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Prediction and control of protein stability using computer experiments

Research Project

Project/Area Number 12680650
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionHirosaki University

Principal Investigator

SAITO Minoru  Hirosaki University, Faculty of Sci. and Tech., Professor, 理工学部, 教授 (60196011)

Project Period (FY) 2000 – 2001
Project Status Completed (Fiscal Year 2001)
Budget Amount *help
¥2,200,000 (Direct Cost: ¥2,200,000)
Fiscal Year 2001: ¥800,000 (Direct Cost: ¥800,000)
Fiscal Year 2000: ¥1,400,000 (Direct Cost: ¥1,400,000)
Keywordsthermal stability / molecular dynamics simulation / prediction / protein / amino acid substitution / parallel computer / parallelization
Research Abstract

The purpose of this project were
(1) Automatically calculating the stability free energies of mutant proteins without interrupting by a user.
(2) Speed up free energy calculations by parallelizing the programs on parallel machines.
(3) Expanding the computational mutagenesis methodology to amino acid mutations between different kinds
(4) Quantitatively predicting the stability of mutant proteins before experimentally observing it.
These purpose were achieved as follows.
(1) Automatic calculation of stability free energy was achieved by making unix shells to control the calculation processes, i.e., computational mutagenesis > molecular dynamics simulation > free energy calculation.
(2) Speed up of calculation was achieved by parallelizing the program COSMOS90 on fujitsu VPP5000 for the molecular dynamics simulation that is the most time consuming part of the stability calculation.
(3) Expansion of computational mutagenesis was successfully performed by amino add mutation from Val (hydrophobia amino acid) to Thr (hydrophilic amino acid) for Myb R2 domain and alpha-lactalbumin.
(4) Predictive calculation of stability was performed to Val>Met and Val>Thr mutations for Myb R2 domain. The calculations successfully predicted the stability of Val>Met mutant but not Val>Thr mutant. The reason of this discrepancy for the Val>Thr calculation was clarified and recalculation gave the correct result.

Report

(3 results)
  • 2001 Annual Research Report   Final Research Report Summary
  • 2000 Annual Research Report
  • Research Products

    (24 results)

All Other

All Publications (24 results)

  • [Publications] Minoru Saito, 他: "Cavity-filling mutations enhance protein stability by lowering the energy of native state"J. Phys. Chem. B,. 104. 3705-3711 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Hidetoshi Kono, 他: "Stability analysis for the cavity-filling mutations of Myb DNA-binding domain by free energy calculations"PROTEINS. 38. 197-209 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Kiyotaka Misoo, 他: "Development of Molecular Dynamics Programs for Protein with Parallelized Barnes-Hut Code"Proc.the Fourth International Conference on High-Performance Computing in Asia-Pacific Region. 2. 1103-1111 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] K.Horii, 他: "Contribution of Thr29 to the thermodynamic stability of goat α-lactalbumin as determined by experimental and theoretical approaches"PROTEINS. 45. 16-29 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] T.Ohumara, 他: "Stabilization of hen egg white lysozyme by a cavity-filling mutation"Protein Saience. 10. 313-320 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] T.Yoda, 他: "Folding-unfolding of goat α-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations"PROTEINS. 42. 49-65 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Y.Taniguchi, 他: "Structure and function of biological systems under extreme conditions : Pressure and temperature effects"Springer. 282 (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] M. Saito, H. Kono, H. Morii, H. Uedaira, Tahir H. Tahirov, K. 0gata, and A. Sarai: "Cavity-filling mutations enhance protein stability by lowering the free energy of native state"J. Phys. Chem.. Vol. 104, No. 15. 3705-3711 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] H. Kono, M. Saito, and A. Sarai: "Stability analysis for the cavity-filling mutations of Myb DNA-binding domain by free energy calculations"PROTEINS. vol. 38. 197-209 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] K. Misoo, Y. Akiyama, Y. Shizawa, and M. Saito: "Development of Molecular Dynamics Programs for Protein with a Parallelized Barnes-Hut Code"Proc. the Fourth International Conference on High-Performance Computing in Asia-Pacific Region. vol. 2. 1103-1111 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] K. Horii, M. Saito, T. Yoda, K. Tsumoto, M. Matsusuna, K. Kuwajima, and I. Kumagai: "Contribution of Thr29 to the thermodynamic stability of goat α-lactalbumin as determined by experimental and theoretical approaches"PROTEINS. vol. 45. 16-29 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] T. Ohmura, T. Ueda, K. Ootsuka, M. Saito, and T. Imoto: "Stabilization of hen egg white lysozyme by a cavity-filling mutation"Protein Science. vol. 10. 313-320 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] T. Yoda, M. Saito, M. Arai, K. Horii, R. Tsumoto, M. Matsusima, I. Kumagai, and K. Kuwajima: "Folding-unfolding of goat α-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations"PROTEINS. vol. 42. 49-65 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] K.Horii, 他: "Contribution of Thr29 to the thermodynamic stability of goat α-lactalbumin as determined by experimental and theoretical approaches"PROTEINS. 45. 16-29 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.Ohmura, 他: "Stabilization of hen egg white lysozyme by a cavity-filling mutation"Protein Science. 10. 313-320 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] T.Yoda, 他: "Folding-unfolding of goat α-lactalbumin studied by stopped-flow circular dichroism and molecular dynamics simulations"PROTEINS. 42. 49-65 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Y.Taniguchi, 他: "Structure and function of biological systems under extreme conditions"Springer. 282 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Minoru Saito 他: "Cavity-filling mutations enhance protein stability by lowering the free energy of native state."J.Phys.Chem.B,. 104. 3705-3711 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Hidetoshi Kono 他: "Stability analysis for the cavity-filling mutations of Myb DNA-binding domain by free energy calculations"PROTEINS : Structure, Function, and Genetics. 38. 197-209 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] 三十尾潔高 他: "並列化Barnes-Hut tree code用いた高精度なタンパク質分子動力学法プログラムの開発"情報処理学会論文誌. 41. 1538-1548 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kiyotaka Misoo 他: "Development of Molecular Dynamics Programs for Protein with a Parallelized Barnes-Hut Code"Proc.the Fourth International Conference on High-Performance Computing in Asia-Pacific Region. 2. 1103-1111 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Takao Yoda 他: "Folding-Unfolding of Goat α-Lactalbumin Studied by Stopped-Flow Circular Dichroism and Molecular Dynamics Simulations"PROTEINS : Structure, Function, and Genetics. 42. 49-65 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Tadahiro Ohmura 他: "Stabilization of hen egg white lysozyme by a cavity-filling mutation"Protein Science. 10. 313-320 (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Y.Taniguchi 他: "Structure and function of biological systems under extreme conditions : Pressure and temperature effects"Springer-Verlag. 320 (2000)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2016-04-21  

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