Ishikura Takakazu, Iwata Yuki, Hatano Tatsuro, Yamato Takahisa
Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, 464-8602, Japan.
J Comput Chem. 2015 Aug 15;36(22):1709-18. doi: 10.1002/jcc.23989. Epub 2015 Jul 6.
Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD-95, and the results were used to illustrate the energy exchange network of inter-residue interactions based on atomistic molecular dynamics simulations. The removal of the α3 helix is known to decrease ligand affinity by 21-fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph.
蛋白质功能不仅受结构调控，还受物理动力学和热涨落的影响。我们开发了计算机程序“蛋白质电流计算”（CURP），用于热涨落蛋白质介质中物理量的流动分析。CURP程序用于计算神经元蛋白PSD - 95的第三个PDZ结构域内的能量流动，结果用于基于原子分子动力学模拟说明残基间相互作用的能量交换网络。已知去除α3螺旋会使配体亲和力降低21倍，而不改变蛋白质整体结构；然而，我们证明该螺旋构成网络图的重要组成部分。
