Authorship：Lead author,　Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：{MDPI} {AG}  

File： J-05-00021-v2.pdf

DOI： 10.3390/j5020021

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

<title>Abstract</title>Non-structural protein 15 (Nsp15) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) forms a homo hexamer and functions as an endoribonuclease. Here, we propose that Nsp15 activity may be inhibited by preventing its hexamerization through drug binding. We first explored the stable conformation of the Nsp15 monomer as the global free energy minimum conformation in the free energy landscape using a combination of parallel cascade selection molecular dynamics (PaCS-MD) and the Markov state model (MSM), and found that the Nsp15 monomer forms a more open conformation with larger druggable pockets on the surface. Targeting the pockets with high druggability scores, we conducted ligand docking and identified compounds that tightly bind to the Nsp15 monomer. The top poses with Nsp15 were subjected to binding free energy calculations by dissociation PaCS-MD and MSM (dPaCS-MD/MSM), indicating the stability of the complexes. One of the identified pockets, which is distinctively bound by inosine analogues, may be an alternative binding site to stabilize viral RNA binding and/or an alternative catalytic site. We constructed a stable RNA structure model bound to both UTP and alternative binding sites, providing a reasonable proposed model of the Nsp15/RNA complex.

File： ae60aa98-1bf7-4bdb-ae2d-e32b028cc28e.pdf

DOI： 10.1038/s41598-022-07792-2

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Other Link： https://www.nature.com/articles/s41598-022-07792-2

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jcim.1c01508

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biophysical Society of Japan  

File： 18_bppb-v18.037.pdf

DOI： 10.2142/biophysico.bppb-v18.037

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Half-turns are shown to be the main determinants of many experimental Alzheimer's Aβ fibril structures. Fibril structures contain three half-turn types, βαRβ, βαLβ and βεβ which each result in a ∼90° bend in a β-strand. It is shown that only these half-turns enable cross-β stacking and thus the right-angle fold seen in fibrils is an intrinsic feature of cross-β. Encoding a strand as a conformational sequence in β, αR, αL and ε(βL), pairwise combination rules for consecutive half-turns are used to decode this sequence to give the backbone path. This reveals how structures would be dramatically affected by a deletion. Using a wild-type Aβ(42) fibril structure and the pairwise combination rules, the Osaka deletion is predicted to result in exposure of surfaces that are mutually shielding from the solvent. Molecular dynamics simulations on an 11-mer β-sheet of Alzheimer's Aβ(40) of the Dutch (E22Q), Iowa (D23N), Arctic (E22G), and Osaka (E22Δ) mutants, show the crucial role glycine plays in the positioning of βαRβ half-turns. Their "in-phase" positions along the sequence in the wild-type, Dutch mutant and Iowa mutant means that the half-folds all fold to the same side creating the same closed structure. Their out-of-phase positions in Arctic and Osaka mutants creates a flatter structure in the former and an S-shape structure in the latter which, as predicted, exposes surfaces on the inside in the closed wild-type to the outside. This is consistent with the gain of interaction model and indicates how domain swapping might explain the Osaka mutant's unique properties.

File： 1-s2.0-S1047847721000976-main.pdf

DOI： 10.1016/j.jsb.2021.107792

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

G-protein-coupled receptors (GPCRs) represent a ubiquitous membrane protein family and are important drug targets. Their diverse signaling pathways are driven by complex pharmacology arising from a conformational ensemble rarely captured by structural methods. Here, fluorine nuclear magnetic resonance spectroscopy (19F NMR) is used to delineate key functional states of the adenosine A2A receptor (A2AR) complexed with heterotrimeric G protein (Gαsβ1γ2) in a phospholipid membrane milieu. Analysis of A2AR spectra as a function of ligand, G protein, and nucleotide identifies an ensemble represented by inactive states, a G-protein-bound activation intermediate, and distinct nucleotide-free states associated with either partial- or full-agonist-driven activation. The Gβγ subunit is found to be critical in facilitating ligand-dependent allosteric transmission, as shown by 19F NMR, biochemical, and computational studies. The results provide a mechanistic basis for understanding basal signaling, efficacy, precoupling, and allostery in GPCRs.

DOI： 10.1016/j.cell.2021.02.041

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File： TranKitaoJCTC2020.pdf

DOI： 10.1021/acs.jctc.9b01203

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/acs.jpcb.8b10309

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DOI： 10.1021/acs.jpcb.8b02756

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：{AIP} Publishing  

DOI： 10.1063/1.5019864

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File： acs.jctc.7b00504.pdf

DOI： 10.1021/acs.jctc.7b00504

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File： acscatal.7b00751.pdf

DOI： 10.1021/acscatal.7b00751

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File： s41598-017-06334-5.pdf

DOI： 10.1038/s41598-017-06334-5

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File： 1-s2.0-S0959440X16301798-main.pdf

DOI： 10.1016/j.sbi.2016.10.014

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Other Link： http://orcid.org/0000-0002-5221-0806

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

File： 1.4813023.pdf

DOI： 10.1063/1.4813023

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DOI： 10.1063/1.4768901

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DOI： 10.1021/jp301100g

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DOI： 10.1021/ja204451g

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Other Link： http://orcid.org/0000-0002-5221-0806

Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1073/pnas.0510285103

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DOI： 10.1021/ja0425886

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DOI： 10.1073/pnas.030540397

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DOI： 10.1016/S0959-440X(99)80023-2

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DOI： 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

DOI： 10.1021/j100141a053

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/0301-0104(91)87082-7

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/jcc.540120309

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jchemed.4c01347

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.jconrel.2025.02.001

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

Biological systems are composed of and regulated by intricate and diverse biomolecular interactions. Experimental and computational approaches have been developed to elucidate the mechanisms of these interactions; however, owing to cost, time, and accuracy issues, large-scale spatiotemporal analyses of molecular pairs remains challenging. Thus, the molecular recognition mechanisms underlying these diverse interactions remain unclear. We successfully simulated the large-scale molecular dynamics (MD) of 4,275 protein–compound pairs by combining a method to accelerate the MD simulations with the supercomputer Fugaku. Our spatiotemporal analysis of generated big MD data revealed universal features underlying molecular recognition and binding processes. This study expands our understanding of the concept of MD simulations from a technique to investigate the dynamic properties of individual protein–drug pairs to an approach to perform large-scale spatiotemporal analysis and compound screening. This study opens an avenue in biological research for subsequent drug discovery.

DOI： 10.1093/pnasnexus/pgaf094

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Authorship：Lead author,　Last author,　Corresponding author   Language：English   Publisher：Springer {US}  

DOI： 10.1007/978-1-0716-3060-0_3

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Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

A protein crystal capturing a ten-amino acid miniprotein was constructed in living cells. The miniprotein immobilized in the scaffold crystal was trapped in a metastable state, which is induced by the intermolecular interactions with the scaffold crystal.

DOI： 10.1039/d2bm01759h

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Authorship：Lead author,　Last author   Publisher：Elsevier  

DOI： 10.1016/b978-0-323-89911-6.00024-8

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DOI： 10.1016/j.bbrc.2022.09.072

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

<jats:p>
Many motile bacteria employ the flagellar type III secretion system (fT3SS) to construct flagella beyond the cytoplasmic membrane. The C-terminal cytoplasmic domain of FlhA (FlhA
<jats:sub>C</jats:sub>
), a transmembrane subunit of the fT3SS, provides binding sites for export substrates and flagellar export chaperones to coordinate flagellar protein export with assembly.
</jats:p>

DOI： 10.1128/spectrum.01110-22

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DOI： 10.1021/acs.jpcb.2c00956

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Language：English   Publishing type：Research paper (scientific journal)  

Signal transduction proteins perceive external stimuli in their sensor module and regulate the biological activities of the effector module, allowing cellular adaptation in response to environmental changes. FixL is a dimeric heme protein kinase that senses the oxygen level in plant root nodules to regulate the transcription of nitrogen fixation genes via the phosphorylation of its cognate transcriptional activator. Dissociation of oxygen from the heme induces conformational changes in the protein, converting it from the inactive form for phosphorylation to the active form. However, how FixL undergoes conformational change to regulate kinase activity upon oxygen dissociation remains poorly understood. Here we report time-resolved ultraviolet resonance Raman spectra showing conformational changes for FixL from Sinorhizobium meliloti. We observed spectral changes with a time constant of about 3 μs, which were oxygen-specific. Furthermore, we found that the conformational changes in the sensor and kinase domains are coupled, enabling allosteric control of kinase activity. Our results demonstrate that concerted structural changes on the microsecond time scale serve as the regulatory switch in FixL.

DOI： 10.1021/acs.jpcb.1c01885

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

<title>Abstract</title>Cell-penetrating peptides have important therapeutic applications in drug delivery, but the variety of known cell-penetrating peptides is still limited. With a promise to accelerate peptide development, artificial intelligence (AI) techniques including deep generative models are currently in spotlight. Scientists, however, are often overwhelmed by an excessive number of unannotated sequences generated by AI and find it difficult to obtain insights to prioritize them for experimental validation. To avoid this pitfall, we leverage molecular dynamics (MD) simulations to obtain mechanistic information to prioritize and understand AI-generated peptides. A mechanistic score of permeability is computed from five steered MD simulations starting from different initial structures predicted by homology modelling. To compensate for variability of predicted structures, the score is computed with sample variance penalization so that a peptide with consistent behaviour is highly evaluated. Our computational pipeline involving deep learning, homology modelling, MD simulations and synthesizability assessment generated 24 novel peptide sequences. The top-scoring peptide showed a consistent pattern of conformational change in all simulations regardless of initial structures. As a result of wet-lab-experiments, our peptide showed better permeability and weaker toxicity in comparison to a clinically used peptide, TAT. Our result demonstrates how MD simulations can support de novo peptide design by providing mechanistic information supplementing statistical inference.

File： s41598-021-90245-z.pdf

DOI： 10.1038/s41598-021-90245-z

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Other Link： http://www.nature.com/articles/s41598-021-90245-z

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High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the CheY-FliM interface. PaCS-MD enabled us to observe pressure-induced dissociation of the CheY-FliM complex at atomic resolution. Pressure dependence of binding free energy indicates that the increase of pressure from 0.1 to 100 MPa significantly weakens the binding. Using high-pressure microscopy, we observed that high hydrostatic pressure fixes the motor rotation to the counter-clockwise direction. In conclusion, the application of pressure enhances hydration of the proteins and weakens the binding of CheY to FliM, preventing reversal of the flagellar motor.

File： s41598-020-59172-3.pdf

DOI： 10.1038/s41598-020-59172-3

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DOI： 10.1063/5.0032465

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Company of Biologists  

<title>ABSTRACT</title>The membrane-shaping ability of PACSIN2 (also known as syndapin II), which is mediated by its F-BAR domain, has been shown to be essential for caveolar morphogenesis, presumably through the shaping of the caveolar neck. Caveolar membranes contain abundant cholesterol. However, the role of cholesterol in PACSIN2-mediated membrane deformation remains unclear. Here, we show that the binding of PACSIN2 to the membrane can be negatively regulated by cholesterol. We prepared reconstituted membranes based on the lipid composition of caveolae. The reconstituted membrane with cholesterol had a weaker affinity for the F-BAR domain of PACSIN2 than a membrane without cholesterol. Consistent with this, upon depletion of cholesterol from the plasma membrane, PACSIN2 localized at tubules that had caveolin-1 at their tips, suggesting that cholesterol inhibits membrane tubulation mediated by PACSIN2. The tubules induced by PACSIN2 could be representative of an intermediate of caveolae endocytosis. Consistent with this, the removal of caveolae from the plasma membrane upon cholesterol depletion was diminished in the PACSIN2-deficient cells. These data suggest that PACSIN2-mediated caveolae internalization is dependent on the amount of cholesterol, providing a mechanism for cholesterol-dependent regulation of caveolae.

<uri xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://doi.org/10.1242/jcs.254656">This article has an associated First Person interview with the first author of the paper.</uri>

DOI： 10.1242/jcs.246785

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/5.0004654

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.str.2019.10.020

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

Computational techniques for accurate and efficient prediction of protein-protein complex structures are widely used for elucidating protein-protein interactions, which play important roles in biological systems. Recently, it has been reported that selecting a structure similar to the native structure among generated structure candidates (decoys) is possible by calculating binding free energies of the decoys based on all-atom molecular dynamics (MD) simulations with explicit solvent and the solution theory in the energy representation, which is called evERdock. A recent version of evERdock achieves a higher-accuracy decoy selection by introducing MD relaxation and multiple MD simulations/energy calculations; however, huge computational cost is required. In this paper, we propose an efficient decoy selection method using evERdock and the best arm identification (BAI) framework, which is one of the techniques of reinforcement learning. The BAI framework realizes an efficient selection by suppressing calculations for nonpromising decoys and preferentially calculating for the promising ones. We evaluate the performance of the proposed method for decoy selection problems of three protein-protein complex systems. Their results show that computational costs are successfully reduced by a factor of 4.05 (in the best case) compared to a standard decoy selection approach without sacrificing accuracy.

DOI： 10.1063/1.5129551

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Phagocytosis is a cellular process for internalization of micron-sized large particles including pathogens. The Bin-Amphiphysin-Rvs167 (BAR) domain proteins, including the FCH-BAR (F-BAR) domain proteins, impose specific morphologies on lipid membranes. Most BAR domain proteins are thought to form membrane invaginations or protrusions by assembling into helical submicron-diameter filaments, such as on clathrin-coated pits, caveolae, and filopodia. However, the mechanism by which BAR domain proteins assemble into micron-scale phagocytic cups was unclear. Here, we show that the two-dimensional sheet-like assembly of Growth Arrest-Specific 7 (GAS7) plays a critical role in phagocytic cup formation in macrophages. GAS7 has the F-BAR domain that possesses unique hydrophilic loops for two-dimensional sheet formation on flat membranes. Super-resolution microscopy reveals the similar assemblies of GAS7 on phagocytic cups and liposomes. The mutations of the loops abolishes both the membrane localization of GAS7 and phagocytosis. Thus, the sheet-like assembly of GAS7 plays a significant role in phagocytosis.

File： s41467-019-12738-w.pdf

DOI： 10.1038/s41467-019-12738-w

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DOI： 10.1074/jbc.ra119.010401

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biophysical Society of Japan  

File： 16_295.pdf

DOI： 10.2142/biophysico.16.0_295

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The bacterial flagellar motor is a unique supramolecular complex which converts ion flow into rotational force. Many biological devices mainly use two types of ions, proton and sodium ion. This is probably because of the fact that life originated in seawater, which is rich in protons and sodium ions. The polar flagellar motor in Vibrio is coupled with sodium ion and the energy converting unit of the motor is composed of two membrane proteins, PomA and PomB. It has been shown that the ion binding residue essential for ion transduction is the conserved aspartic acid residue (PomB-D24) in the PomB transmembrane region. To reveal the mechanism of ion selectivity, we identified essential residues, PomA-T158 and PomA-T186, other than PomB-D24, in the Na+-driven flagellar motor. It has been shown that the side chain of threonine contacts Na+ in Na+-coupled transporters. We monitored the Na+-binding specific structural changes using ATR-FTIR spectroscopy. The signals were abolished in PomA-T158A and -T186A, as well as in PomB-D24N. Molecular dynamics simulations further confirmed the strong binding of Na+ to D24 and showed that T158A and T186A hindered the Na+ binding and transportation. The data indicate that two threonine residues (PomA-T158 and PomA-T186), together with PomB-D24, are important for Na+ conduction in the Vibrio flagellar motor. The results contribute to clarify the mechanism of ion recognition and conversion of ion flow into mechanical force.

File： s41598-019-46038-6.pdf

DOI： 10.1038/s41598-019-46038-6

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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.

File： acsomega.9b01480.pdf

DOI： 10.1021/acsomega.9b01480

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BACKGROUND: Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations. SCOPE OF REVIEW: First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure. MAJOR CONCLUSIONS: Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening. GENERAL SIGNIFICANCE: MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.

DOI： 10.1016/j.bbagen.2019.07.004

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DOI： 10.1016/j.bpj.2019.06.007

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DOI： 10.1021/acs.jcim.9b00112

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Bacteria use a type III protein export apparatus for construction of the flagellum, which consists of the basal body, the hook, and the filament. FlhA forms a homo-nonamer through its C-terminal cytoplasmic domains (FlhAC) and ensures the strict order of flagellar assembly. FlhAC goes through dynamic domain motions during protein export, but it remains unknown how it occurs. Here, we report that the FlhA(G368C) mutation biases FlhAC toward a closed form, thereby reducing the binding affinity of FlhAC for flagellar export chaperones in complex with their cognate filament-type substrates. The G368C mutations also restrict the conformational flexibility of a linker region of FlhA (FlhAL), suppressing FlhAC ring formation. We propose that interactions of FlhAL with its neighboring subunit converts FlhAC in the ring from a closed conformation to an open one, allowing the chaperon/substrate complexes to bind to the FlhAC ring to form the filament at the hook tip.

DOI： 10.1016/j.str.2019.03.017

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Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Informa {UK} Limited  

DOI： 10.1080/07391102.2018.1477626

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Biophysical Society of Japan  

DOI： 10.2142/biophysico.16.0_240

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DOI： 10.2139/ssrn.3471315

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

DOI： 10.1063/1.5055799

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DOI： 10.1021/acs.jpcb.8b07048

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DOI： 10.1021/acs.jpcb.8b03518

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Authorship：Lead author,　Corresponding author   Language：English   Publisher：Springer Nature  

DOI： 10.1007/s12551-017-0338-7

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry ({RSC})  

File： Jake.pdf

DOI： 10.1039/c7cp06355e

DOI： 10.1039/C7CP06355E

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DOI： 10.1016/j.jmgm.2017.09.017

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DOI： 10.1021/acs.jpcb.6b10668

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File： acscatal.6b01094.pdf

DOI： 10.1021/acscatal.6b01094

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DOI： 10.1021/acs.biochem.6b00361

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DOI： 10.1038/onc.2015.211

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Authorship：Last author,　Corresponding author   Language：English   Publisher：The Biophysical Society of Japan  

<p>We examine the dynamic features of non-trivial allosteric binding sites to elucidate potential drug binding sites. These allosteric sites were previously found to be allosteric after determination of the protein-drug co-crystal structure. After comprehensive search in the Protein Data Bank, we identify 10 complex structures with allosteric ligands whose structures are very similar to their functional forms. Then, possible pockets on the protein surface are searched as potential ligand binding sites. To mimic ligand binding to the pocket, complex models are generated to fill out each pocket with pseudo ligand blocks consisting of spheres. Normal mode analysis of the elastic network model is performed for the complex models and unbound structures to assess the change of protein dynamics induced by ligand binding. We examine nine profiles to describe the dynamic and positional characteristics of the pockets, and identify the change of fluctuation around the ligand, ΔMSF_bs, as the best profile for distinguishing the allosteric sites from the other sites in 8 structures. These cases should be considered as examples of dynamics-driven allostery, which accompanies significant changes in protein dynamics. ΔMSF_bs is suggested to be used for the search of potential dynamics-driven allosteric sites in proteins for drug discovery.</p>

File： 13_117.pdf

DOI： 10.2142/biophysico.13.0_117

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DOI： 10.1073/pnas.1502991112

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DOI： 10.1016/j.bmc.2014.11.027

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DOI： 10.1021/acs.jctc.5b00723

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DOI： 10.1021/acs.jctc.5b00215

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File： ncomms5994.pdf

DOI： 10.1038/ncomms5994

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DOI： 10.1016/j.bpj.2014.07.049

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File： 1.4844235.pdf

DOI： 10.1063/1.4844235

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File： 1.4823743.pdf

DOI： 10.1063/1.4823743

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DOI： 10.1002/prot.24252

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DOI： 10.1107/S0907444913002102

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DOI： 10.1039/c3cp42761g

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DOI： 10.1016/j.cplett.2012.12.063

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DOI： 10.1021/ct200363h

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DOI： 10.1016/j.cplett.2011.09.006

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DOI： 10.1016/j.cplett.2011.09.006

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Authorship：Lead author,　Last author,　Corresponding author   Language：English  

DOI： 10.1063/1.3642607

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DOI： 10.1063/1.3613676

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DOI： 10.1021/jp2008623

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DOI： 10.1016/j.cplett.2011.01.017

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DOI： 10.1016/j.jsb.2010.09.022

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DOI： 10.1063/1.3498745

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DOI： 10.1016/j.bpj.2010.01.017

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/j.1365-2958.2010.07097.x

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DOI： 10.1016/j.jmgm.2009.11.007

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DOI： 10.1016/j.bpj.2009.08.019

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DOI： 10.1002/jcc.21186

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File： btp396.pdf

DOI： 10.1093/bioinformatics/btp396

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File： btp032.pdf

DOI： 10.1093/bioinformatics/btp032

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File： btp023.pdf

DOI： 10.1093/bioinformatics/btp023

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DOI： 10.1529/biophysj.107.118042

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DOI： 10.1529/biophysj.107.123927

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DOI： 10.1021/jp710039p

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DOI： 10.1529/biophysj.107.128546

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DOI： 10.1021/jp0756247

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DOI： 10.1073/pnas.0708199104

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DOI： 10.1103/PhysRevE.75.041912

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DOI： 10.1016/j.jsb.2006.10.006

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DOI： 10.1016/j.msea.2005.12.082

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DOI： 10.1529/biophysj.106.085910

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DOI： 10.1002/mrc.1839

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DOI： 10.1038/nature02997

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.physb.2004.03.167

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

DOI： 10.1093/protein/gzg083

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Test accounts  

DOI： 10.1080/1023816021000020608

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Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.

DOI： 10.1063/1.1308516

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DOI： 10.1007/s002490000103

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DOI： 10.1016/S0006-3495(98)77661-1

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1002/(SICI)1097-0134(19980301)30:4<388::AID-PROT6>3.0.CO;2-F

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DOI： 10.1021/jp972847w

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DOI： 10.1002/(SICI)1097-0134(199703)27:3<425::AID-PROT10>3.0.CO;2-N

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DOI： 10.1002/prot.340230207

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DOI： 10.1021/ja00093a034

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DOI： 10.1002/pro.5560030608

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DOI： 10.1016/0301-4622(94)00070-0

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/j100141a052

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1006/jmbi.1993.1671

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DOI： 10.1039/c8cp90010h

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DOI： 10.1016/j.bpj.2016.11.327

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Language：English   Publishing type：Research paper, summary (international conference)  

DOI： 10.1016/j.bpj.2016.11.213

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Language：English   Publisher：Humana Press Inc.  

DOI： 10.1007/978-1-4939-6927-2_10

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Other Link： http://orcid.org/0000-0002-5221-0806

Language：English   Publishing type：Research paper, summary (international conference)  

DOI： 10.1016/j.bpj.2015.11.3436

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Language：English  

DOI： 10.1063/1.4968639

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.55.262

CiNii Books

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Other Link： https://jlc.jst.go.jp/DN/JLC/20015396233?from=CiNii

Language：Japanese  

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Language：English  

DOI： 10.1016/j.bpj.2014.09.012

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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DOI： 10.2142/biophys.54.167

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Language：English   Publishing type：Research paper, summary (international conference)  

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S152_6

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S166_2

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DOI： 10.1063/1.4897682

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DOI： 10.2142/biophys.53.S128_6

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J-GLOBAL

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.53.S130_2

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.52.S127_3

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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CiNii Books

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S131_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S130_4

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S130_5

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DOI： 10.2142/biophys.51.S130_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S121_5

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.50.S84_6

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.50.S157_2

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.50.S88_1

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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DOI： 10.2142/biophys.50.S62_3

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DOI： 10.2142/biophys.50.S171_2

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.49.S66_6

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.49.S168_4

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.49.S182_5

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.48.S84_2

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.48.S16_1

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.48.S145_4

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S81_2

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S137_3

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.48.S136_4

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Language：Japanese   Publisher：The Biophysical Society of Japan  

The bacterial flagellar filament controls the swimming mode of bacteria by its polymorphic structural change. We investigated dynamics of the flagellar filament by massive molecular dynamic simulation and found that three types of inter-molecular interactions, permanent, sliding and switch interactions, play essential roles in the structural change. The polymorphic structure of the flagellar filament is thought to be due to energy frustration between intra- and inter-molecular interactions.

DOI： 10.2142/biophys.48.011

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.47.S25_2

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.47.S184_2

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.47.S116_2

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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Language：Japanese   Publisher：The Physical Society of Japan  

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DOI： 10.2142/biophys.47.S35_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.47.S43_2

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Language：English   Publisher：Elsevier BV  

DOI： 10.1016/j.physb.2006.05.130

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.46.S313_3

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Language：English   Publisher：The Biophysical Society of Japan  

DOI： 10.2142/biophys.46.S158_1

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Language：English   Publisher：The Biophysical Society of Japan  

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Publisher：8  

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J-GLOBAL

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J-GLOBAL

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J-GLOBAL

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Language：Japanese   Publisher：The Physical Society of Japan  

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DOI： 10.11436/mssj1998.8.35_44

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DOI： 10.2142/biophys.46.S317_3

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DOI： 10.2142/biophys.46.S293_2

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S156_1

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.46.S361_2

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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Publisher：10 Suppl  

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Language：Japanese   Publisher：10 Suppl  

PubMed

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S213_2

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S56_4

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S41_1

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S219_3

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Language：Japanese   Publisher：共立出版  

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Other Link： http://search.jamas.or.jp/link/ui/2006022478

Language：Japanese   Publisher：共立出版(株)  

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Other Link： https://search.jamas.or.jp/index.php?module=Default&action=Link&pub_year=2005&ichushi_jid=J00808&link_issn=&doc_id=20050801270007&doc_link_id=40006857289&url=http%3A%2F%2Fci.nii.ac.jp%2Fnaid%2F40006857289&type=CiNii&icon=https%3A%2F%2Fjk04.jamas.or.jp%2Ficon%2F00003_1.gif

Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.45.S253_2

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DOI： 10.2142/biophys.44.S214_2

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DOI： 10.2142/biophys.44.S49_4

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DOI： 10.2142/biophys.44.S43_4

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DOI： 10.2142/biophys.44.S143_3

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DOI： 10.2142/biophys.43.S54_4

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DOI： 10.2142/biophys.43.S11_1

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.43.S74_3

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DOI： 10.2142/biophys.43.S50_2

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DOI： 10.2142/biophys.42.S179_4

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Language：Japanese   Publisher：The Japanese Society for Neutron Science  

DOI： 10.5611/hamon.12.80

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.42.S58_2

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DOI： 10.2142/biophys.42.S65_2

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DOI： 10.2142/biophys.41.S5_2

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Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.41.S110_2

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DOI： 10.2142/biophys.41.S103_2

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Language：Japanese   Publisher：The Physical Society of Japan (JPS)  

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A novel method has been developed in order to determine both structure and dynamics of proteins using a molecular simulation and experimental data. This is based on the concept of the Jumping-Among-Minima model. In this method, inter-substate fluctuations are determined by molecular simulation and inter-substate motions are determined so as to reproduce experimental data. Slow dynamics of proteins and its relation to protein functions are discussed.

DOI： 10.2142/biophys.40.167

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DOI： 10.2142/biophys.40.S26_4

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DOI： 10.2142/biophys.40.S31_3

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