Developments of methods for predicting transitions of proteins based on structural fluctuations

2015 Fiscal Year Final Research Report

• Project/Area Number: 26840056
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biophysics
• Research Institution: University of Tsukuba
• Principal Investigator: Harada Ryuhei 筑波大学, 数理物質系, 特別研究員(PD) (60612174)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Keywords: 分子動力学シミュレーション / タンパク質の天然構造予測 / タンパク質の構造変化予測

Outline of Final Research Achievements

Methods for predicting conformational transitions have been developed based on structural fluctuations of proteins. As computational schemes, the following two processes are repeated: (I) Selections of structures of proteins that have high potential to transit to other meta-stable states, where the candidates are selected based on a set of appropriate reaction coordinates. (II) Short-time molecular dynamics simulations restarting from the structures as conformational search. The above processes are powerful for predicting conformational transitions of proteins efficiently.
According to the strategy, we have developed several sampling methods for predicting conformational transitions, and applied them to biological systems. For instance, our methods have successfully predicted the native state of a mini-protein, chignolin. Furthermore, large-amplitude domain motions of T4 lysozyme in explicit water have been reproduced with our methods.

Free Research Field

生物物理学