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Bajpai S, Petkov BK, Tong M, Abreu CRA, Nair NN, Tuckerman ME. An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package. J Comput Chem 2023; 44:2166-2183. [PMID: 37464902 DOI: 10.1002/jcc.27182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023]
Abstract
Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. In this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open-source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state-of-the-art thermostats and multiple time-stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high-dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra-N-methylglycine (tetra-sarcosine) peptoid in implicit solvent, and the Trp-cage mini protein in explicit water.
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Affiliation(s)
- Shitanshu Bajpai
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India
| | - Brian K Petkov
- Department of Chemistry, New York University (NYU), New York, New York, USA
| | - Muchen Tong
- Department of Chemistry, New York University (NYU), New York, New York, USA
| | - Charlles R A Abreu
- Chemical Engineering Department, Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India
| | - Mark E Tuckerman
- Department of Chemistry, New York University (NYU), New York, New York, USA
- Courant Institute of Mathematical Sciences, New York University (NYU), New York, New York, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China
- Simons Center for Computational Physical Chemistry, New York University, New York, New York, USA
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2
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Yamaguchi SI, Xie Q, Ito F, Terao K, Kato Y, Kuroiwa M, Omori S, Taniura H, Kinoshita K, Takahashi T, Toyokuni S, Kasahara K, Nakayama M. Carbon nanotube recognition by human Siglec-14 provokes inflammation. NATURE NANOTECHNOLOGY 2023:10.1038/s41565-023-01363-w. [PMID: 37024598 DOI: 10.1038/s41565-023-01363-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/28/2023] [Indexed: 06/15/2023]
Abstract
For the design and development of innovative carbon nanotube (CNT)-based tools and applications, an understanding of the molecular interactions between CNTs and biological systems is essential. In this study, a three-dimensional protein-structure-based in silico screen identified the paired immune receptors, sialic acid immunoglobulin-like binding lectin-5 (Siglec-5) and Siglec-14, as CNT-recognizing receptors. Molecular dynamics simulations showed the spatiotemporally stable association of aromatic residues on the extracellular loop of Siglec-5 with CNTs. Siglec-14 mediated spleen tyrosine kinase (Syk)-dependent phagocytosis of multiwalled CNTs and the subsequent secretion of interleukin-1β from human monocytes. Ectopic in vivo expression of human Siglec-14 on mouse alveolar macrophages resulted in enhanced recognition of multiwalled CNTs and exacerbated pulmonary inflammation. Furthermore, fostamatinib, a Syk inhibitor, blocked Siglec-14-mediated proinflammatory responses. These results indicate that Siglec-14 is a human activating receptor recognizing CNTs and that blockade of Siglec-14 and the Syk pathway may overcome CNT-induced inflammation.
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Affiliation(s)
- Shin-Ichiro Yamaguchi
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
- CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
| | - Qilin Xie
- CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
- Computational Structural Biology Laboratory, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Fumiya Ito
- CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuki Terao
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Yoshinobu Kato
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Miki Kuroiwa
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Satoshi Omori
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Hideo Taniura
- Laboratory of Neurochemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of In Silico Analyses, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
| | - Takuya Takahashi
- Computational Structural Biology Laboratory, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Shinya Toyokuni
- CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Center for Low Temperature Plasma Science, Nagoya University, Nagoya, Japan
| | - Kota Kasahara
- CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan.
- Computational Structural Biology Laboratory, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan.
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki, Japan.
| | - Masafumi Nakayama
- Laboratory of Immunology and Microbiology, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan.
- CREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan.
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3
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Fukuda I, Nakamura H. Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference. Biophys Rev 2022; 14:1315-1340. [PMID: 36659982 PMCID: PMC9842848 DOI: 10.1007/s12551-022-01029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023] Open
Abstract
In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cutoff-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology. In particular, we take into account the reaction field (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cutoff-based methods are based on different physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cutoff region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the artificial effects, generated near the boundary, from the cutoff sphere. Nonetheless, we find physical and/or mathematical similarities between these methods. In particular, the modified RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.
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Affiliation(s)
- Ikuo Fukuda
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima, Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
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4
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Bekker GJ, Kamiya N. Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking. Biophys Rev 2022; 14:1349-1358. [PMID: 36659995 PMCID: PMC9842809 DOI: 10.1007/s12551-022-01010-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/14/2022] [Indexed: 11/20/2022] Open
Abstract
Multicanonical molecular dynamics (McMD)-based dynamic docking is a powerful tool to not only predict the native binding configuration between two flexible molecules, but it can also be used to accurately simulate the binding/unbinding pathway. Furthermore, it can also predict alternative binding sites, including allosteric ones, by employing an exhaustive sampling approach. Since McMD-based dynamic docking accurately samples binding/unbinding events, it can thus be used to determine the molecular mechanism of binding between two molecules. We developed the McMD-based dynamic docking methodology based on the powerful, but woefully underutilized McMD algorithm, combined with a toolset to perform the docking and to analyze the results. Here, we showcase three of our recent works, where we have applied McMD-based dynamic docking to advance the field of computational drug design. In the first case, we applied our method to perform an exhaustive search between Hsp90 and one of its inhibitors to successfully predict the native binding configuration in its binding site, as we refined our analysis methods. For our second case, we performed an exhaustive search of two medium-sized ligands and Bcl-xL, which has a cryptic binding site that differs greatly between the apo and holo structures. Finally, we performed a dynamic docking simulation between a membrane-embedded GPCR molecule and a high affinity ligand that binds deep within its receptor's pocket. These advanced simulations showcase the power that the McMD-based dynamic docking method has, and provide a glimpse of the potential our methodology has to unravel and solve the medical and biophysical issues in the modern world. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-022-01010-z.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Narutoshi Kamiya
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
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5
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Fukunishi Y, Higo J, Kasahara K. Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles. Biophys Rev 2022; 14:1423-1447. [PMID: 36465086 PMCID: PMC9703445 DOI: 10.1007/s12551-022-01015-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/06/2022] [Indexed: 11/29/2022] Open
Abstract
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.
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Affiliation(s)
- Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo 650-0047 Japan ,Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
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6
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Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule. Sci Rep 2022; 12:13792. [PMID: 35963875 PMCID: PMC9376114 DOI: 10.1038/s41598-022-17920-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/02/2022] [Indexed: 11/08/2022] Open
Abstract
A GA-guided multidimensional virtual-system coupled molecular dynamics (GA-mD-VcMD) simulation was conducted to elucidate binding mechanisms of a middle-sized flexible molecule, bosentan, to a GPCR protein, human endothelin receptor type B (hETB). GA-mD-VcMD is a generalized ensemble method that produces a free-energy landscape of the ligand-receptor binding by searching large-scale motions accompanied with stable maintenance of the fragile cell-membrane structure. All molecular components (bosentan, hETB, membrane, and solvent) were represented with an all-atom model. Then sampling was conducted from conformations where bosentan was distant from the binding site in the hETB binding pocket. The deepest basin in the resultant free-energy landscape was assigned to native-like complex conformation. The following binding mechanism was inferred. First, bosentan fluctuating randomly in solution is captured using a tip region of the flexible N-terminal tail of hETB via nonspecific attractive interactions (fly casting). Bosentan then slides occasionally from the tip to the root of the N-terminal tail (ligand–sliding). During this sliding, bosentan passes the gate of the binding pocket from outside to inside of the pocket with an accompanying rapid reduction of the molecular orientational variety of bosentan (orientational selection). Last, in the pocket, ligand–receptor attractive native contacts are formed. Eventually, the native-like complex is completed. The bosentan-captured conformations by the tip-region and root-region of the N-terminal tail correspond to two basins in the free-energy landscape. The ligand-sliding corresponds to overcoming of a free-energy barrier between the basins.
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7
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Pal A, Pal S, Verma S, Shiga M, Nair NN. Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes. J Comput Chem 2021; 42:1996-2003. [DOI: 10.1002/jcc.26727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/28/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022]
Affiliation(s)
- Asit Pal
- Department of Chemistry Indian Institute of Technology Kanpur Kanpur India
| | - Subhendu Pal
- Department of Chemistry Indian Institute of Technology Kanpur Kanpur India
| | - Shivani Verma
- Department of Chemistry Indian Institute of Technology Kanpur Kanpur India
| | - Motoyuki Shiga
- Center for Computational Science and E‐Systems Japan Atomic Energy Agency Chiba Japan
| | - Nisanth N. Nair
- Department of Chemistry Indian Institute of Technology Kanpur Kanpur India
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8
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Higo J, Takashima H, Fukunishi Y, Yoshimori A. Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. J Comput Chem 2021; 42:956-969. [PMID: 33755222 DOI: 10.1002/jcc.26516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/30/2022]
Abstract
A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Importantly, the molecular orientation of mS-11 is ordering in a wide region around mSin3B. The resultant binding scenario is: When mS-11 is distant from the binding site of mSin3B, mS-11 descends the free-energy slope toward the binding site maintaining the molecular orientation to be advantageous for binding. Then, finally a long and flexible hydrophobic sidechain of mS-11 fits into the binding site, which is the lowest-free-energy complex structure inhibiting NRSF/REST binding to mSin3B.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Hajime Takashima
- Department of Research and Development, PRISM BioLab Co., Ltd., Fujisawa, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Atsushi Yoshimori
- Chemoinformatics & AI Research Group, Institute for Theoretical Medicine, Inc., Fujisawa, Japan
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9
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Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities. Sci Rep 2021; 11:6178. [PMID: 33731831 PMCID: PMC7971087 DOI: 10.1038/s41598-021-85612-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/19/2021] [Indexed: 11/08/2022] Open
Abstract
A preceding experiment suggested that a compound, which inhibits binding of the REST/NRSF segment to the cleft of a receptor protein mSin3B, can be a potential drug candidate to ameliorate many neuropathies. We have recently developed an enhanced conformational sampling method, genetic-algorithm-guided multi-dimensional virtual-system-coupled canonical molecular dynamics, and in the present study, applied it to three systems consisting of mSin3B and one of three compounds, sertraline, YN3, and acitretin. Other preceding experiments showed that only sertraline inhibits the binding of REST/NRSF to mSin3B. The current simulation study produced the spatial distribution of the compounds around mSin3B, and showed that sertraline and YN3 bound to the cleft of mSin3B with a high propensity, although acitretin did not. Further analyses of the simulation data indicated that only the sertraline-mSin3B complex produced a hydrophobic core similar to that observed in the molecular interface of the REST/NRSF-mSin3B complex: An aromatic ring of sertraline sunk deeply in the mSin3B's cleft forming a hydrophobic core contacting to hydrophobic amino-acid residues located at the bottom of the cleft. The present study proposes a step to design a compound that inhibits competitively the binding of a ligand to its receptor.
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10
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Higo J, Kusaka A, Kasahara K, Kamiya N, Hayato I, Qilin X, Takahashi T, Fukuda I, Mori K, Hata Y, Fukunishi Y. GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics. Biophys Physicobiol 2021; 17:161-176. [PMID: 33585149 DOI: 10.2142/biophysico.bsj-2020008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/22/2020] [Indexed: 12/01/2022] Open
Abstract
We introduced a conformational sampling method in an earlier report: The multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD) enhances conformational sampling of a biomolecular system by computer simulations. Herein, new sampling method, a subzone-based mD-VcMD, is presented as an extension of mD-VcMD. Then, the subzone-based method is extended further using a genetic algorithm (GA) named the GA-guided mD-VcMD. In these methods, iterative simulation runs are performed to increase the sampled region gradually. The new methods have the following benefits: (1) They are free from a production run: i.e., all snapshots from all iterations are useful for analyses. (2) They are free from fine tuning of a weight function (probability distribution function or potential of mean force). (3) A canonical ensemble (i.e., a thermally equilibrated ensemble) is generated from a simple procedure. A thermodynamic weight is assigned to each snapshot. (4) Selective sampling can be performed for particularly addressing a poorly sampled region without breaking the proportion of the canonical ensemble if the poorly sampled conformational region emerges in sampling. By applying the methods to a simple system that involves an energy barrier between potential-energy minima, we demonstrated that the new methods have considerably higher sampling efficiency than the original mD-VcMD does.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Itaya Hayato
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Xie Qilin
- College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Kentaro Mori
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan.,National Institute of Technology, Maizuru College, Maizuru, Kyoto 625-8511, Japan
| | - Yutaka Hata
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, 135-0064, Japan
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11
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Higo J, Kawabata T, Kusaka A, Kasahara K, Kamiya N, Fukuda I, Mori K, Hata Y, Fukunishi Y, Nakamura H. Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. J Chem Inf Model 2020; 60:4867-4880. [PMID: 32910853 DOI: 10.1021/acs.jcim.0c00551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Enhanced conformational sampling, a genetic-algorithm-guided multidimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semistable complex structures and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3ε, and a flexible peptide, phosphorylated myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3ε. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3ε surface and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spot are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding constant changes resulting from the alanine mutation experiment for the residues. We also performed a simulation of nonphosphorylated peptide and 14-3-3ε, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3ε.
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Affiliation(s)
- Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kentaro Mori
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Maizuru College, 234 Shiroya, Maizuru, Kyoto 625-8511 Japan
| | - Yutaka Hata
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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12
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Kasahara K, Terazawa H, Itaya H, Goto S, Nakamura H, Takahashi T, Higo J. myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling. Biophys Physicobiol 2020; 17:140-146. [PMID: 33240741 PMCID: PMC7671739 DOI: 10.2142/biophysico.bsj-2020013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/10/2020] [Indexed: 12/03/2022] Open
Abstract
The molecular dynamics (MD) method is a promising approach for investigating the molecular mechanisms of microscopic phenomena. In particular, generalized ensemble MD methods can efficiently explore the conformational space with a rugged free-energy surface. However, the implementation and acquisition of technical knowledge for each generalized ensemble MD method are not straightforward for end-users. Here, we present a new version of the myPresto/omegagene software, which is an MD simulation engine tailored for a series of generalized ensemble methods, which are virtual-system coupled multicanonical MD (V-McMD), virtual-system coupled adaptive umbrella sampling (V-AUS), and virtual-system coupled canonical MD (VcMD). This program has been applied in several studies analyzing free-energy landscapes of a variety of molecular systems with all-atom simulations. The updated version provides new functionality for coarse-grained simulations powered by the hydrophobicity scale method. The software package includes a step-by-step tutorial document for enhanced conformational sampling of the poly-glutamine (poly-Q) oligomer expressed as a one-bead per residue model. The myPresto/omegagene software is freely available at the following URL: https://github.com/kotakasahara/omegagene under the Apache2 license.
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Affiliation(s)
- Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hiroki Terazawa
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hayato Itaya
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Satoshi Goto
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo 650-0047, Japan
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