Homo sapiens (HTIM), and tested if they kill the parasite. METHODOLOGY/PRINCIPAL FINDINGS Dithiodianiline (DTDA) at nanomolar concentrations completely inactivates recombinant TIM of T. cruzi (TcTIM). It also inactivated HTIM, but at concentrations around 400 times higher. DTDA was also tested on four TcTIM mutants with each of its four cysteines replaced with either valine or alanine. The sensitivity of the mutants to DTDA was markedly similar to that of the wild type. The crystal structure of the TcTIM soaked in DTDA at 2.15 A resolution, and the data on the mutants showed that inactivation resulted from alterations of the dimer interface. DTDA also prevented the growth of Escherichia coli cells transformed with TcTIM, had no effect on normal E. coli, and also killed T. cruzi epimastigotes in culture. CONCLUSIONS/SIGNIFICANCE By targeting on the dimer interface of oligomeric enzymes from parasites, it is possible to discover small molecules that selectively thwart the life of the parasite. Also, the conformational changes that DTDA induces in the dimer interface of the trypanosomal enzyme are unique and identify a region of the interface that could be targeted for drug discovery.
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Affiliation(s)
- Vanesa Olivares-Illana
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Ingeborg Becker
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miriam Berzunza
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Juventino García
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ruy Pérez-Montfort
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Nallely Cabrera
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Armando Gómez-Puyou
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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40
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Sacquin-Mora S, Laforet E, Lavery R. Locating the active sites of enzymes using mechanical properties. Proteins 2007; 67:350-9. [PMID: 17311346 DOI: 10.1002/prot.21353] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have applied the calculation of mechanical properties to a dataset of almost 100 enzymes to determine the extent to which catalytic residues have distinct properties. Specifically, we have calculated force constants describing the ease of moving any given amino acid residue with respect to the other residues in the protein. The results show that catalytic residues are invariably associated with high force constants. Choosing an appropriate cutoff enables the detection of roughly 80% of catalytic residues with only 25% of false positives. It is shown that neither multidomain structures, nor the presence or absence of bound ligands hinder successful detections. It is however noted that active sites near the protein surface are more difficult to detect and that non-catalytic, but structurally key residues may also exhibit high force constants.
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Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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41
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Zomosa-Signoret V, Aguirre-López B, Hernández-Alcántara G, Pérez-Montfort R, de Gómez-Puyou MT, Gómez-Puyou A. Crosstalk between the subunits of the homodimeric enzyme triosephosphate isomerase. Proteins 2007; 67:75-83. [PMID: 17221869 DOI: 10.1002/prot.21242] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Homodimeric triosephosphate isomerase (TIM) from Trypanosoma cruzi (TcTIM) and T. brucei (TbTIM) are markedly similar in amino acid sequence and three-dimensional structure. In their dimer interfaces, each monomer has a Cys15 that is surrounded by loop3 of the adjoining subunit. Perturbation of Cys15 by methylmethane thiosulfonate (MMTS) induces abolition of catalysis and structural changes. In the two TIMs, the structural arrangements of their Cys15 are almost identical. Nevertheless, the susceptibility of TcTIM to MMTS is nearly 100-fold higher than in TbTIM. To ascertain the extent to which the characteristics of the interface Cys depend on the dynamics of its own monomer or on those of the adjacent monomer, we studied MMTS action on mutants of TcTIM that had the interface residues of TbTIM, and hybrids that have only one interfacial Cys15 (C15ATcTIM-wild type TbTIM). We found that the solvent exposure of the interfacial Cys depends predominantly on the characteristics of the adjoining monomer. The maximal inhibition of activity induced by perturbation of the sole interface Cys in the C15ATcTIM-TbTIM hybrid is around 60%. Hybrids formed with C15ATcTIM monomers and catalytically inert TbTIM monomers (E168DTbTIM) were also studied. Their activity drops by nearly 50% when the only interfacial Cys is perturbed. These results in conjunction with those on C15ATcTIM-wild type TbTIM hybrid indicate that about half of the activity of each monomer depends on the integrity of each of the two Cys15-loop3 portions of the interface. This could be another reason of why TIM is an obligatory dimer.
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Affiliation(s)
- Viviana Zomosa-Signoret
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70243, 04510 México, D. F., Mexico
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Amyes TL, Richard JP. Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion. Biochemistry 2007; 46:5841-54. [PMID: 17444661 PMCID: PMC2556868 DOI: 10.1021/bi700409b] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
More than 80% of the rate acceleration for enzymatic catalysis of the aldose-ketose isomerization of (R)-glyceraldehyde 3-phosphate (GAP) by triosephosphate isomerase (TIM) can be attributed to the phosphodianion group of GAP [Amyes, T. L., O'Donoghue, A. C., and Richard, J. P. (2001) J. Am. Chem. Soc. 123, 11325-11326]. We examine here the necessity of the covalent connection between the phosphodianion and triose sugar portions of the substrate by "carving up" GAP into the minimal neutral two-carbon sugar glycolaldehyde and phosphite dianion pieces. This "two-part substrate" preserves both the alpha-hydroxycarbonyl and oxydianion portions of GAP. TIM catalyzes proton transfer from glycolaldehyde in D2O, resulting in deuterium incorporation that can be monitored by 1H NMR spectroscopy, with kcat/Km = 0.26 M-1 s-1. Exogenous phosphite dianion results in a very large increase in the observed second-order rate constant (kcat/Km)obsd for turnover of glycolaldehyde, and the dependence of (kcat/Km)obsd on [HPO32-] exhibits saturation. The data give kcat/Km = 185 M-1 s-1 for turnover of glycolaldehyde by TIM that is saturated with phosphite dianion so that the separate binding of phosphite dianion to TIM results in a 700-fold acceleration of proton transfer from carbon. The binding of phosphite dianion to the free enzyme (Kd = 38 mM) is 700-fold weaker than its binding to the fleeting complex of TIM with the altered substrate in the transition state (Kd = 53 muM); the total intrinsic binding energy of phosphite dianion in the transition state is 5.8 kcal/mol. We propose a physical model for catalysis by TIM in which the intrinsic binding energy of the substrate phosphodianion group is utilized to drive closing of the "mobile loop" and a protein conformational change that leads to formation of an active site environment that is optimally organized for stabilization of the transition state for proton transfer from alpha-carbonyl carbon.
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Affiliation(s)
- Tina L Amyes
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, USA
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43
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Ayton GS, Noid WG, Voth GA. Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol 2007; 17:192-8. [PMID: 17383173 DOI: 10.1016/j.sbi.2007.03.004] [Citation(s) in RCA: 305] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 02/21/2007] [Accepted: 03/13/2007] [Indexed: 02/07/2023]
Abstract
Considerable progress has been recently achieved in the multiscale modeling of complex biological processes. Multiscale models have now investigated the structure and dynamics of lipid membranes, proteins, peptides and DNA over length and time scales ranging from the atomic to the macroscopic. Serial multiscale methods that parameterize low-resolution coarse-grained models with data from high-resolution models have studied long time or length scale phenomena that cannot be investigated with atomically detailed models. Parallel multiscale methods that directly couple high- and low-resolution models have efficiently explored slow structural transitions and the importance of long-wavelength fluctuations for biological molecules. The success of such models relies upon new theories and methods for constructing accurate multiscale bridges that transfer information between models with different resolutions.
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Affiliation(s)
- Gary S Ayton
- Center for Biological Modeling and Simulation, University of Utah, Salt Lake City, UT 84112-0850, USA
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Doruker P, Nilsson L, Kurkcuoglu O. Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations. J Biomol Struct Dyn 2006; 24:1-16. [PMID: 16780370 DOI: 10.1080/07391102.2006.10507093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Anisotropic network model (ANM) is used to analyze the collective motions of restriction enzyme EcoRI in free form and in complex with DNA. For comparison, three independent molecular dynamics (MD) simulations, each of 1.5 ns duration, are also performed for the EcoRI-DNA complex in explicit water. Although high mobility (equilibrium fluctuations) of inner and outer loops that surround the DNA is consistent in both methods and experiments, MD runs sample different conformational subspaces from which reliable collective dynamics cannot be extracted. However, ANM employed on different conformations from MD simulations indicates very similar collective motions. The stems of the inner loops are quite immobile even in the free enzyme and form a large, almost fixed, pocket for DNA binding. As a result, the residues that make specific and non-specific interactions with the DNA exhibit very low fluctuations in the free enzyme. The vibrational entropy difference between the EcoRI complex and free protein + unkinked DNA is positive (favorable), which may partially counteract the unfavorable enthalpy difference of DNA kink formation. Dynamic domains in EcoRI complex and cross-correlations between residue fluctuations indicate possible means of communication between the distal active sites.
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Affiliation(s)
- Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek 34342, Istanbul, Turkey.
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Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL. The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. J Chem Theory Comput 2006; 2:696-704. [PMID: 17710199 PMCID: PMC1948848 DOI: 10.1021/ct600060d] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually focused on the level of one point per residue. In this work, we compare the applicability of elastic network models over a broader range of representational scales. We apply normal mode analysis for multiple scales on a high-resolution protein data set using various cutoff radii to define the residues considered to be interacting, or the extent of cooperativity of their motions. These scales include the residue-, atomic-, proton-, and explicit solvent-levels. Interestingly, atomic, proton, and explicit solvent level calculations all provide similar results at the same cutoff value, with the computed mean-square fluctuations showing only a slightly higher correlation (0.61) with the experimental temperature factors from crystallography than the results of the residue-level coarse-graining. The qualitative behavior of each level of coarse graining is similar at different cutoff values. The correlations between these fluctuations and the number of internal contacts improve with increased cutoff values. Our results demonstrate that atomic level elastic network models provide an improved representation for the collective motions of proteins compared to the coarse-grained models.
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Affiliation(s)
- Taner Z. Sen
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Yaping Feng
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011
| | - John V. Garcia
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
| | - Andrzej Kloczkowski
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
| | - Robert L. Jernigan
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011-3020
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
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