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Development of a method to predict protein 3D structures based on correlations of distances between amino acids in proteins

开发基于蛋白质中氨基酸之间距离的相关性来预测蛋白质 3D 结构的方法

基本信息

批准号：
12680664
负责人：
KIKUCHI Takeshi
金额：
$ 1.28万
依托单位：
Kurashiki University of Science and the Arts
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2000
资助国家：
日本
起止时间：
2000 至 2002
项目状态：
已结题

项目摘要

The purpose of the present study was to explore the basic principle for development of a method to predict protein 3D structures. The following two topics were discussed in this study. One topic was investigation of the protein 3D structure formation by examination of physics of ideal no- frustrated spin systems assuming that the properties of protein folding are attributed to the minimal frustration effect. Another topic was elucidation of the actual protein structure formation principle by consideration of the behaviors of the spin systems obtained in this study. I studied this problem by the elucidation of the distance correlations between residues with the simulations of protein denatured states using a simplified effective potential. I further tried to investigate the possibility to develop a new protein 3D structure prediction method from the present technique. The following conclusion were obtained by the present study; (1) In the no frustrated spin system, the weak but slowly decaying pair correlation functions are dominant in the formation of the basic state. (2) The slowly decaying pair correlation functions are attributed to the convergence of the spin motions into one mode state. (3) In the actual model of the protein simulation, the residue pair correlations corresponding to the native structure appear in a specific temperature range. (4) This type of residue pair correlations can be regarded as the motion of a specific mode and the pair correlations corresponding to the native contacts are especially strong. These results suggest strongly the existence of a specific temperature range which means the condition of the transition to the native structure in denatured states, and we are encouraged to expect the possibility to establish a new method of protein 3D structure predictions

本研究的目的是探索开发预测蛋白质 3D 结构的方法的基本原理。本研究讨论了以下两个主题。其中一个主题是通过检查理想无受挫自旋系统的物理学来研究蛋白质 3D 结构的形成，假设蛋白质折叠的特性归因于最小的受挫效应。另一个主题是通过考虑本研究中获得的自旋系统的行为来阐明实际蛋白质结构形成原理。我通过使用简化的有效势模拟蛋白质变性状态来阐明残基之间的距离相关性来研究这个问题。我进一步尝试研究利用现有技术开发新的蛋白质 3D 结构预测方法的可能性。本研究得出以下结论； (1) 在无受挫自旋系统中，弱但缓慢衰减的对相关函数在基本态的形成中占主导地位。 (2) 缓慢衰减的对相关函数归因于自旋运动收敛到一种模式状态。 (3)在蛋白质模拟的实际模型中，与天然结构对应的残基对相关性出现在特定的温度范围内。 (4)这种残基对相关性可以被视为特定模式的运动，并且与本地接触对应的对相关性特别强。这些结果强烈表明特定温度范围的存在，这意味着变性状态下向天然结构转变的条件，并且我们鼓励期待建立一种新的蛋白质 3D 结构预测方法的可能性