Multi-strand beta-sheet of Alzheimer Abeta(1-40) folds to beta-strip helix: Implication for protofilament formation
Steven Hayward(University of East Anglia), Akio Kitao(School of Life Science and Technology, Tokyo Institute of Technology)
Journal of Biomolecular Structure and Dynamics, pp.1-11 (2018), DOI:10.1080/07391102.2018.1477626

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations
Ai Shinobu(School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan), Kazuhiro Takemura(School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan), Nobuyuki Matubayasi(Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan), Akio Kitao(School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan)
The Journal of Chemical Physics, Vol.149, pp.195101 (2018), DOI:10.1063/1.5055799

Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases
Hisham M. Dokainish(School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan), Akio Kitao(School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan)
The Journal of Physical Chemistry B, Vol.122(36), pp.8537-8547 (2018), DOI:10.1021/acs.jpcb.8b07048

ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation
Kazuhiro Takemura(School of Life Science and Technology, Tokyo Institute of Technology, 2 Chome-12-1, Ookayama, Meguro, Tokyo 152-8550, Japan), Chika Sato(The University of Tokyo), Akio Kitao(School of Life Science and Technology, Tokyo Institute of Technology, 2 Chome-12-1, Ookayama, Meguro, Tokyo 152-8550, Japan)
The Journal of Physical Chemistry B, 122(29), pp.7191-7200 (2018), DOI:10.1021/acs.jpcb.8b02756

Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays
Shuhei Watanabe(Kyoto University), Yuichi Mishima(Osaka University), Masahiro Shimizu(Kyoto University), Isao Suetake(Osaka University), Shoji Takada(Kyoto University)
Biophysical Journal, Vol.114, pp.2336-2351(2018), DOI:10.1016/j.bpj.2018.03.025

Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data
Cheng Tan(Kyoto University), Shoji Takada(Kyoto University)
Journal of Chemical Theory and Computation, Vol.14, pp.3877-3889 (2018), DOI:10.1021/acs.jctc.8b00299

Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics
TRAN, Phuoc Duy(Tokyo Tech.), TAKEMURA, Kazuhiro(Univ. Tokyo), KUWATA, Kazuo(Gifu Univ.), KITAO, Akio(Tokyo Tech.)
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14, 404-417, DOI:10.1021/acs.jctc.7b00504

Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein-DNA Complexes
Masahiro Shimizu(Kyoto University), Shoji Takada(Kyoto University)
Journal of Chemical Theory and Computation, Vol.14, pp.1682-1694 (2018), DOI:10.1021/acs.jctc.7b00954

Binding free energy analysis of protein-protein docking model structures by evERdock
Kazuhiro Takemura(The University of Tokyo), Nobuyuki Matubayasi(Osaka University), Akio Kitao(The University of Tokyo, Tokyo Institute of Technology)
The Journal of Chemical Physics, Vol.148, 105101(2018), DOI:10.1063/1.5019864

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
Giovanni B Brandani(Kyoto University), Toru Niina(Kyoto University), Cheng Tan(Kyoto University), Shoji Takada(Kyoto University)
Nucleic Acids Research, Vol.46, pp.2788-2801 (2018), DOI:10.1093/nar/gky158

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase
Suyong Re(RIKEN), Shigehisa Watabe(RIKEN), Wataru Nishima(RIKEN), Eiro Muneyuki(Chuo Univ.), Yoshiki Yamaguchi(RIKEN), Alexander D. MacKerell Jr.(Univ. Maryland), Yuji Sugita(RIKEN)
Scientific Reports, 8, 1644 (2018), DOI:10.1038/s41598-018-20012-0

Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics
TRAN, Phuoc Duy(Tokyo Tech.), TAKEMURA, Kazuhiro(Univ. Tokyo), KUWATA, Kazuo(Gifu Univ.), KITAO, Akio(Tokyo Tech.)
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2018,14, 404-417, DOI:10.1021/acs.jctc.7b00504

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
Toru Niina(Kyoto University), Giovanni B. Brandani(Kyoto University), Cheng Tan(Kyoto University), Shoji Takada(Kyoto University)
PLOS Computational Biology, Vol.13, pp.e1005880 (2017), DOI:10.1371/journal.pcbi.1005880

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation
Grzegorz Nawrocki (1), Po-hung Wang (2), Isseki Yu (2,3), Yuji Sugita (2,3,4,5), Michael Feig (1)
(1) Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
(2) RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
(3) RIKEN iTHES, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
(4) RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minaotojima-Minamimachi, Chuo-ku, Kobe, Hyogo
650-0047, Japan
(5) RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
Journal of Physical Chemistry B, 2017,121, 11072-11084, DOI:10.1021/acs.jpcb.7b08785

Molecular dynamics simulation of bacterial flagella
Akio Kitao(Tokyo Institute of Technology), Hiroaki Hata(The University of Tokyo)
Biophysical Reviews, pp.1-13 (2017), DOI:10.1007/s12551-017-0338-7

Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
Shintaroh Kubo(Kyoto University), Wenfei Li(Nanjin University), Shoji Takada(Kyoto University)
PLOS Computational Biology, Vol.13, e1005748(2017), DOI:10.1371/journal.pcbi.1005748

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations
Michael Feig, Grzegorz Nawrocki(Department of Biochemistry and Molecular Biology, Michigan State University), Isseki Yu(iTHES Research Group, RIKEN, and Theoretical Molecular Science Laboratory, RIKEN), Po-hung Wang(Theoretical Molecular Science Laboratory, RIKEN), Yuji Sugita(Theoretical Molecular Science Laboratory, RIKEN, Advanced Institute for Computational Science, RIKEN, Quantitative Biology Center, RIKEN, and iTHES Research Group, RIKEN)
Journal of Physical Chemistry B, vol.121, 8009-8025, 2017, DOI:10.1021/acs.jpcb.7b03570

Atomistic modeling of alternating access of a mitochondrial ADP/ATP membrane transporter with molecular simulations
Koichi Tamura(Kyoto University), Shigehiko Hayashi(Kyoto University)
PLOS ONE, 12, e0181489 (2017), DOI:10.1371/journal.pone.0181489

Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature
Kazuhiro Takemura(The University of Tokyo), Kyoko Hanawa-Suetsugu(Nara Advanced Institute of Science and Technology), Shiro Suetsugu(Nara Advanced Institute of Science and Technology), Akio KItao(The University of Tokyo)
Scientific Reports 7, Article number: 6808, DOI:10.1038/s41598-017-06334-5

How one-dimensional diffusion of transcription factors are affected by obstacles: coarse-grained molecular dynamics study
Mami Saito(Kyoto University), Tsuyoshi Terakawa(Columbia University), Shoji Takada(Kyoto University)
Molecular Simulation, Vol.43, pp.1315-1321, DOI:10.1080/08927022.2017.1334885

Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems
Jaewoon Jung(RIKEN AICS, RIKEN), Yuji Sugita(RIKEN AICS, RIKEN, RIKEN QBiC, RIKEN iTHES)
Journal of Computational Chemistry, Vol. 38, pp. 1410-1418, DOI:10.1002/jcc.24511

Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair
Hisham M. Dokainish(The University of Tokyo), Daichi Yamada(Nagoya Institute of Technology), Tatsuya Iwata(Nagoya Institute of Technology), Hideki Kandori(Nagoya Institute of Technology), Akio Kitao(The University of Tokyo)
ACS Catalysis, Vol.7 pp4835－4845 (2017), DOI:10.1021/acscatal.7b00751

The structural basis of a high affinity ATP binding epsilon subunit from a bacterial ATP synthase
Alexander Krah(Korea Institute for Advanced Study), Yasuyuki Kato-Yamada(Rikkyo University), Shoji Takada(Kyoto University)
PLOS ONE, Vol.12, e0177907(2017), DOI:10.1371/journal.pone.0177907

QM/MM geometry optimization on extensive free-energy surfaces for examination of enzymatic reactions and design of novel functional properties of proteins
Shigehiko Hayashi(Kyoto University), Yoshihiro Uchida(Kyoto University), Taisuke Hasegawa(Kyoto University), Masahiro Higashi(University of the Ryukyus), Takahiro Kosugi(Institute for Molecular Science), Motoshi Kamiya(Kyoto University)
Annual Review of Physical Chemistry,Vol. 68:135-154 (Volume publication date May 2017) , DOI:10.1146/annurev-physchem-052516-050827

Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation
Motoshi Kamiya(Kyoto University), Shigehiko Hayashi(Kyoto University)
J. Phys. Chem. B, 2017, 121 (15), pp 3842–3852, DOI:10.1021/acs.jpcb.6b13050

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics
Raimondas Galvelis(Theoretical Molecular Science, RIKEN), Yuji Sugita(Theoretical Molecular Science, RIKEN)
J. Chem. Theory Comput., 2017, 13 (6), pp 2489–2500, DOI:10.1021/acs.jctc.7b00188

Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics
Raimondas Galvelis, Suyong Re, and Yuji Sugita.
J. Chem. Theory Comput.,13, 5, 1934-1942 (2017), DOI:10.1021/acs.jctc.7b00079

Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding
Po-hung Wang(Theoretical Molecular Science Laboratory, RIKEN), Isseki Yu(iTHES Research Group. RIKEN, Theoretical Molecular Science Laboratory, RIKEN), Yuji Sugita(Theoretical Molecular Science Laboratory, RIKEN)
Chemical Physics Letters Volume,671, March 2017, Pages 63-70, DOI:10.1016/j.cplett.2017.01.012

Communication: Constant uncertainty molecular dynamics: A simple and efficient algorithm to incorporate quantum nature into a real-time molecular dynamics simulation
Taisuke Hasegawa(Kyoto University)
The Journal of Chemical Physics,145, 171101 (2016), DOI:10.1063/1.4966917

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm
Isseki Yu(iTHES Research Group, RIKEN, Theoretical Molecular Science Laboratory, RIKEN), Takaharu Mori(Theoretical Molecular Science Laboratory, RIKEN), Tadashi Ando(Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center), Ryuhei Harada(Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science), Jaewoon Jung(Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science), Yuji Sugita(Theoretical Molecular Science Laboratory, RIKEN, iTHES Research Group, RIKEN, Theoretical Molecular Science Laboratory, RIKEN, Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science), Michael Feig(Department of Biochemistry and Molecular Biology, Michigan State University)
eLife, 5, e19274 (2016), DOI:10.7554/eLife.19274

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights
Masahiro Shimizu(Kyoto University), Yasunori Noguchi(Kyushu University), Yukari Sakiyama(Kyushu University), Hironori Kawakami(Kyushu University), Tsutomu Katayama(Kyushu University), Shoji Takada(Kyoto University)
Proceedings of the National Academy of Sciences USA, vol.113, E8021-E8030 (2016), DOI:10.1073/pnas.1609649113

Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations
Le Chang(kyoto University), Shoji Takada(kyoto University)
Scientific Reports, 6: 34441 (13 pages) (2016), DOI:10.1038/srep34441

Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model
Tadashi Ando(RIKEN, Japan; RIKEN Quantitative Biology Center, Japan.), Isseki Yu(RIKEN, Japan), Michael Feig(Michigan State University, United States), Yuji Sugita(RIKEN, Japan; RIKEN Quantitative Biology Center, Japan; RIKEN Advanced Institute for Computational Science, Japan;)
J. Phys. Chem., 120, 11856-11865.(2016), DOI:10.1021/acs.jpcb.6b06243

Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics
Cheng Tan(Kyoto University), Tsuyoshi Terakawa(Columbia University), Shoji Takada(Kyoto University)
Journal of the American Chemical Society, Vol.138 (27), pp.8512-8522(2016),DOI:10.1021/jacs.6b03729

Non-targeted parallel cascade selection molecular dynamics (nt-PaCS-MD) for enhancement of the conformational sampling of proteins
Ryuhei Harada, Akio Kitao
J. Chem. Theory Comput.,11,pp 5493–5502 (2015),DOI:10.1021/acs.jctc.5b00723