Stable conformation search of Collagen-like peptides using improved simulated annealing by Tsallis statistics

Abstract

Simulated Annealing improved by Tsallis statistics was applied to search a globally stable conformation of collagen-like oligopeptides. Recently the structures of two collagen model peptides were determined by X-ray crystallography. One of them is made of a repeating unit of L-Pro-L-Hyp-Gly. They form triple helical coils as were described in many textbooks. On the other hand, we analyzed a model peptide Boc-L-Pro-L-Pro-Gly by X-ray crystallography. Its conformation is same as the conformation of repeating unit of collagen. It suggests the helical conformation of collagen molecule is determined in the stage of single strand. The new statistical dynamics by Tsallis generalizes the ordinary thermodynamic and is going to be applied in various fields including simulated annealing. We tried the search of globally stable conformations of six model peptides, Boc-(L-Pro-L-Pro-Gly)n-methylamide, acetyl-(L-Pro-L-Hyp-Gly)n-methylamide, n = 1,2 and 3, using the improved transition and acceptance probabilities based upon Tsallis entropy. Semiempirical molecular orbital calculation package(WinMopac) was used as an energy minimizer. X-ray structures could be searched for the model peptides successfully. We conclude that the simulated annealing algorithm with semiempirical MO calculations gives globally stable conformations for collagen-like oligopeptides.