Effect of Crystal Environment on Protein Structures: Molecular Dynamics Simulations and Database Analysis

2014 Fiscal Year Final Research Report

• Project/Area Number: 25891031
• Research Category: Grant-in-Aid for Research Activity Start-up
• Allocation Type: Single-year Grants
• Research Field: Biophysics
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: MIYASHITA Osamu 独立行政法人理化学研究所, 計算科学研究機構, 上級研究員 (10620528)
• Research Collaborator: AHLSTROM Logan
• Project Period (FY): 2013-08-30 – 2015-03-31
• Keywords: 計算機生物物理 / 計算機構造生物 / 結晶構造 / 分子動力学シミュレーション / データベース解析

Outline of Final Research Achievements

Effects of crystal environment on the structure and dynamics of protein molecules were examined, by combining molecular dynamics simulations and statistical analysis of protein structure database. In particular, we studied cyanovirin-N and BPTI, for which multiple high-resolution X-ray structures are available. Molecular dynamics simulations were performed to obtain the conformational ensemble in solution. In addition, simulations of proteins in crystal environment were performed in comparison to examine the effect of crystal packing quantitatively. These data were then compared with the available protein X-ray structures to examine the effect of crystal formation conditions. A large number of available structures were analyzed to obtain statistics of crystal structures and compared against the conformational ensemble from simulations. These results provide valuable insight into the interpretation of X-ray structures to discuss protein dynamics and functions.

Free Research Field

計算機生物物理