Itoh Kazuhito, Sasai Masaki
Department of Computational Science and Engineering, Nagoya University, Nagoya 464-8603, Japan.
J Chem Phys. 2009 Apr 14;130(14):145104. doi: 10.1063/1.3097018.
Theory of multidimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in terms of cooperativity within individual regions and interactions among multiple regions and thus obtained classification is used to analyze the folding process of several example proteins. Ribosomal protein S6, src-SH3 domain, CheY, barnase, and BBL domain are analyzed with the two-dimensional representation by using a structure-based Hamiltonian model. The extension to the higher dimensional representation leads to the finer description of the folding process. Barnase, NtrC, and an ankyrin repeat protein are examined with the three-dimensional representation. The multidimensional representation allows us to directly address questions on folding pathways, intermediates, and transition states.
通过采用蛋白质中多个区域的结构序参作为多个坐标，发展了蛋白质折叠自由能面的多维表示理论。根据各个区域内的协同性以及多个区域之间的相互作用，对各种折叠情况进行分类，然后利用得到的分类来分析几个示例蛋白质的折叠过程。通过基于结构的哈密顿模型，用二维表示法分析了核糖体蛋白S6、src-SH3结构域、CheY、巴纳酶和BBL结构域。向更高维表示的扩展导致对折叠过程更精细的描述。用三维表示法研究了巴纳酶、NtrC和一个锚蛋白重复序列蛋白。多维表示使我们能够直接解决关于折叠途径、中间体和过渡态的问题。
