JB Steinfeld , O Belan , Y Kwon , T Terakawa , A Al-Zain , MJ Smith , JB Crickard , Z Qi , W Zhao , R Rothstein , LS Symington , P Sung , SJ Boulton , EC Greene

Genes & Development 33 : 1191

Gō model revisited

S Takada

Biophysics and Physicobiology 16 : 248

Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins

R Kanada , T Terakawa , H Kenzaki , S Takada

Biophysical journal 116 : 2285

Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration

W Li , J Wang , J Zhang , S Takada , W Wang

Physical Review Letters 122 : 238102

Langmuir-Blodgett technique for anisotropic colloids: Young investigator perspective

T Li , K Lilja , RJ Morris , GB Brandani

Journal of Colloid and Interface Science 540 : 420

2018

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

GB Brandani , S Takada

PLoS computational biology 14 : e1006512

Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

C Tan , S Takada

Journal of chemical theory and computation 14 : 3877

Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays

S Watanabe , Y Mishima , M Shimizu , I Suetake , S Takada

Biophysical journal 114 : 2336

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

GB Brandani , T Niina , C Tan , S Takada

Nucleic acids research 46 : 2788

Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein–DNA Complexes

M Shimizu , S Takada

Journal of chemical theory and computation 14 : 1682

2017

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

T Niina , GB Brandani , C Tan , S Takada

PLoS computational biology 13 : e1005880

Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations

S Kubo , W Li , S Takada

PLoS computational biology 13 : e1005748

The condensin complex is a mechanochemical motor that translocates along DNA

T Terakawa , S Bisht , JM Eeftens , C Dekker , CH Haering , EC Greene

Science 358 : 672

Sequential eviction of crowded nucleoprotein complexes by the exonuclease RecBCD molecular motor

T Terakawa , S Redding , TD Silverstein , EC Greene

Proceedings of the National Academy of Sciences 114 : E6322

How one-dimensional diffusion of transcription factors are affected by obstacles: coarse-grained molecular dynamics study

M Saito , T Terakawa , S Takada

Molecular Simulation 43 : 1315

The structural basis of a high affinity ATP binding ε subunit from a bacterial ATP synthase

A Krah , Y Kato-Yamada , S Takada

PloS one 12 : e0177907

Adsorption of the natural protein surfactant Rsn-2 onto liquid interfaces

GB Brandani , SJ Vance , M Schor , A Cooper , MW Kennedy , BO Smith , CE MacPhee , DL Cheung

Physical Chemistry Chemical Physics 19 : 8584

2016

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights

M Shimizu , Y Noguchi , Y Sakiyama , H Kawakami , T Katayama , S Takada

Proceedings of the National Academy of Sciences 113 : E8021

Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

L Chang , S Takada

Scientific Reports 6 : 34441

The Conformation of Interfacially Adsorbed Ranaspumin-2 Is an Arrested State on the Unfolding Pathway

RJ Morris , GB Brandani , V Desai , BO Smith , M Schor , CE MacPhee

Biophysical Journal 111 : 732

Dynamic coupling among protein binding, sliding, and DNA bending revealed by molecular dynamics

C Tan , T Terakawa , S Takada

Journal of the American Chemical Society 138 : 8512

On the ATP binding site of the ε subunit from bacterial F-type ATP synthases

A Krah , S Takada

Biochimica et Biophysica Acta (BBA)-Bioenergetics 1857 : 332

2015

p53 dynamics upon response element recognition explored by molecular simulations

T Terakawa , S Takada

Scientific reports 5 : 17107

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

S Takada , R Kanada , C Tan , T Terakawa , W Li , H Kenzaki

Accounts of Chemical Research 48 : 3026

The Bacterial Hydrophobin BslA is a Switchable Ellipsoidal Janus Nanocolloid

GB Brandani , M Schor , R Morris , N Stanley-Wall , CE MacPhee , D Marenduzzo , U Zachariae

Langmuir 31 : 11558

DNA RECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases

JY Lee , T Terakawa , Z Qi , JB Steinfeld , S Redding , Y Kwon , WA Gaines , W Zhao , P Sung , EC Greene

Science 349 : 977

Partial unwrapping and histone tail dynamics in nucleosome revealed by coarse-grained molecular simulations

H Kenzaki , S Takada

PLoS computational biology 11 : e1004443

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations

T Tanaka , N Hori , S Takada

PLoS Comput Biol 11 : e1004356

On the Mg2+ binding site of the ε subunit from bacterial F-type ATP synthases

A Krah , S Takada

Biochimica et Biophysica Acta (BBA)-Bioenergetics 1847 : 1101

Couplings between hierarchical conformational dynamics from multi-time correlation functions and two-dimensional lifetime spectra: Application to adenylate kinase

J Ono , S Takada , S Saito

The Journal of Chemical Physics 142 : 212404

Dimer domain swapping versus monomer folding in apo-myoglobin studied by molecular simulations

K Ono , M Ito , S Hirota , S Takada

Physical Chemistry Chemical Physics 17 : 5006

Applying a grid technology to protein structure predictor "ROKKY".

K Fujikawa , W Jin , SJ Park , T Furuta , S Takada , H Arikawa , S Date , S Shimojo

Studies in health technology and informatics 112 : 27

2014

Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53

T Terakawa , J Higo , S Takada

Biophysical journal 107 : 721

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

W Li , W Wang , S Takada

Proceedings of the National Academy of Sciences 111 : 10550

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins

T Terakawa , S Takada

Journal of Chemical Theory and Computation 10 : 711

2013

Bayesian Parameter Inference by Markov Chain Monte Carlo with Hybrid Fitness Measures: Theory and Test in Apoptosis Signal Transduction Network

Y Murakami , S Takada

PloS one 8 : e74178

ATP hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations

MJ McGrath , IFW Kuo , S Hayashi , S Takada

J. Am. Chem. Soc. 135 : 8908

Quantifying disorder through conditional entropy: an application to fluid mixing

GB Brandani , M Schor , CE Macphee , H Grubmuller , U Zachariae , D Marenduzzo

PLoS One 8 : e65617

Protein‐specific force field derived from the fragment molecular orbital method can improve protein–ligand binding interactions

L Chang , T Ishikawa , K Kuwata , S Takada

Journal of computational chemistry 34 : 1251

Folding Coupled with Assembly in Split Green Fluorescent Proteins Studied by Structure-based Molecular Simulations

M Ito , T Ozawa , S Takada

The Journal of Physical Chemistry B 117 : 13212

Drug uptake pathways of multidrug transporter AcrB studied by molecular simulations and site-directed mutagenesis experiments

XQ Yao , N Kimura , S Murakami , S Takada

Journal of the American Chemical Society 135 : 7474

Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin

R Kanada , T Kuwata , H Kenzaki , S Takada

PLoS computational biology 9 : e1002907

2012

p53 searches on DNA by rotation-uncoupled sliding at C-terminal tails and restricted hopping of core domains

T Terakawa , H Kenzaki , S Takada

Journal of the American Chemical Society 134 : 14555

Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching

N Hori , S Takada

Journal of Chemical Theory and Computation 8 : 3384

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

W Li , T Terakawa , W Wang , S Takada

Proceedings of the National Academy of Sciences 109 : 17789

Coarse-grained molecular simulations of large biomolecules

S Takada

Current opinion in structural biology 22 : 130

2011

Rigor of cell fate decision by variable p53 pulses and roles of cooperative gene expression by p53.

Y Murakami , S Takada

Biophysics 8 : 41

Multiscale ensemble modeling of intrinsically disordered proteins: p53 N-terminal domain

T Terakawa , S Takada

Biophysical journal 101 : 1450

CafeMol: a coarse-grained biomolecular simulator for simulating proteins at work

H Kenzaki , N Koga , N Hori , R Kanada , W Li , K Okazaki , XQ Yao , S Takada

Journal of Chemical Theory and Computation 7 : 1979

Structural Comparison of F1-ATPase: Interplay among Enzyme Structures, Catalysis, and Rotations

K Okazaki , S Takada

Structure 19 : 588

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

W Li , PG Wolynes , S Takada

Proceedings of the National Academy of Sciences 108 : 3504

2010

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

T Terakawa , T Kameda , S Takada

Journal of computational chemistry 32 : 1228

Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations

XQ Yao , H Kenzaki , S Murakami , S Takada

Nature communications 1 : 117

Characterizing Protein Energy Landscape by Self-Learning Multiscale Simulations: Application to a Designed β-Hairpin

W Li , S Takada

Biophysical journal 99 : 3029

Multiscale methods for protein folding simulations

W Li , H Yoshii , N Hori , T Kameda , S Takada

Methods 52 : 106

2009

Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

N Koga , T Kameda , K Okazaki , S Takada

Proceedings of the National Academy of Sciences 106 : 18237

Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins

T Niwa , BW Ying , K Saito , WZ Jin , S Takada , T Ueda , H Taguchi

Proceedings of the National Academy of Sciences 106 : 4201

Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously

W Li , S Takada

The Journal of chemical physics 130 : 214108

Folding energy landscape and network dynamics of small globular proteins

N Hori , G Chikenji , RS Berry , S Takada

Proceedings of the National Academy of Sciences 106 : 73

2008

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

K Okazaki , S Takada

Proceedings of the National Academy of Sciences 105 : 11182

In silico chaperonin-like cycle helps folding of proteins for structure prediction

T Furuta , Y Fujitsuka , G Chikenji , S Takada

Biophysical journal 94 : 2558

Asymmetry in membrane protein sequence and structure: Glycine outside rule

W Jin , S Takada

Journal of molecular biology 377 : 74

2006

Secondary structure provides a template for the folding of nearby polypeptides

T Kameda , S Takada

Proceedings of the National Academy of Sciences 103 : 17765

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

K Okazaki , N Koga , S Takada , JN Onuchic , PG Wolynes

Proceedings of the National Academy of Sciences 103 : 11844

Folding-based molecular simulations reveal mechanisms of the rotary motor F1–ATPase

N Koga , S Takada

Proceedings of the National Academy of Sciences 103 : 5367

Protein Grabs a Ligand by Extending Anchor Residues: Molecular Simulation for Ca2+ Binding to Calmodulin Loop

C Kobayashi , S Takada

Biophysical journal 90 : 3043

Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study

G Chikenji , Y Fujitsuka , S Takada

Proceedings of the National Academy of Sciences 103 : 3141

SimFold energy function for de novo protein structure prediction: consensus with Rosetta

Y Fujitsuka , G Chikenji , S Takada

Proteins 62 : 381

2005

Present and future prospects of protein structure prediction

S Park , G Chikenji , T Hirokawa , K Tomii , S Takada

JOURNAL-JAPANESE SOCIETY FOR ARTIFICIAL INTELLIGENCE 20 : 479

2004

Protein folding mechanisms and energy landscape of src SH3 domain studied by a structure prediction toolbox

G Chikenji , Y Fujitsuka , S Takada

Chemical physics 307 : 157

Guiding the search for a protein's maximum rate of folding

Y Zhu , X Fu , T Wang , A Tamura , S Takada , JG Saven , F Gai

Chemical physics 307 : 99

Roles of physical interactions in determining protein‐folding mechanisms: Molecular simulation of protein G and α spectrin SH3

S Yup Lee , Y Fujitsuka , DH Kim , S Takada

Proteins 55 : 128

Optimizing physical energy functions for protein folding

Y Fujitsuka , S Takada , ZA Luthey‐Schulten , PG Wolynes

Proteins 54 : 88

2003

Competition between protein folding and aggregation with molecular chaperones in crowded solutions: insight from mesoscopic simulations

AR Kinjo , S Takada

Biophysical journal 85 : 3521

A reversible fragment assembly method for de novo protein structure prediction

G Chikenji , Y Fujitsuka , S Takada

The Journal of chemical physics 119 : 6895

How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations

F Takagi , N Koga , S Takada

Proceedings of the National Academy of Sciences 100 : 11367

De novo design of foldable proteins with smooth folding funnel: Automated negative design and experimental verification

W Jin , O Kambara , H Sasakawa , A Tamura , S Takada

Structure 11 : 581

2002

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: dynamics

AR Kinjo , S Takada

Physical Review E 66 : 051902

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: statics

AR Kinjo , S Takada

Physical Review E 66 : 031911

On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction

H Fukunishi , O Watanabe , S Takada

The Journal of chemical physics 116 : 9058

2001

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model

N Koga , S Takada

Journal of molecular biology 313 : 171

Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach

JJ Portman , S Takada , PG Wolynes

The Journal of Chemical Physics 114 : 5069

Protein folding simulation with solvent‐induced force field: Folding pathway ensemble of three‐helix‐bundle proteins

S Takada

Proteins 42 : 85

2000

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics

JJ Portman , S Takada , PG Wolynes

The Journal of Chemical Physics 114 : 5082

Simulating folding of helical proteins with coarse grained models

S Takada

Progress of Theoretical Physics Supplement 138 : 366

1999

Gō-ing for the prediction of protein folding mechanisms

S Takada

Proceedings of the National Academy of Sciences 96 : 11698

Folding dynamics with nonadditive forces: a simulation study of a designed helical protein and a random heteropolymer

S Takada , Z Luthey-Schulten , PG Wolynes

The Journal of chemical physics 110 : 11616

1998

Variational theory for site resolved protein folding free energy surfaces

JJ Portman , S Takada , PG Wolynes

Physical review letters 81 : 5237

1997

Microscopic theory of critical folding nuclei and reconfiguration activation barriers in folding proteins

S Takada , PG Wolynes

The Journal of chemical physics 107 : 9585

Statics, metastable states, and barriers in protein folding: A replica variational approach

S Takada , PG Wolynes

Physical Review E 55 : 4562

An elementary mode coupling theory of random heteropolymer dynamics

S Takada , JJ Portman , PG Wolynes

Proceedings of the National Academy of Sciences 94 : 2318

Glassy dynamics of random heteropolymers

S Takada , PG Wolynes

Progress of Theoretical Physics Supplement 126 : 49

1995

Multidimensional tunneling in terms of complex classical mechanics: Wave functions, energy splittings, and decay rates in nonintegrable systems

S Takada

The Journal of Chemical Physics 104 : 3742

Transfer-matrix approach to tunneling between Kolmogorov-Arnold-Moser tori

S Takada , PN Walker , M Wilkinson

Physical Review A 52 : 3546

1994

Effects of vibrational excitation on multidimensional tunneling: General study and proton tunneling in tropolone

S Takada , H Nakamura

The Journal of chemical physics 102 : 3977

WKB Theory of Tunneling between Tori

S Takada , H Nakamura

Progress of Theoretical Physics Supplement 116 : 295

Effects of Potential Energy Surface Topography and Isotope Substitution in Atom-Diatom Chemical Reactions: the CL + H2 and D + H2 Systems

S Takada , K Tsuda , A Ohsaki , H Nakamura

Advances in molecular vibrations and collision dynamics 2 : 245

1993

Constant centrifugal potential approximation for atom–diatom chemical reaction dynamics

K Moribayashi , S Takada , H Nakamura

The Journal of chemical physics 100 : 4284

Wentzel–Kramers–Brillouin theory of multidimensional tunneling: General theory for energy splitting

S Takada , H Nakamura

The Journal of chemical physics 100 : 98

1991

Reaction dynamics of D+ H2→ DH+ H: Effects of potential energy surface topography and usefulness of the constant centrifugal potential approximation

S Takada , A Ohsaki , H Nakamura

The Journal of chemical physics 96 : 339