[Method for calculation of low-energy conformations of alpha-helical pairs of globular proteins]

The computer model of folding of two alpha-helices of globular proteins was developed. The radicals of amino acids were approximated by spheres with centers located in C beta-atoms. The functional of energy took into account the hydrophobic interactions of alpha-helices, electrostatic contacts of charged and polar side groups of amino acid, Van der Waals' interactions. The conformations with minimum energies of two-helical superstructures G--H from alpha- and beta-chains of horse hemoglobin, sperm whale myoglobin, and erythrocruorin were computed. They have mean deviation 0.7--1.8 A from native conformations of these proteins. Hence, at the self-organization process alpha-helices firstly are "roughly" oriented by hydrophobic interactions, but the choice of stable conformation occurs by Van der Waals' and electrostatic interactions. On this stage the low-energy conformation becomes "frozen" and cannot be significantly rearranged later. The mutual orientation of secondary protein structures are determined mainly by amino acid radical volumes, their hydrophobicity and charge.