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Analysis of stability and dynamics of tertiary structure of nucleic acid molecules by using computer simulation

Research Project

Project/Area Number 16570132
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionThe University of Tokyo

Principal Investigator

NAKAMURA Shugo  The University of Tokyo, Graduate School of Agricultural and Life Sciences, Associate Professor, 大学院・農学生命科学研究科, 助教授 (90272442)

Project Period (FY) 2004 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥3,100,000 (Direct Cost: ¥3,100,000)
Fiscal Year 2005: ¥1,400,000 (Direct Cost: ¥1,400,000)
Fiscal Year 2004: ¥1,700,000 (Direct Cost: ¥1,700,000)
Keywordsnucleic acids / mini hairpin molecule / generalized ensemble method / folding / マルチカノニカル分子動力学法
Research Abstract

This research is about the analysis of the stability of nucleic acids hairpin structures by large scale structure sampling using multicanonical molecular dynamics simulation and local enhanced sampling (LES). Target molecules are dGC(GAA)GC and its mutants at tri-loop region. Starting from unfold structure, folding event was found in the trajectories of a multicanonical molecular dynamics simulation, and this folding/unfolding pathway was analyzed in detail. Sorin et al. proposed two folding pathways, zipping and compaction, for RNA tetra-loop hairpins. According to the analysis in this research, the folding pathway for dGC(GAA)GC was compaction-type. Structure sampling using LES was also applied to stable dGC(GNA)GC (N=A,G,T,C) and unstable dGC(GAG)GC and dGC(GAC)GC. Similar folding pathways were observed in dGC(GNA)GC trajectories : first, A5 stacks on the stem (G6), then G3 stacks on the stem (C2), and finally, N4 stacks on G3. For dGC(GNA)GC, structures were converged to near-native hairpin in 10 ns simulation. For dGC(GAG)GC and dGC(GAC)GC, structures were not converged, that corresponds to the fact that these molecules cannot form stable hairpin structures. These analysis may be able to extend to the stability analysis of other nucleic acid molecules.

Report

(3 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • Research Products

    (13 results)

All 2005 2004

All Journal Article (13 results)

  • [Journal Article] Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand2005

    • Author(s)
      T.Murata, et al.
    • Journal Title

      FEBS Journal 272

      Pages: 4938-4948

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase2005

    • Author(s)
      H.Nojiri, et al.
    • Journal Title

      Journal of Molecular Biology 351

      Pages: 355-370

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Crystal structure of the terminal cumene dioxygenase component of Pseudomonas fluorescens IP012005

    • Author(s)
      X.Dong, et al.
    • Journal Title

      Journal of Bacteriology 187

      Pages: 2483-2490

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions2005

    • Author(s)
      K.Sumikoshi, et al.
    • Journal Title

      Proceedings of the 16th International Conference on Genome Informatics (GIW 2005) 16

      Pages: 161-173

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase2005

    • Author(s)
      H.Nojiri et al.
    • Journal Title

      Journal of Molecular Biology 351

      Pages: 355-370

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand2005

    • Author(s)
      T.Murata et al.
    • Journal Title

      FEBS J. 272(19)

      Pages: 4938-4948

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase2005

    • Author(s)
      H.Nojiri et al.
    • Journal Title

      J.Mol.Biol. 351(2)

      Pages: 355-370

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Crystal structure of the terminal cumene dioxygenase component of Pseudomonas fluorescens IP012005

    • Author(s)
      X.Dong et al.
    • Journal Title

      J.Bachteriol. 187(7)

      Pages: 2483-2490

    • Related Report
      2005 Annual Research Report
  • [Journal Article] A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions2005

    • Author(s)
      K.Sumikoshi et al.
    • Journal Title

      Proceedings of the 16th International Conference on Genome Informatics (GIW 2005) 16(2)

      Pages: 161-173

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Distributed shared arrays : Portable shared-memory programming interface for multiple computer systems2005

    • Author(s)
      A.Nomoto, Y.Watanabe, W.Kaneko, T.Terada, S.Nakamura, K.Shimizu
    • Journal Title

      Proceedings of the 2004 Symposium on Applications & the Internet (印刷中)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Improvement of accuracy of free-energy landscapes of peptids calculated with generalized Born model by using numerical solutions of Poisson's equation2004

    • Author(s)
      T.Ishizuka, et al.
    • Journal Title

      Chemical Physics Letters 393

      Pages: 546-551

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Distributed shared arrays : Portable shared-memory programming interface for multiple computer systems2004

    • Author(s)
      A.Nomoto, et al.
    • Journal Title

      Proceedings of the 2004 Symposium on Applications & the Internet

      Pages: 630-635

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Improvement of accuracy of free-energy landscapes of peptids calculated with generalized Born model by using numerical solutions of Poisson's equation2004

    • Author(s)
      T.Ishizuka, T.Terada, S.Nakamura, K.Shimizu
    • Journal Title

      Chemical Physics Letters 393

      Pages: 546-551

    • Related Report
      2004 Annual Research Report

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Published: 2004-04-01   Modified: 2016-04-21  

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