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

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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