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Hata H, Phuoc Tran D, Marzouk Sobeh M, Kitao A. Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model. Biophys Physicobiol 2022; 18:305-316. [PMID: 35178333 PMCID: PMC8694779 DOI: 10.2142/biophysico.bppb-v18.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
We recently proposed a computational procedure to simulate the dissociation of protein/ligand complexes using the dissociation Parallel Cascade Selection Molecular Dynamics simulation (dPaCS-MD) method and to analyze the generated trajectories using the Markov state model (MSM). This procedure, called dPaCS-MD/MSM, enables calculation of the dissociation free energy profile and the standard binding free energy. To examine whether this method can reproduce experimentally determined binding free energies for a variety of systems, we used it to investigate the dissociation of three protein/ligand complexes: trypsin/benzamine, FKBP/FK506, and adenosine A2A receptor/T4E. First, dPaCS-MD generated multiple dissociation pathways within a reasonable computational time for all the complexes, although the complexes differed significantly in the size of the molecules and in intermolecular interactions. Subsequent MSM analyses produced free energy profiles for the dissociations, which provided insights into how each ligand dissociates from the protein. The standard binding free energies obtained by dPaCS-MD/MSM are in good agreement with experimental values for all the complexes. We conclude that dPaCS-MD/MSM can accurately calculate the binding free energies of these complexes.
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Affiliation(s)
- Hiroaki Hata
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Duy Phuoc Tran
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Mohamed Marzouk Sobeh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Physics Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
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Aida H, Shigeta Y, Harada R. Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD. MATERIALS 2022; 15:ma15041490. [PMID: 35208030 PMCID: PMC8878848 DOI: 10.3390/ma15041490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 01/09/2023]
Abstract
Parallel cascade selection molecular dynamics (PaCS-MD) is a rare-event sampling method that generates transition pathways between a reactant and product. To sample the transition pathways, PaCS-MD repeats short-time MD simulations from important configurations as conformational resampling cycles. In this study, PaCS-MD was extended to sample ligand binding pathways toward a target protein, which is referred to as LB-PaCS-MD. In a ligand-concentrated environment, where multiple ligand copies are randomly arranged around the target protein, LB-PaCS-MD allows for the frequent sampling of ligand binding pathways. To select the important configurations, we specified the center of mass (COM) distance between each ligand and the relevant binding site of the target protein, where snapshots generated by the short-time MD simulations were ranked by their COM distance values. From each cycle, snapshots with smaller COM distance values were selected as the important configurations to be resampled using the short-time MD simulations. By repeating conformational resampling cycles, the COM distance values gradually decreased and converged to constants, meaning that a set of ligand binding pathways toward the target protein was sampled by LB-PaCS-MD. To demonstrate relative efficiency, LB-PaCS-MD was applied to several proteins, and their ligand binding pathways were sampled more frequently than conventional MD simulations.
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Affiliation(s)
- Hayato Aida
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan;
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan;
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan;
- Correspondence:
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Hua XF, Du XZ, Zhang ZY. Ligand binding and release investigated by contact-guided iterative multiple independent molecular dynamics simulations. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2010181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xin-fan Hua
- National Science Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Xin-zheng Du
- National Science Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Zhi-yong Zhang
- National Science Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
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4
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Abstract
The analysis of folding trajectories for proteins is an open challenge. One of the problems is how to describe the amount of folded secondary structure in a protein. We extend the use of Estradas' folding degree (Bioinformatics 2002, 18, 697) for the analysis of the evolution of the folding stage during molecular dynamics (MD) simulation. It is shown that residue contribution to the total folding degree is a predominantly local property, well-defined by the backbone dihedral angles at the given residue, without significant contribution from the backbone conformation of other residues. Moreover, the magnitude of this residue contribution can be quite easily associated with characteristic motifs of secondary protein structures such as the α-helix, β-sheet (hairpin), and so on by means of a Ramachandran-like plot as a function of backbone dihedral angles φ,ψ. Additionally, the understanding of the free energy profile associated with the folding process becomes much simpler. Often a 1D profile is sufficient to locate global minima and the corresponding structure for short peptides.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry - Centre for Glycomics, Dubravska cesta 9, 84538 Bratislava, Slovakia.,Agency for Medical Research and Development (AMED), Chiyoda-ku, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
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Ghanbari-Ardestani S, Khojasteh-Band S, Zaboli M, Hassani Z, Mortezavi M, Mahani M, Torkzadeh-Mahani M. The effect of different percentages of triethanolammonium butyrate ionic liquid on the structure and activity of urate oxidase: Molecular docking, molecular dynamics simulation, and experimental study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111318] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Shin K, Tran DP, Takemura K, Kitao A, Terayama K, Tsuda K. Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method. ACS OMEGA 2019; 4:13853-13862. [PMID: 31497702 PMCID: PMC6714528 DOI: 10.1021/acsomega.9b01480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/01/2019] [Indexed: 05/13/2023]
Abstract
This paper proposes a novel molecular simulation method, called tree search molecular dynamics (TS-MD), to accelerate the sampling of conformational transition pathways, which require considerable computation. In TS-MD, a tree search algorithm, called upper confidence bounds for trees, which is a type of reinforcement learning algorithm, is applied to sample the transition pathway. By learning from the results of the previous simulations, TS-MD efficiently searches conformational space and avoids being trapped in local stable structures. TS-MD exhibits better performance than parallel cascade selection molecular dynamics, which is one of the state-of-the-art methods, for the folding of miniproteins, Chignolin and Trp-cage, in explicit water.
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Affiliation(s)
- Kento Shin
- Graduate School
of Frontier Sciences, The University of
Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
| | - Duy Phuoc Tran
- Graduate School
of Frontier Sciences, The University of
Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
| | - Kazuhiro Takemura
- School
of Life Sciences and Technology, Tokyo Institute
of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Akio Kitao
- School
of Life Sciences and Technology, Tokyo Institute
of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kei Terayama
- RIKEN Center for
Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Medical Sciences
Innovation Hub Program, RIKEN Cluster for Science, Technology and
Innovation Hub, Kanagawa 230-0045, Japan
- Department
of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
- E-mail: (Kei Terayama)
| | - Koji Tsuda
- Graduate School
of Frontier Sciences, The University of
Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
- RIKEN Center for
Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Research
and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Ibaraki 305-0047, Japan
- E-mail: . Phone: +81(4)-7136-3983. Fax: +81(4)-7136-3975 (Koji Tsuda)
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Harada R, Shigeta Y. Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations. J Chem Theory Comput 2018; 15:680-687. [PMID: 30468705 DOI: 10.1021/acs.jctc.8b00802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A protocol for calculating free energy landscapes (FELs) is proposed based on a combination of two cascade-type molecular dynamics (MD) methods, parallel cascade selection MD (PaCS-MD) and outlier flooding method (OFLOOD), with the help of a Markov state model (MSM). The former rapidly generates approximated transition paths directly connecting reactants with products, and the latter complementary resamples marginal conformational subspaces. Trajectories obtained by them give reliable microstates in MSM providing accurate FEL with low computational costs. As a demonstration, the present method was applied to a miniprotein (Chignolin and Trp-cage) in explicit water and successfully elucidated multiple folding paths on their free energy landscapes. Our method could be applicable to a wide variety of biological systems to estimate their free energy profiles.
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Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences , University of Tsukuba , 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
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Hu D, Guan X, Wang Y. Weighted least square analysis method for free energy calculations. J Comput Chem 2018; 39:2397-2404. [DOI: 10.1002/jcc.25580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Dan Hu
- School of Mathematical Sciences, Institute of Natural Sciences, and MOE-LSC; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Xiaoqing Guan
- Institute of Natural Sciences, Shanghai Jiao Tong University; Shanghai 200240 China
| | - Yukun Wang
- Institute of Natural Sciences, Shanghai Jiao Tong University; Shanghai 200240 China
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Harada R. Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180170] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
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