Name

WAKO, Hiroshi

Official Title

Professor

Affiliation

(School of Social Sciences)

Contact Information

Mail Address

Mail Address
wako@waseda.jp

URL

Web Page URL

http://www.f.waseda.jp/wako/

Grant-in-aids for Scientific Researcher Number
60158607

Sub-affiliation

Sub-affiliation

Faculty of Social Sciences(Graduate School of Social Sciences)

Research Council (Research Organization)/Affiliated organization(Global Education Center)

Affiliated Institutes

理工学総合研究センター

兼任研究員 1989-2006

バイオインフォマティクス研究所

研究員 2004-2006

ITバイオ研究所

研究員 2005-2009

ITバイオ・マイニング研究所

研究所員 2010-2013

理工学術院総合研究所(理工学研究所)

兼任研究員 2006-2018

理工学術院総合研究所(理工学研究所)

兼任研究員 2018-

Educational background・Degree

Educational background

-1973 Waseda Universsity Faculty of Science and Engineering Department of Physics
-1978 Waseda University Graduate School, Division of Science and Engineering Physics and Applied Physics

Degree

Dr. of Science Coursework Waseda University

Career

1978-1981Cornell University, Post-doctoral associate
1982-1985Waseda University, Research Assistant
1985-1986Juntendo University, Research Assistant
1986-1988Waseda University, Lecturer
1988-1993Waseda University, Assistant Professor
1993-Waseda University, Professor

Academic Society Joined

The Biophysical Society of Japan

The Physical Society of Japan

Protein Science Society of Japan

Japanese Society for Bioinformatics

The Chem-Bio Informatics Society

Research Field

Keywords

Protein folding, Bioinformatics

Grants-in-Aid for Scientific Research classification

Biology / Biological Science / Biophysics

Research interests Career

Theoretical Study on Protein Folding

Current Research Theme Keywords:Protein,Molecular Mechanics and Dynamics,Computer Simulation

Individual research allowance

Paper

Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model

Wako Hiroshi;Abe Haruo

Biophysics and Physicobiology 13(0) p.263 - 2792016-2016

CiNii

Detail

Outline:

The Φ-value analysis approach provides information about transition-state structures along the folding pathway of a protein by measuring the effects of an amino acid mutation on folding kinetics. Here we compared the theoretically calculated Φ values of 27 proteins with their experimentally observed Φ values; the theoretical values were calculated using a simple statistical-mechanical model of protein folding. The theoretically calculated Φ values reflected the corresponding experimentally observed Φ values with reasonable accuracy for many of the proteins, but not for all. The correlation between the theoretically calculated and experimentally observed Φ values strongly depends on whether the protein-folding mechanism assumed in the model holds true in real proteins. In other words, the correlation coefficient can be expected to illuminate the folding mechanisms of proteins, providing the answer to the question of which model more accurately describes protein folding: the framework model or the nucleation-condensation model. In addition, we tried to characterize protein folding with respect to various properties of each protein apart from the size and fold class, such as the free-energy profile, contact-order profile, and sensitivity to the parameters used in the Φ-value calculation. The results showed that any one of these properties alone was not enough to explain protein folding, although each one played a significant role in it. We have confirmed the importance of characterizing protein folding from various perspectives. Our findings have also highlighted that protein folding is highly variable and unique across different proteins, and this should be considered while pursuing a unified theory of protein folding.

Calculation of Free-Energy Profiles, Folding Rates, and Ö Values by Means of a Simple Statistical-Mechanical Model of Protein Folding

H. Wako and H. Abe

Advances in Protein Folding Research/ Nova Science Publisher p.19 - 632015-

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

H. Wako and S. Endo

Comp. Biol. Chem. 44p.22 - 302013-

DOI

Dynamic features of homodimer interfaces calculated by normal-mode analysis

Y. Tsuchiya, K. Kinoshita, S. Endo, and H. Wako

Protein Science 21(10) p.1503 - 15132012-

DOI

ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins

H. Wako and S. Endo

The Open Bioinformatics Journal 6p.9 - 192012-

DOI

Study of Folding/Unfolding Kinetics of Lattice Proteins by Applying a Simple Statistical Mechanical Model for Protein Folding

H. Wako and H. Abe

Protein Folding / Nova Science Publisher p.349 - 3762011-

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

H. Wako and S. Endo

Biophys. Chem. 159p.257 - 2662011-

DOI

Prediction of protein motions from amino acid sequence and its application to protein-protein interaction.

S. Hirose, K. Yokota, Y. Kuroda, H. Wako, S. Endo, S. Kanai, and T. Noguchi

BMC Structural Biology 10(20) 2010-

DOI

Folding/unfolding kinetics of lattice proteins studied using a simple statistical mechanical model for protein folding, I: Dependence on native structures and amino acid sequences

H. Abe and H. Wako

Physica A 388p.3442 - 34542009-

DOI

Statistical mechanical theory of protein conformation and its transition

Y. Kobayashi, H. Wako, and N. Saito

J. Phys. Soc. Jpn 76(7) p.0748022007-

DOI

Single amino acid substitutions in lattice proteins using statistical mechanical model for protein folding

H. Wako and H. Abe

J Phys. Soc. Jpn 76(10) p.1048012007-

DOI

Analyses of simulations of three-dimensional lattice proteins in comparison with a simplified statistical mechanical model of protein folding

H. Abe and H. Wako

Physical Review E 74p.0119132006-

Application of a statistical mechanical model for protein folding to a three-dimensional lattice protein

H. Abe andH. Wako

J. Phys. Soc. Jpn 73(5) p.1143 - 11462004-

ProMode: a database of normal mode analyses on protein molecules with a full-atom model

H. Wako, M. Kato and S. Endo

Bioinformatics 20(13) p.2035 - 20432004-

Environment-dependent and position-specific frequencies of amino acid occurrences in α-helices

H. Wako, J. An, and A. Sarai

Chem-Bio Info. J 3(2) p.58 - 772003-

Analysis of structural motifs of proteins using sets of codes, describing local structures

J. An, H. Wako, and A. Sarai

Mol. Biol. (Mosk) 35p.1056 - 10622001-

Sampling efficiency of molecular dynamics and Monte Carlo method in protein simulation

H. Yamashita, S. Endo, H. Wako, and A. Kidera

Chem. Phys. Lett. 342p.382 - 3862001-

Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis.

H. Kikuchi, H. Wako, K. Yura, M. Go, and M. Mimuro

Biophys. J. 79p.1587 - 16002000-

Nobel method to detect a motif of local structures in different protein conformations

H. Wako and T. Yamato

Protein Engineering 11p.981 - 9901998-

Conformational Analysis of Nucleic Acid Molecules with Flexible Furanose Rings in Dihedral Angle Space

M. Tomimoto, N. Go, and H. Wako

J. Comp. Chem. 17p.71996-

New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue

S. Endo, J. Higo, K. Nagayama, and H. Wako

J. Comp. Chem. 17(4) p.4761996-

A Comparative Study of Dynamic Structures Between Phage 434 Cro and Repressor Proteins by Normal Mode Analysis

H. Wako, M. Tachikawa, and A. Ogawa

PROTEINS: Struc. Func. Genet. 261996-

Dynamic Relationships among Economic Variables Examined by the Embedding Method

T. Inaba, Y. Nagai, and H. Wako

Dynamical Systems and Chaos (N. Aoki et al. ed.) / World Scientific 1995-

Secondary structure prediction of β-subunits of the gonadotropin-thyrotropin family from its aligned sequences using environment-dependent amino-acid substitution tables and conformational propensities

H. Wako and S. Ishii

Biochimica et Biophysica Acta 1247p.1041995-

FEDER/2: Program for Static and Dynamic Conformational Energy Analysis of Macro-Molecules in Dihedral Angle Space

H. Wako, S. Endo, K. Nagayama, and N. Go

Comp. Phys. Comm. 911995-

Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins I. Solvent accessibility class

H. Wako and T.L. Blundell

Journal of Molecular Biology 238p.6821994-

Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins II. Secondary structures

H. Wako and T.L. Blundell

Journal of Molecular Biology 238p.6931994-

The recognition of protein structure and function from sequence : adding value to genome data

A.C. May, M.S. Johnson, S.D. Rufino, H. Wako, Z.Y. Zhu, R. Sowdhamini, N. Srinivasan, M.A. Rodionov, and T.L. Blundell

Phil. Trans. R. Soc. Lond. B 344p.3731994-

Molecular biology of gonadotropins.

S. Ishii, H. Ando, H. Wako, and Y. Kubota

Avian Endocrinology (P.J. Sharp ed.) /J of Endocrinology Ltd, Bristol p.123 - 1341993-

A new version of DADAS (DistanceAnalysis in Dihedral Angle Space) and its performance.

S. Endo, H. Wako, K. Nagayama, and N. Go

Computational Aspects of the Study of Biological Macromoleculesby Nuclear Magnetic Resonance Spectroscopy (J.C.. Hoch et al. ed.) / Plenum Press, New York p.233 - 2511991-

Distance-constraint approachto higher-order structures of globular proteins with empirically determineddistances between amino acid residues.

H. Wako and Y. Kubota

J. Protein Chem. 10p.233 - 2431991-

Protein conformation in terms of conformational energy analysis.

H. Wako

Protein Structural Analysis, Folding and Design (H.. Hatano ed.) / Japan Scientific Societies Press and Elsevier p.3 - 171990-

Inspection of three-dimensional structures of proteins with dynamical information from the normal mode analysis

H. Wako

Prot. Seq. Data Anal. 2p.175 - 1801989-

A fractal model of protein conformationsand spectral exponents for the densities of low-frequency normal modesof vibration.

H. Wako

J. Phys. Soc. Jpn 58p.1926 - 19291989-

Monte Carlo simulations of aprotein molecule with and without hydration energy calculated by the hydration-shellmodel.

H. Wako

J. Protein Chem. 8p.733 - 7471989-

Dynamic structures of globularproteins with respect to correlative movements of residues calculated inthe normal mode analysis.

H. Wako

J. Protein Chem. 8p.589 - 6071989-

Inspection of three-dimensionalstructures of proteins with dynamical information from the normal modeanalysis.

H. Wako

Protein Seq. Data Anal. 2p.175 - 1801989-

Algorithm for rapid calculationof hessian of conformational energy function of proteins by supercomputer.

H. Wako and N. Go

J. Comp. Chem. 8p.625 - 6351987-

Development of software tools for protein structure design.

H. Nakamura, T. Yamazaki, H. Abe, T. Noguti, Y. Seno, H. Wako, and N. Go

J. Mol. Graph. 4p.180 - 1811986-

Unfolding of tertiary structuresof proteins.

H. Wakana, H. Yokomizo, H. Wako, Y. Isogai, K. Kosuge, and N. Saito

Int. J. Pept. Protein Res. 23p.657 - 6701984-

Monte Carlo study on local andsmall-amplitude conformational fluctuation in hen egg white lysozyme.

H. Wakana, H. Wako, and N. Saito

Int. J. Pept. Protein Res. 23p.315 - 3231984-

Hydrophobic interaction and the prediction of the tertiary structures of proteins.

N. Saito, H. Wako, T. Akutsu, and Y. Oyama

Studies Phys. Theor. Chem. 27p.325 - 3381983-

Statistical mechanical treatmentof α-helices and extended structures in proteins with inclusion of short-and medium-range interactions.

H. Wako, N. Saito, and H.A. Scheraga

J. Protein Chem. 2p.221 - 2491983-

Cis-trans isomerizationof proline in the peptide (His 105-Val 124) of ribonuclease A containingthe primary nucleation site.

R.P. Mathew, F. Gerewitz, H. Wako and H.A. Scheraga

J. Protein Chem. 2p.131 - 1461983-

Distance-constraint approachto protein folding. II. Prediction of three-dimensional structure of bovinepancreatic trypsin inhibitor

H. Wako and H.A. Scheraga

J. Protein Chem. 1p.85 - 1171982-

Distance-constraint approachto protein folding. I. Statistical analysis of protein conformations interms of distances between residues.

H. Wako and H.A. Scheraga

J. Protein Chem. 1p.5 - 451982-

Visualization of the natureof protein folding by a study of a distance constraint approach in two-dimensionalmodels.

H. Wako and H.A. Scheraga

Biopolymers 21p.611 - 6321982-

On the use of distance constraintsto fold a protein.

H. Wako and H.A. Scheraga

Macromolecules 14p.961 - 9691981-

Statistical mechanical theoryof the protein conformation II. Folding pathway for protein.

H. Wako and N. Saito

J. Phys. Soc. Jpn 44p.1939 - 19451978-

Statistical mechanical theoryof the protein conformation I. General considerations and the applicationto homopolymers.

H. Wako and N. Saito

J. Phys. Soc. Jpn 44p.1931 - 19381978-

Tertiary structures of gastrin-like tetrapeptides.

T. Yamada, H. Wako, N. Saito, Y. Isogai, and H. Watari

Int. J. Pept. Protein Res. 8p.607 - 6141976-

Dynamic features of homodimer interfaces calculated by normal-mode analysis

Tsuchiya, Yuko;Kinoshita, Kengo;Endo, Shigeru;Wako, Hiroshi

PROTEIN SCIENCE 21(10) p.1503 - 15132012-2012

DOIWoS

Detail

ISSN:0961-8368

Memorial Issue for Professor Nobuhiko Saitô

Yura Kei;Wako Hiroshi

Biophysics and Physicobiology 13(0) p.243 - 2432016-2016

CiNii

Statistical Mechanical Theory of the Protein Conformation. I. General Considerations and the Application to Homopolymers

Wako Hiroshi;Saitô Nobuhiko

Journal of the Physical Society of Japan 44(6)

CiNii

Detail

ISSN:0031-9015

A Fractal Model of Protein Conformations and Spectral Exponents for the Densities of Low-Frequency Normal Modes of Vibration

Wako Hiroshi

Journal of the Physical Society of Japan 58(6)

CiNii

Detail

ISSN:0031-9015

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables.

Wako Hiroshi;Endo Shigeru

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables. 442013-2013

DOI

Detail

ISSN:1476-928X

Outline::We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein-DNA complex, a protein-tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system.

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

Kinjo, Akira R.; Bekker, Gert Jan; Wako, Hiroshi; Endo, Shigeru; Tsuchiya, Yuko; Sato, Hiromu; Nishi, Hafumi; Kinoshita, Kengo; Suzuki, Hirofumi; Kawabata, Takeshi; Yokochi, Masashi; Iwata, Takeshi; Kobayashi, Naohiro; Fujiwara, Toshimichi; Kurisu, Genji; Nakamura, Haruki

Protein Science 27(1) p.95 - 1022018/01-2018/01

PubMedDOIScopus

Detail

ISSN:09618368

Outline:© 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated. Here, we report the new RDB PDBj Mine 2, the WebGL molecular viewer Molmil, the ProMode-Elastic server for normal mode analysis, a virtual reality system for the eF-site protein electrostatic molecular surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.

Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank

Wako, Hiroshi; Endo, Shigeru

Biophysical Reviews 9(6) p.877 - 8932017/12-2017/12

DOIScopus

Detail

ISSN:18672450

Outline:© 2017, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany. Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein dynamics using data from the Protein Data Bank (PDB). We developed an elastic network model-based NMA program using dihedral angles as independent variables. Compared to the NMA programs that use Cartesian coordinates as independent variables, key attributes of the proposed program are as follows: (1) chain connectivity related to the folding pattern of a polypeptide chain is naturally embedded in the model; (2) the full-atom system is acceptable, and owing to a considerably smaller number of independent variables, the PDB data can be used without further manipulation; (3) the number of variables can be easily reduced by some of the rotatable dihedral angles; (4) the PDB data for any molecule besides proteins can be considered without coarse-graining; and (5) individual motions of constituent subunits and ligand molecules can be easily decomposed into external and internal motions to examine their mutual and intrinsic motions. Its performance is illustrated with an example of a DNA-binding allosteric protein, a catabolite activator protein. In particular, the focus is on the conformational change upon cAMP and DNA binding, and on the communication between their binding sites remotely located from each other. In this illustration, NMA creates a vivid picture of the protein dynamics at various levels of the structures, i.e., atoms, residues, secondary structures, domains, subunits, and the complete system, including DNA and cAMP. Comparative studies of the specific protein in different states, e.g., apo- and holo-conformations, and free and complexed configurations, provide useful information for studying structurally and functionally important aspects of the protein.

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

Wako, Hiroshi;Endo, Shigeru

COMPUTATIONAL BIOLOGY AND CHEMISTRY 44p.22 - 302013-2013

DOIWoS

Detail

ISSN:1476-9271

Statistical Mechanical Theory of the Protein Conformation. II. Folding Pathway for Protein

Wako Hiroshi;Saitô Nobuhiko

Journal of the Physical Society of Japan 44(6)

CiNii

Detail

ISSN:0031-9015

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis.

Wako Hiroshi;Endo Shigeru

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis. 159(2-3) 2011-2011

DOI

Detail

ISSN:1873-4200

Outline::The conformational change of a protein upon ligand binding was examined by normal mode analysis (NMA) based on an elastic-network model (ENM) for a full-atom system using dihedral angles as independent variables. Specifically, we investigated the extent to which conformational change vectors of atoms from an apo form to a holo form of a protein can be represented by a linear combination of the displacement vectors of atoms in the apo form calculated for the lowest-frequency m normal modes (m=1, 2,…, 20). In this analysis, the latter vectors were best fitted to the former ones by the least-squares method. Twenty-two paired proteins in the holo and apo forms, including three dimer pairs, were examined. The results showed that, in most cases, the conformational change vectors were reproduced well by a linear combination of the displacement vectors of a small number of low-frequency normal modes. The conformational change around an active site was reproduced as well as the entire conformational change, except for some proteins that only undergo significant conformational changes around active sites. The weighting factors for 20 normal modes optimized by the least-squares fitting characterize the conformational changes upon ligand binding for these proteins. The conformational changes sampled around the apo form of a protein by the linear combination of the displacement vectors obtained by ENM-based NMA may help solve the flexible-docking problem of a protein with another molecule because the results presented herein suggest that they have a relatively high probability of being involved in an actual conformational change.

Application of a Statistical Mechanical Model for Protein Folding to a Three-Dimensional Lattice Protein

Abe Haruo;Wako Hiroshi

Journal of the Physical Society of Japan 73(5)

CiNii

Detail

ISSN:0031-9015

Books And Publication

Study of Folding/Unfolding Kinetics of Lattice Proteins by Applying a Simple Statistical Mechanical Model for Protein Folding

H. Wako and H. Abe

Nova Biomedical2011/01-

Detali

ISBN:978-1-61761-922-9

トポロジーデザイニング 新しい幾何学からはじめる物質・材料設計(分担執筆): 「タンパク質のモチーフ構造解析 」

輪湖 博

(株)エヌ・ティー・エヌ2009/04-

Detali

ISBN:978-4-86034-162-4

科学技術は社会とどう共生するか(分担執筆): 「科学技術ジャーナリストの課題」(パネルディスカッションの記録)

高橋真理子・渡部潤一・輪湖 博・小山慶太

東京電機大学出版局2009/04-

Detali

ISBN:978-4-501-62430-9

複雑系の構造と予測 (分担執筆): 「タンパク質分子の立体構造転移」

輪湖 博、安部晴男

共立出版2006/06-

バイオインフォマティクス事典 (分担執筆): 「構造エネルギー最適化法」「基準振動解析」の項目

輪湖 博

共立出版2006/06-

物理学辞典三訂版 (分担執筆): 「アンフィンゼンのドグマ」「タンパク質の折りたたみ過程」「ディスタンス・ジオメトリー」の項目

輪湖 博

培風館2005/09-

タンパク質のかたちと物性 (分担執筆): 「タンパク質という複雑系へのアプローチ」

輪湖 博

共立出版1997-

社会人間学 (分担執筆): 「生命倫理学と人間行動」

那須 政玄、輪湖 博

成文堂1997-

時間と変化の経済学 (共訳)

有賀裕二、浅田統一郎、稲葉敏夫、輪湖 博

中央大学出版部1994-

アイザック・アシモフの科学と発見の年表 (共訳)

小山慶太、輪湖 博

丸善1992-

機能性食品タンパク質工学ハンドブック (分担執筆): 「タンパク質の高次構造と機能-計算化学・計算物理学からのアプローチ」

輪湖 博

サイエンスフォーラム1991-

計算物理学と計算化学 (分担執筆): 「蛋白質の立体構造シミュレーション」(共著)

輪湖 博、郷 信広

海文堂1988-

遺伝情報の科学

輪湖 博

成文堂1990-

BASICによる生物 (共著)

荻原利彦、小林謙三、永井喜則、土屋尚、輪湖 博

共立出版1987-

『Protein Structural Analysis, Folding and Design』(分担執筆)、Protein Conformation in terms of conformational energy analysis

Japan Scientific Societies Press & Elsvier1990-

『Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy』(分担執筆)、A new version of DADAS(Distance Analysis in Dihedral Angle Space)and its performance(共著)

Plenum1991-

Lecture And Oral

Development and Releasing of New Databases forProtein Dynamics: ProMode-Oligomer and ProMode-Elastic.

2011/11/08

Detail

Poster presentation

Characterization of a conformational change of protein with elastic-network-model based normal mode analysis in dihedral angle space.

17th International Biophysics Congress2011/10/31

Detail

Poster presentation

Conformational change reproduced by a linear combination of displacement vectors obtained from normal mode analysis

2011/09/18

Detail

Oral presentation(general)

Structure deviation analyses of proteins complexed with various ATP analogs.

InCob 20102010/09/26

Detail

Poster presentation

ProMode-Elastic: database of elastic-network-model based normal mode analysis

InCob 20102010/09/26

Detail

Poster presentation

Dynamic structures of proteins characterized by networks formed by connecting positively correlated residues in normal mode vibrations

Fifth East Asian Biopyhsics Symposium2006/11

Detail

Poster presentation

Normal mode analyses of multimeric proteins with symmetry in dihedral angle space

Fifth East Asian Biopyhsics Symposium2006/11

Detail

Poster presentation

Structural alignment with Delaunay codes characterizing local structures and structural motifs identified by the alignment

Fifth East Asian Biopyhsics Symposium2006/11

Detail

Poster presentation

Effect of single amino acid substitutions on kinetic properties of folding studied by a statistical mechanical model of lattice proteins

Fifth East Asian Biopyhsics Symposium2006/11

Detail

Poster presentation

Comparisons between dynamic properties of homologous protein structure in ProMode (Database of normal mode analyses on proteins)

GIW20052005/12

Detail

Poster presentation

ProMode: a collection and comparison of normal mode analysis results of protein molecules

The 1st Pacific-Rim International Conference on Protein Science2004/04

Detail

Poster presentation

A Statictical Mechanical Model for Protein Folding: A Study on Three-Dimensional Lattice Proteins

The 1st Pacific-Rim International Conference on Protein Science2004/04

Detail

Poster presentation

Development of Energy-Minimization and Molecular Simulation Algorithm Considering Solvation Effects in Dihedral Angles Space

The 1st Pacific-Rim International Conference on Protein Science2004/04

Detail

Poster presentation

Reflection of knowledge information in ProMode (a database of normal mode analyses on proteins)

GIW20042004/12

Detail

Poster presentation

Improvements in ProMode (a database of normal mode analyses of proteins)

GIW20032003/12

Detail

Poster presentation

ProMode: A database of normal mode analysis of proteins.

GIW20022002/12

Detail

Poster presentation

Exploration of the structural space of proteins by molecular dynamics directed initially to normal modes

4-th International Conferenece on Biological Physics2001/07

Detail

Poster presentation

Rigid local structure motifs in proteins detected by the Delaunay tessellation method.

4-th International Conferenece on Biological Physics2001/07

Detail

Poster presentation

Geometrical analysis of protein structures

4-th International Conferenece on Biological Physics2001/07

Detail

Poster presentation

Analysis of structural motifs in proteins

BGRS 20002000/08

Detail

Poster presentation

Research Grants & Projects

Grant-in-aids for Scientific Research Adoption Situation

Research Classification:

Normal mode analysis of proteins using an elastic network model in dihedral angle space

Allocation Class:¥4320000

Research Classification:

Analyses of binding normal modes in protein complexes and registration to the database ProMode

Allocation Class:¥3100000

Research Classification:

A comparative study of dynamic structures of proteins by using normal mode analysis database.

Allocation Class:¥3500000

Research Classification:

The dynamic structure of protein molecules based on coupling among normal modes

Allocation Class:¥2500000

Research Classification:

Classification and analysis of local structure motifs in protein conformations

Allocation Class:¥3200000

Research Classification:

Evolution of Gonadotropic Hormones : Molecular and Morphological Approaches

Allocation Class:¥10500000

Research Classification:

Protein structure, comparison, prediction, and design

Allocation Class:¥340200000

Research Classification:

Administration of researches on principles of protein architecture

Allocation Class:¥49700000

Research Classification:

Evolution of pituitary hormones

Allocation Class:¥23500000

On-campus Research System

Special Research Project

基準振動解析によるタンパク質ダイナミクスの比較研究

2002

Research Results Outline: タンパク質立体構造の構築原理を明らかにし、構造と機能の関係を理解することは、構造生物学、バイオインフォーマティクスなどにおけるポスト・ゲノムの重要な タンパク質立体構造の構築原理を明らかにし、構造と機能の関係を理解することは、構造生物学、バイオインフォーマティクスなどにおけるポスト・ゲノムの重要な研究課題の一つである。そこでは、静的構造のみならず、動的構造を考慮した研究が不可欠であることが広く... タンパク質立体構造の構築原理を明らかにし、構造と機能の関係を理解することは、構造生物学、バイオインフォーマティクスなどにおけるポスト・ゲノムの重要な研究課題の一つである。そこでは、静的構造のみならず、動的構造を考慮した研究が不可欠であることが広く認識されているものの、ダイナミクスに関する研究の多くは個別のタンパク質に関するもので、より多くのタンパク質のダイナミクスを比較研究することによって、より大局的な視点から解析したものは殆んどないのが現状である。そこで本研究では、われわれが現在構築中のタンパク質の基準振動解析データベースを利用して、多くのタンパク質の動的構造を比較し、立体構造の構築原理、そして構造・機能相関の問題にアプローチすることを目的として研究を行ってきた。 本年度は、まず、より多くのタンパク質について基準振動解析を行い、そのデータを蓄積した。 その上で、タンパク質の立体構造を構成する部品としての局所構造の性格をダイナミクスの観点から明らかにするために、各基準振動モードについて、各原子ペアのゆらぎベクトルの内積をとり、正の相関が強い原子がそれぞれ一つの集合を構成するようクラスター化することによってドメインを定義する方法を開発した。これまで、動的なドメインを定義する方法にはDynDomというソフトがよく使われているが、この方法では、見た目あきらかにドメインが存在すると思われる場合でも定義されない場合が多く、その後の解析ができないという欠点があった。本研究で開発した方法はそれを補うことができ、ダイナミクスの観点からドメインを定義し、タンパク質立体構造の構築原理を考える上で、新たな視点を提供することができると思う。今後、得られたドメインを分類し、性格付けしていく予定である。

二面角空間でのタンパク質の分子動力学シミュレーション

1997

Research Results Outline:タンパク質の立体構造をその立体構造エネルギーという観点から解析し、研究するために、これまで、エネルギーの最小化、基準振動解析、モンテカルロ・シミュレータンパク質の立体構造をその立体構造エネルギーという観点から解析し、研究するために、これまで、エネルギーの最小化、基準振動解析、モンテカルロ・シミュレーションを二面角を変数として実行するプログラムFEDERの開発を行ってきた。しかし、二面角を変数とす...タンパク質の立体構造をその立体構造エネルギーという観点から解析し、研究するために、これまで、エネルギーの最小化、基準振動解析、モンテカルロ・シミュレーションを二面角を変数として実行するプログラムFEDERの開発を行ってきた。しかし、二面角を変数とする分子動力学計算に関しては、変数の3乗に比例する計算量が必要と考えられ、実用的でなかったため、プログラムの開発を見送ってきた経緯がある。しかし、近年、変数の1乗に比例する計算量で可能なアルゴリズムが相次いで発表されたことを受けて、われわれのプログラムFEDERにもその機能を付加し、分子動力学シミュレーションを行ってみることとした。 結果的に2つのアルゴリズムを試すこととなった。最初に採用したJainらのアルゴリズムは、シミュレーションを続けるうちに運動量が変動し、計算が不安定になる欠点があることがわかった。そこで新たにMazurらのアルゴリズムを採用したプログラムを開発した。こちらは、運動量保存がアルゴリズム的に保証されており、現在までに行ったテストの結果では、少なくとも通常の環境設定でのシミュレーションはJainらのものより安定に進行することがわかった。しかし、非常にエネルギーが高い初期値、非常な高温、非常に大きな系でのシミュレーションにはついてはまだ十分に検討しておらず、改良が必要となる可能性もある。また、並行して、最小エネルギー構造のまわりでの基準振動モードにそったゆらぎのシミュレーションについてもテスト計算を行った。 今後、プログラムの改良とともに、具体的なタンパク質を設定してシミュレーションを行う予定である。

Lecture Course

Course TitleSchoolYearTerm
Mathematical ScienceSchool of Social Sciences2019spring semester
Life Science 1School of Social Sciences2019spring semester
Life Science 2School of Social Sciences2019fall semester
Introduction to EntropySchool of Social Sciences2019fall semester
SeminarII (Study of Life Science/spring semester)School of Social Sciences2019spring semester
SeminarII (Study of Life Science/fall semester)School of Social Sciences2019fall semester
SeminarIII (Study of Life Science/spring semester)School of Social Sciences2019spring semester
SeminarIII (Study of Life Science/fall semester)School of Social Sciences2019fall semester
Life Science IGraduate School of Social Sciences2019spring semester
Life Science IIGraduate School of Social Sciences2019fall semester
Life Science I(spring semester)Graduate School of Social Sciences2019spring semester
Life Science I(fall semester)Graduate School of Social Sciences2019fall semester
Life science II(spring semester)Graduate School of Social Sciences2019spring semester
Life science II(fall semester)Graduate School of Social Sciences2019fall semester