Computational research for development of mechanistic principle in carbohydrate binding proteins: molecular recognition and catalytic mechanism

2017 Fiscal Year Final Research Report

• Project/Area Number: 26410031
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: ISHIDA TOYOKAZU 国立研究開発法人産業技術総合研究所, 材料・化学領域, 主任研究員 (70443166)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Keywords: QM/MM計算 / 自由エネルギー計算 / 電子状態計算 / 分子動力学計算 / 糖鎖認識 / レクチン / キャプシドタンパク質 / 分子間相互作用

Outline of Final Research Achievements

Carbohydrates in general play important roles in various aspects of biological functions from the molecular level to macro-scale biological phenomena. In these processes, the atomistic basis of carbohydrate function is considered to be a molecular interaction between complex carbohydrates and target proteins. In contrast to their importance in various biological functions, atomistic details of carbohydrate recognition remain elusive at present. To advance our knowledge of carbohydrate recognitions, we have proposed a hybrid computational modeling strategy which combines MD sampling and QM/MM calculations.

First, we applied our methodology to one important system, the virus infection process by the norovirus capsid protein. Based on hybrid modeling analysis, we discuss the molecular basis of carbohydrate recognition between the capsid protein domain and Lewis antigens. We also mention another enzymatic system that hydrolyzes carbohydrate chains in a biomass degrading process.

Free Research Field

理論化学、計算化学