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2006 Fiscal Year Final Research Report Summary

Geometry optimizations of proteins using the ab initio fragment molecular orbital method

Research Project

Project/Area Number 16350017
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionNational Institute of Advanced Industrial Science and Technology (AIST)

Principal Investigator

KITAURA Kazuo  National Institute of Advanced Industrial Science and Technolog, Reserch Institute for Computational Sciences, Principal Reserch Scientist, 計算科学研究部門, 上席研究員 (30132723)

Co-Investigator(Kenkyū-buntansha) UEBAYASI Masami  National Institute of Advanced Industrial Science and Technolog, Institute for Biological Resources and Functions, Reserch Scientist, 生物機能工学部門, 主任研究員 (70356559)
NEMOTO Tadasi  National Institute of Advanced Industrial Science and Technolog, Biological Information Research Center, Reserch Scientist, 生物情報解析センター, 主任研究員 (70357739)
Project Period (FY) 2004 – 2006
Keywordsfragment MO method / protein / geometry optimization / ab initio molecular orbital / FMO method
Research Abstract

We have developed the fragment molecular orbital method (FMO) for the electronic structure calculations of large molecules such as proteins. In the FMO method, a molecule is divided into small fragments and ab initio MO calculations are performed on the fragment monomers and their dimers to obtain the total energy and other properties of while molecule. In this work, we have developed the analytic derivative of the electrostatic interaction between far separated fragments necessary for practical gradient calculations of large systems, and performed a number of geometry optimizations using FMO and ab initio methods. In particular, the α-helix, β-turn and extended conformers of 10-residue polyalanine were studied, and the good FMO accuracy established (RMSD for the former two forms were about 0.2 Å and for the latter structure 10^<-3> Å). Met-enkephalin dimer used as a model for polypeptide binding was computed at the 3-21G and 6-31G^* levels and a similar accuracy was achieved; the error in the binding energy predictions (FMO vs ab initio) was 1-3 kcal/mol. Chignolin (PDB : luao) and an agonist polypeptide of erythropoietin receptor protein (emp1) were optimized at the 3-21(+)G level, with the RMS deviation from ab initio of about 0.2 Å, or 0.5^O° in terms of bond angles. It is shown that the FMO method can be practically used for the geometry optimization of real proteins.

  • Research Products

    (19 results)

All 2007 2006 2005 2004 Other

All Journal Article (18 results) Book (1 results)

  • [Journal Article] The fragment molecular orbital method for geometry optimizations of polypeptides and proteins2007

    • Author(s)
      Dmitri G.Fedorov, Toyokazu Ishida, Masami Uebayasi, Kazuo Kitaura
    • Journal Title

      J. Phys. Chem. A 111

      Pages: 2722-2732

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Change in a protein's electronic structure induced by an explicit solvent : an ab initio Fragment Molecular Orbital (FMO) study of ubiquitin2007

    • Author(s)
      Yuto Komeiji, Toyokazu Ishida, Dmitri G. Fedorov, Kazuo Kitaura
    • Journal Title

      J. Comp. Chem. 28

      Pages: 1750-1762

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Molecular recognition mechanism of FK506 binding protein (FKBP) : All electron fragment molecular orbital (FMO) study2007

    • Author(s)
      Isao Nakanishi, Dmitri G. Fedorov, Kazuo Kitaura
    • Journal Title

      Proteins : Struct. Funct. Bioinfo. 68

      Pages: 145-158

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] On the accuracy of the three-body fragment molecular orbital method (FMO) applied to Moller-Plesset perturbation theory2007

    • Author(s)
      Dmitri G.Fedorov, Kazuya Ishimura, Toyokazu Ishida, Kazuo Kitaura, Peter Pulay, Shigeru Nagase
    • Journal Title

      J. Comp. Chem. 28

      Pages: 1476-1484

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Pair interaction energy decomposition analysis2007

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      J. Comp. Chem. 28

      Pages: 222-237

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] On the accuracy of the three-body fragment molecular orbital method (FMO) applied to Moller-Plesset perturbation theory2007

    • Author(s)
      Dmitri G.Fedorov, Kazuya Ishimura, Toyokazu Ishida, Kazuo Kitaura, Peter Pulay, Shigeru Nagase
    • Journal Title

      J. Comp.Chem. 28

      Pages: 1476-1484

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Three-body fragment molecular orbital method for accurate calculations of large systems2006

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      Chem. Phys. Lett. 433

      Pages: 182-187

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] The polarisable continuum model (PCM) combined with the fragment molecular orbital method (FMO)2006

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura, Hui Li, Jan H.Jensen, Mark S.Gordon
    • Journal Title

      J. Comp. Chem. 27

      Pages: 976-985

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] All electron quantum chemical calculation of the entire enzyme system confirms a collective catalytic device in the chorismate mutase reaction2006

    • Author(s)
      Toyokazu Ishida, Dmitri G. Fedorov, Kazuo Kitaura
    • Journal Title

      J. Phys. Chem. B 110

      Pages: 1457-1463

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Three-body fragment molecular orbital method for accurate calculations of large systems2006

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      Chem. Phys. Lett 433

      Pages: 182-187

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein2005

    • Author(s)
      Tadashi Nemoto, Dmitri G.Fedorov, Masami Uebayasi, Kenji Kanazawa, Kazuo Kitaura, Yuto Komeiji
    • Journal Title

      Comput. Bio. Chem. 29

      Pages: 434-439

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Coupled-cluster theory based upon the fragment molecular orbital method2005

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      J. Chem. Phys. 123

      Pages: 134103-134112

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Multilayer formulation of the fragment molecular orbital method (FMO)2005

    • Author(s)
      Dmitri G.Fedorov, Toyokazu Ishida, Kazuo Kitaura
    • Journal Title

      J. Phys Chem. A 109

      Pages: 2638-2646

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Multiconfiguration self consistent field theory based upon the fragment molecular orbital method2005

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      J. Chem. Phys. 122

      Pages: 54108-54117

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Second order Moller-Plesset perturbation theory based upon the fragment molecular orbital method (FMO)2004

    • Author(s)
      D.G.Fedorov, K.Kitaura
    • Journal Title

      J.Chem.Phys. 121

      Pages: 2483-2490

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Second order Moller Plesset perturbation theory based upon the fragment molecular orbital method (FMO)2004

    • Author(s)
      D.G.Fedorov, K.Kitaura
    • Journal Title

      J.Chem.Phys. 121

      Pages: 2483-2490

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Extending the power of quanum chemistry to large systems with the fragment molecular orbital method

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      J. Phys. Chem. A (in press)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Extending the power of quanum chemistry to large systems with the fragment molecular orbital method

    • Author(s)
      Dmitri G.Fedorov, Kazuo Kitaura
    • Journal Title

      J. Phys. Chem. A (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Book] "Theoretical development of the fragment molecular orbital (FMO) method" in "Modern methods for theoretical physical chemistry and biopolymers"(edited by E. Starikow, S. Tanaka and J. Lewis)2006

    • Author(s)
      D.G.Fedorov, Kazuo Kitaura
    • Total Pages
      3-38
    • Publisher
      Elsevier, Amsterdam
    • Description
      「研究成果報告書概要(和文)」より

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Published: 2008-05-27  

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