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

本研究的目的是探索蛋白质三维结构预测方法的基本原理。本研究讨论了以下两个主题。一个主题是通过检查理想无阻挫自旋系统的物理来研究蛋白质3D结构的形成，假设蛋白质折叠的性质归因于最小阻挫效应。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的形成原理。我研究了这个问题，阐明了残基之间的距离相关性与蛋白质变性状态的模拟使用一个简化的有效势。我进一步尝试研究从现有技术开发新的蛋白质3D结构预测方法的可能性。研究结果表明：（1）在无阻挫自旋系统中，弱但缓慢衰减的对关联函数在基态的形成中起主导作用。(2)缓慢衰减的对关联函数归因于自旋运动收敛到一个模态。(3)在蛋白质模拟的实际模型中，对应于天然结构的残基对相关性出现在特定的温度范围内。(4)这种残基对相关可以看作是特定模式的运动，并且与原生接触相对应的残基对相关特别强。这些结果有力地表明存在一个特定的温度范围，这意味着在变性状态下向天然结构转变的条件，我们受到鼓舞，期待建立一种新的蛋白质三维结构预测方法的可能性

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