Role of water molecules in biomolecular functions and interactions

2015 Fiscal Year Final Research Report

• Project/Area Number: 26800227
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biological physics/Chemical physics/Soft matter physics
• Research Institution: Keio University
• Principal Investigator: Tomotaka Oroguchi 慶應義塾大学, 理工学部, 講師 (90589821)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Keywords: 生体分子 / 機能的構造揺らぎ / 水和構造 / 水素結合ネットワーク / 分子動力学シミュレーション

Outline of Final Research Achievements

In this study, we investigated how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, glutamate dehydrogenase (GDH), through molecular dynamics simulation supported by structural analyses and biochemical experiments. The results show that ‘wetting’/’drying’ and ‘adsorption’/’dissociation’ of a few water molecules at an active-site cleft worked as a switch for the functional motions of GDH. Thus, this study demonstrates the importance of water molecules in understanding protein functions.
In addition, we are now developing a new MD potential parameter set, which can account experimental hydration structures around protein surfaces. Our analyses using MD and quantum-chemistry calculation show that the potential parameter set, which explicitly consider loan pairs of polar atoms, is necessary to reproduce the hydration structures obtained by X-ray crystal structural analyses.

Free Research Field

生物物理