Development of new molecular dynamics simulation methods and application to protein folding problem

2014 Fiscal Year Final Research Report

• Project/Area Number: 23740325
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biophysics/Chemical physics
• Research Institution: Okazaki Research Facilities, National Institutes of Natural Sciences
• Principal Investigator: OKUMURA HISASHI 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 計算科学研究センター, 准教授 (80360337)
• Project Period (FY): 2011-04-28 – 2015-03-31
• Keywords: 分子動力学 / タンパク質 / ペプチド

Outline of Final Research Achievements

Biomolecules such as proteins have complicated free energy surfaces with many local minima. Conventional molecular dynamics simulations tend to get trapped in these local-minimum states. One of the powerful techniques to avoid this difficulty is the replica-exchange method.
We proposed a new type of the replica-exchange method, which is referred to as helix-strand replica-exchange molecular dynamics method. In this method umbrella potential which enhances alpha-helix or beta-strand conformation is exchanged. We applied this method to a design peptide and compared the results with those obtained by usual replica-exchange method.
We also proposed a better alternative to the replica-exchange method, which we refer to as the replica-permutation method. In replica-permutation method, not only exchanges between two replicas but also permutations among more than two replicas are performed.

Free Research Field

理論生物物理学