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Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2015年第31期36卷 2344-2349页

作者： Mori, Yoshiharu Okumura, Hisashi Natl Inst Nat Sci Inst Mol Sci Dept Theoret & Computat Mol Sci Okazaki Aichi 4448585 Japan Natl Inst Nat Sci Inst Mol Sci Res Ctr Computat Sci Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Struct Mol Sci Okazaki Aichi 4448585 Japan

Simulated tempering (ST) is a useful method to enhance sampling of molecular simulations. When ST is used, the Metropolis algorithm, which satisfies the detailed balance condition, is usually applied to calculate the transition probability. Recently, an alternative method that satisfies the global balance condition instead of the detailed balance condition has been proposed by Suwa and Todo. In this study, ST method with the Suwa-Todo algorithm is proposed. Molecular dynamics simulations with ST are performed with three algorithms (the Metropolis, heat bath, and Suwa-Todo algorithms) to calculate the transition probability. Among the three algorithms, the Suwa-Todo algorithm yields the highest acceptance ratio and the shortest autocorrelation time. These suggest that sampling by a ST simulation with the Suwa-Todo algorithm is most efficient. In addition, because the acceptance ratio of the Suwa-Todo algorithm is higher than that of the Metropolis algorithm, the number of temperature states can be reduced by 25% for the Suwa-Todo algorithm when compared with the Metropolis algorithm. (c) 2015 Wiley Periodicals, Inc.

关键词： molecular simulation molecular dynamics generalized-ensemble algorithm random walk correlation

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Origin of the kinetic HDAC2-selectivity of an HDAC inhibitor

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2023年第18期44卷 1604-1609页

作者： Mishima, Hirokazu Itoh, Yukihiro Kurohara, Takashi Suzuki, Takayoshi Asada, Naoya Kusakabe, Ken-ichi Okamoto, Yuko Nagoya Univ Grad Sch Sci Dept Phys Nagoya Aichi 4648602 Japan Japan Sci & Technol Agcy JST Core Res Evolut Sci & Technol CREST Saitama Japan Osaka Univ SANKEN Osaka Japan Shionogi Pharmaceut Res Ctr Lab Med Chem Res Osaka Japan Nagoya Univ Informat Technol Ctr High Performance Comp Div Nagoya Aichi Japan Nagoya Univ Global Engagement Ctr Int Affairs Nagoya Aichi Japan

A newly synthesized small molecule, KTT-1, exhibits kinetically selective inhibition of histone deacetylase 2, HDAC2, over its homologous enzyme, HDAC1. KTT-1 is hard to be released from the HDAC2/KTT-1 complex, compared to the HDAC1/KTT-1 complex and the residence time of KTT-1 in HDAC2 is longer than that in HDAC1. To explore the physical origin of this kinetic selectivity, we performed replica-exchange umbrella sampling molecular dynamics simulations for formation of both complexes. The calculated potentials of mean force suggest that KTT-1 is stably bound to HDAC2 and that it is easily disassociated from HDAC1. In the direct vicinity of the KTT-1 binding site in both enzymes, there exists a conserved loop consisting of four consecutive glycine residues (Gly304-307 for HDAC2;Gly299-302 for HDA1). The difference between the two enzymes comes from a single un-conserved residue behind this loop, namely, Ala268 in HDAC2 and Ser263 in HDAC1. The Ala268 contributes to the tight binding of KTT-1 to HDAC2 by the linear orientation of Ala268, Gly306, and one carbon atom in KTT-1. On the other hand, Ser263 cannot stabilize the binding of KTT-1 to HDAC1, because it is relatively further away from the glycine loop and because the directions of the two forces are not in line.

关键词： epigenetics generalized-ensemble algorithm histone deacetylase moleculer dynamics simulation replica-exchange umbrella sampling

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Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

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BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016年第7期1858卷 1635-1651页

作者： Mori, Takaharu Miyashita, Naoyuki Im, Wonpil Feig, Michael Sugita, Yuji RIKEN iTHES Res Grp 2-1 Hirosawa Wako Saitama 3510198 Japan RIKEN Theoret Mol Sci Lab 2-1 Hirosawa Wako Saitama 3510198 Japan RIKEN Lab Biomol Funct Simulat Quantitat Biol Ctr Chuo Ku Integrated Innovat Bldg 7F Kobe Hyogo 6500047 Japan KINDAI Univ Fac Biol Oriented Sci & Technol 930 Nishimitani Wakayama 6496493 Japan Univ Kansas Dept Mol Sci 2030 Becker Dr Lawrence KS 66047 USA Univ Kansas Ctr Computat Biol 2030 Becker Dr Lawrence KS 66047 USA Michigan State Univ Dept Biochem & Mol Biol E Lansing MI 48824 USA Michigan State Univ Dept Chem E Lansing MI 48824 USA RIKEN Adv Inst Computat Sci Computat Biophys Res Team Chou Ku 7-1-26 Minatojima Minamimachi Kobe Hyogo 6500047 Japan

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. (C) 2016 The Authors. Published by Elsevier B.V.

关键词： generalized Born (GB) model generalized-ensemble algorithm Replica-exchange molecular dynamics (REMD) Replica-exchange umbrella sampling (REUS) Surface-tension REMD Replica exchange with solute tempering (REST)

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Key Residue for Aggregation of Amyloid-β Peptides

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ACS CHEMICAL NEUROSCIENCE 2022年第22期13卷 3139-3151页

作者： Itoh, Satoru G. Yagi-Utsumi, Maho Kato, Koichi Okumura, Hisashi Natl Inst Nat Sci Inst Mol Sci Okazaki Aichi 4448787 Japan Natl Inst Nat Sci Exploratory Res Ctr Life & Living Syst ExCELLS Okazaki Aichi 4448787 Japan SOKENDAI Grad Univ Adv Studies Dept Struct Mol Sci Okazaki Aichi 4448787 Japan Nagoya City Univ Grad Sch Pharmaceut Sci Nagoya Aichi 4658603 Japan

It is known that oligomers of amyloid-beta (A beta) peptide are associated with Alzheimer's disease. A beta has two isoforms: A beta 40 and A beta 42. Although the difference between A beta 40 and A beta 42 is only two additional C-terminal residues, A beta 42 aggregates much faster than A beta 40. It is unknown what role the C-terminal two residues play in accelerating aggregation. Since A beta 42 is more toxic than A beta 40, its oligomerization process needs to be clarified. Moreover, clarifying the differences between the oligomerization processes of A beta 40 and A beta 42 is essential to elucidate the key factors of oligomerization. Therefore, to investigate the dimerization process, which is the early oligomerization process, Hamiltonian replica-permutation molecular dynamics simulations were performed for A beta 40 and A beta 42. We identified a key residue, Arg5, for the A beta 42 dimerization. The two additional residues in A beta 42 allow the C-terminus to form contact with Arg5 because of the electrostatic attraction between them, and this contact stabilizes the beta-hairpin. This beta-hairpin promotes dimer formation through the intermolecular beta-bridges. Thus, we examined the effects of amino acid substitutions of Arg5, thereby confirming that the mutations remarkably suppressed the aggregation of A beta 42. Moreover, the mutations of Arg5 suppressed the A beta 40 aggregation. It was found by analyzing the simulations that Arg5 is important for A beta 40 to form intermolecular contacts. Thus, it was clarified that the role of Arg5 in the oligomerization process varies due to the two additional C-terminal residues.

关键词： molecular dynamics simulation generalized-ensemble algorithm amyloid-beta peptide protein aggregation

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Determination of the structural ensemble of the molten globule state of a protein by computer simulations

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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2019年第8期87卷 635-645页

作者： Shimizu, Masahiro Kajikawa, Yukihito Kuwajima, Kunihiro Dobson, Christopher M. Okamoto, Yuko Nagoya Univ Grad Sch Sci Dept Phys Nagoya Aichi 4648602 Japan Univ Tokyo Grad Sch Sci Dept Phys Tokyo Japan Korea Inst Adv Study KIAS Sch Computat Sci Seoul South Korea Univ Cambridge Ctr Misfolding Dis Dept Chem Cambridge England Nagoya Univ Informat Technol Ctr Nagoya Aichi Japan Nagoya Univ Struct Biol Res Ctr Grad Sch Sci Nagoya Aichi Japan Nagoya Univ Ctr Computat Sci Grad Sch Engn Nagoya Aichi Japan JST CREST Nagoya Aichi Japan

We have used computer simulations to investigate the structural nature of the molten globule (MG) state of canine milk lysozyme. To sample the conformational space efficiently, we performed replica-exchange umbrella sampling simulations with the radius of gyration as a reaction coordinate. We applied the Weighted Histogram Analysis Method to the trajectory of the simulations to obtain the potential of mean force, from which we identified representative structures corresponding to local minima in the free energy surface. The representative structures obtained in this way are in accord with the characteristics of the MG state reported previously by experimental studies. We conjecture that the MG state comprises a series of partially structured states undergoing relatively fast conformational interchange.

关键词： canine milk lysozyme folding intermediate state generalized-ensemble algorithm molecular dynamics simulation molten globule protein folding replica-exchange umbrella sampling

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Molecular dynamics of the structural changes of helical peptides induced by pressure

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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2014年第11期82卷 2970-2981页

作者： Mori, Yoshiharu Okumura, Hisashi Inst Mol Sci Dept Theoret & Computat Mol Sci Okazaki Aichi 4448585 Japan Inst Mol Sci Res Ctr Computat Sci Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Struct Mol Sci Okazaki Aichi 4448585 Japan

An AK16 peptide and a C-peptide analog are experimentally known to form more helical structures under high-pressure conditions than those at atmospheric pressure, even though most proteins usually unfold at high pressure. To understand the pressure-induced structural changes of the two peptides, molecular dynamics simulations with the simulated tempering method for the isobaric-isothermal ensemble were performed in a wide pressure range from 0.1 MPa to 1.4 GPa. We found that the fraction of the folded state decreases once and then increases with increasing pressure for both peptides. The partial molar volume change of both peptides from the folded state to the unfolded state increases monotonically from a negative value to a positive value as pressure increases. By calculating the radius of gyration and interatomic distances of the AK16 peptide and the C-peptide analog, we found that these peptides are compressed under high-pressure conditions, which causes the folded state to be more stable at high pressure. Furthermore, we found that the salt bridge of the C-peptide analog is broken under high pressure. Proteins 2014;82:2970-2981. (c) 2014 Wiley Periodicals, Inc.

关键词： AK16 peptide C-peptide generalized-ensemble algorithm simulated tempering pressure dependence salt bridge

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Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

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MOLECULAR SIMULATION 2007年第1-2期33卷 97-102页

作者： Kawashima, Y. Sasaki, Y. C. Sugita, Y. Yoda, T. Okamoto, Y. Japan Sci & Technol Agcy CREST Sasaki Tokyo 1900012 Japan Nagoya Univ Sch Sci Dept Phys Chikusa Ku Nagoya Aichi 4648602 Japan JASRI SPring8 Mikazuki Hyogo 6795198 Japan Univ Tokyo Inst Mol & Cellular Biosci Bunkyo Ku Tokyo 1130032 Japan Nagahama Inst Biosci & Technol Shiga 5260829 Japan Inst Mol Sci Res Ctr Computat Sci Okazaki Aichi 444 Japan

We examine the effects of the nanocrystal covalently bonded to one end, utilizing replica-exchange molecular dynamics simulation of a peptide with the sequence Ac-YGKAAAAKAAAAKAAAAKC-amide, to simulate the diffraction X-ray tracking (DXT) method. We performed three different simulations in this study. A simulation with no constraint, a simulation with one end fixed, and a simulation with one end fixed and also considering the effect of the nanocrystal by changing the mass of the sulfur atom in the C-terminus, which covalently bonded with the An nanocrystal in diffraction DXT method, was performed. The average configuration parameters of the three simulations are compared and discussed. We analyzed our simulation results utilizing principal component analysis. The obtained free-energy landscape indicated that the condition of the DXT technique will not affect the global-minimum state, however, it may affect the folding pathway.

关键词： generalized-ensemble algorithm REMD diffracted X-ray tracking DXT

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Protein folding simulations and structure predictions

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COMPUTER PHYSICS COMMUNICATIONS 2001年第1-3期142卷 55-63页

作者： Okamoto, Y Inst Mol Sci Dept Theoret Studies Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Funct Mol Sci Okazaki Aichi 4448585 Japan

In complex systems such as spin glasses and proteins, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the simulated annealing method and generalized-ensemble algorithms in order to overcome this multiple-minima problem. Besides simulated annealing, three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods. (C) 2001 Elsevier Science B.V. All rights reserved.

关键词： protein folding simulated annealing generalized-ensemble algorithm multicanonical algorithm simulated tempering replica-exchange method

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Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

Replica-exchange molecular dynamics simulation of diffracted...

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Symposium on Progress and Future Prospects in Molecular Dynamics Simulation