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Fujisaki H. Multiscale aspects of molecular motions: From molecular vibrations, conformational changes of biomolecules to cellular dynamics. J NIPPON MED SCH 2021; 89:9-15. [PMID: 34526452 DOI: 10.1272/jnms.jnms.2022_89-116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular aspects of living systems are important because it is the most basic aspects of life as exemplified in biochemistry and structural biology. Since molecules move due to interactive forces between atoms, physics plays an important role to understand the dynamic phenomena of living systems. Here we review our multiscale approaches for computationally treating different levels of molecular motions: vibrational dynamics of molecules, conformational change of biomolecules, and cellular dynamics using statistical-mechanics-based models.
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Affiliation(s)
- Hiroshi Fujisaki
- Department of Physics, Nippon Medical School.,AMED-CREST, Japan Agency for Medical Research and Development
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2
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Mandelli D, Parrinello M. A modified nudged elastic band algorithm with adaptive spring lengths. J Chem Phys 2021; 155:074103. [PMID: 34418926 DOI: 10.1063/5.0059593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a modified version of the nudged elastic band (NEB) algorithm to find minimum energy paths connecting two known configurations. We show that replacing the harmonic band-energy term with a discretized version of the Onsager-Machlup action leads to a NEB algorithm with adaptive spring lengths that automatically increase the resolution of the minimum energy path around the saddle point of the potential energy surface. The method has the same computational cost per optimization step of the standard NEB algorithm and does not introduce additional parameters. We present applications to the isomerization of alanine dipeptide, the elimination of hydrogen from ethane, and the healing of a 5-77-5 defect in graphene.
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Affiliation(s)
- D Mandelli
- Atomistic Simulations, Italian Institute of Technology, Via Morego, 30 16163 Genova, Italy
| | - M Parrinello
- Atomistic Simulations, Italian Institute of Technology, Via Morego, 30 16163 Genova, Italy
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3
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Moritsugu K, Yamamoto N, Yonezawa Y, Tate SI, Fujisaki H. Path Ensembles for Pin1-Catalyzed Cis-Trans Isomerization of a Substrate Calculated by Weighted Ensemble Simulations. J Chem Theory Comput 2021; 17:2522-2529. [PMID: 33769826 DOI: 10.1021/acs.jctc.0c01280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pin1 enzyme protein recognizes specifically phosphorylated serine/threonine (pSer/pThr) and catalyzes the slow interconversion of the peptidyl-prolyl bond between cis and trans forms. Structural dynamics between the cis and trans forms are essential to reveal the underlying molecular mechanism of the catalysis. In this study, we apply the weighted ensemble (WE) simulation method to obtain comprehensive path ensembles for the Pin1-catalyzed isomerization process. Associated rate constants for both cis-to-trans and trans-to-cis isomerization are calculated to be submicroseconds time scales, which are in good agreement with the calculated free energy landscape where the cis form is slightly less favorable. The committor-like analysis indicates the shift of the transition state toward trans form (at the isomerization angle ω ∼ 110°) compared to the intrinsic position for the isolated substrate (ω ∼ 90°). The calculated structural ensemble clarifies a role of both the dual-histidine motif, His59/His157, and the basic residues, Lys63/Arg68/Arg69, to anchor both sides of the peptidyl-prolyl bond, the aromatic ring in Pro, and the phosphate in pSer, respectively. The rotation of the torsion angle is found to be facilitated by relaying the hydrogen-bond partner of the main-chain oxygen in pSer from Cys113 in the cis form to Arg68 in the trans form, through Ser154 at the transition state, which is really the cause of the shift in the transition state. The role of Ser154 as a driving force of the isomerization is confirmed by additional WE and free energy calculations for S154A mutant where the isomerization takes place slightly slower and the free energy barrier increases through the mutation. The present study shows the usefulness of the WE simulation for substantial path samplings between the reactant and product states, unraveling the molecular mechanism of the enzyme catalysis.
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Affiliation(s)
- Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Norifumi Yamamoto
- Department of Applied Chemistry, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Yasushige Yonezawa
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Shin-Ichi Tate
- Department of Mathematical and Life Sciences, School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hiroshi Fujisaki
- Department of Physics, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-0023, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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4
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Jalalypour F, Sensoy O, Atilgan C. Perturb-Scan-Pull: A Novel Method Facilitating Conformational Transitions in Proteins. J Chem Theory Comput 2020; 16:3825-3841. [PMID: 32324386 DOI: 10.1021/acs.jctc.9b01222] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Conformational transitions in proteins facilitate precise physiological functions. Therefore, it is crucial to understand the mechanisms underlying these processes to modulate protein function. Yet, studying structural and dynamical properties of proteins is notoriously challenging due to the complexity of the underlying potential energy surfaces (PES). We have previously developed the perturbation-response scanning (PRS) method to identify key residues that participate in the communication network responsible for specific conformational transitions. PRS is based on a residue-by-residue scan of the protein to determine the subset of residues/forces which provide the closest conformational change leading to a target conformational state, inasmuch as linear response theory applies to these motions. Here, we develop a novel method to further evaluate if conformational transitions may be triggered on the PES. We aim to study functionally relevant conformational transitions in proteins by using results obtained from PRS and feeding them as inputs to steered molecular dynamics simulations. The success and the transferability of the method are evaluated on three protein systems having different complexities of motion on the PES: calmodulin, adenylate kinase, and bacterial ferric binding protein. We find that the method captures the target conformation, while providing key residues and the optimum paths with relatively low free energy profiles.
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Affiliation(s)
- Farzaneh Jalalypour
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Ozge Sensoy
- School of Engineering and Natural Sciences, Istanbul Medipol University, 34810, Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey.,Sabanci University Nanotechnology Research and Application Center, SUNUM, 34956, Istanbul, Turkey
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5
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Fujisaki H, Moritsugu K, Matsunaga Y. Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions. Int J Mol Sci 2018; 19:E3177. [PMID: 30326661 PMCID: PMC6213965 DOI: 10.3390/ijms19103177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 01/07/2023] Open
Abstract
To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its atomistic details are hard to obtain both experimentally and computationally. Here, we review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: one is the Onsager⁻Machlup action method, and the other is the weighted ensemble method. Some applications of the above methods to biomolecular systems are also discussed and illustrated.
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Grants
- JPMJPR1679 Japan Science and Technology Agency
- 16K00059 Ministry of Education, Culture, Sports, Science and Technology
- 17KT0101 Ministry of Education, Culture, Sports, Science and Technology
- 25840060 Ministry of Education, Culture, Sports, Science and Technology
- 15K18520 Ministry of Education, Culture, Sports, Science and Technology
- JP18am0101109 Japan Agency for Medical Research and Development
- 17gm0810012h0001 Japan Agency for Medical Research and Development
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Affiliation(s)
- Hiroshi Fujisaki
- Department of Physics, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-0023, Japan.
- AMED-CREST, Japan Agency for Medical Research and Development, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan.
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Yasuhiro Matsunaga
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
- JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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6
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Hayami T, Kasahara K, Nakamura H, Higo J. Molecular dynamics coupled with a virtual system for effective conformational sampling. J Comput Chem 2018; 39:1291-1299. [PMID: 29464736 DOI: 10.1002/jcc.25196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 11/12/2022]
Abstract
An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Tomonori Hayami
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Lee J, Lee IH, Joung I, Lee J, Brooks BR. Finding multiple reaction pathways via global optimization of action. Nat Commun 2017; 8:15443. [PMID: 28548089 PMCID: PMC5458546 DOI: 10.1038/ncomms15443] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/24/2017] [Indexed: 12/25/2022] Open
Abstract
Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barriers via crossovers and mutations of pathways and finds all possible pathways of small systems without initial guesses on pathways. The rank order and the transition time distribution of multiple pathways are in good agreement with those of long Langevin dynamics simulations. The lowest action folding pathway of FSD-1 is consistent with recent experiments. The results show that Action-CSA is an efficient and robust computational approach to study the multiple pathways of complex reactions and large-scale conformational changes.
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Affiliation(s)
- Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - In-Ho Lee
- Center for Materials Genome, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
- Center for In Silico Protein Science, School of Computational Science, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - InSuk Joung
- Center for In Silico Protein Science, School of Computational Science, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Jooyoung Lee
- Center for In Silico Protein Science, School of Computational Science, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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8
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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9
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Fujisaki H, Moritsugu K, Matsunaga Y, Morishita T, Maragliano L. Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review. Front Bioeng Biotechnol 2015; 3:125. [PMID: 26389113 PMCID: PMC4558547 DOI: 10.3389/fbioe.2015.00125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/10/2015] [Indexed: 01/12/2023] Open
Abstract
Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.
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Affiliation(s)
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | | | - Tetsuya Morishita
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Luca Maragliano
- Center for Synaptic Neuroscience, Istituto Italiano di Tecnologia, Genova, Italy
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10
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Lee KH, Chen J. Multiscale enhanced sampling of intrinsically disordered protein conformations. J Comput Chem 2015; 37:550-7. [PMID: 26052838 DOI: 10.1002/jcc.23957] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/03/2015] [Accepted: 05/11/2015] [Indexed: 12/24/2022]
Abstract
In a recently developed multiscale enhanced sampling (MSES) technique, topology-based coarse-grained (CG) models are coupled to atomistic force fields to enhance the sampling of atomistic protein conformations. Here, the MSES protocol is refined by designing more sophisticated Hamiltonian/temperature replica exchange schemes that involve additional parameters in the MSES coupling restraint potential, to more carefully control how conformations are coupled between the atomistic and CG models. A specific focus is to derive an optimal MSES protocol for simulating conformational ensembles of intrinsically disordered proteins (IDPs). The efficacy of the refined protocols, referred to as MSES-soft asymptote (SA), was evaluated using two model peptides with various levels of residual helicities. The results show that MSES-SA generates more reversible helix-coil transitions and leads to improved convergence on various ensemble conformational properties. This study further suggests that more detailed CG models are likely necessary for more effective sampling of local conformational transition of IDPs. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Kuo Hao Lee
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
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11
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Moritsugu K, Terada T, Kidera A. Multiscale enhanced sampling driven by multiple coarse-grained models. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Kar P, Feig M. Recent advances in transferable coarse-grained modeling of proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:143-80. [PMID: 25443957 PMCID: PMC5366245 DOI: 10.1016/bs.apcsb.2014.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems is employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multiscale hybrid all-atom/CG simulations of proteins.
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Affiliation(s)
- Parimal Kar
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA; Department of Chemistry, Michigan State University, East Lansing, Michigan, USA.
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13
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Zhou HX. Theoretical frameworks for multiscale modeling and simulation. Curr Opin Struct Biol 2014; 25:67-76. [PMID: 24492203 DOI: 10.1016/j.sbi.2014.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 12/25/2013] [Accepted: 01/10/2014] [Indexed: 02/08/2023]
Abstract
Biomolecular systems have been modeled at a variety of scales, ranging from explicit treatment of electrons and nuclei to continuum description of bulk deformation or velocity. Many challenges of interfacing between scales have been overcome. Multiple models at different scales have been used to study the same system or calculate the same property (e.g., channel conductance). Accurate modeling of biochemical processes under in vivo conditions and the bridging of molecular and subcellular scales will likely soon become reality.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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