A simple method for the calculation of low energy packings of α-helices—A threshold approximation. I. The use of the method to estimate the effects of amino acid substitutions, deletions and insertions in globins

Abstract

A simple method is developed for computing low energy packings in alpha-helical proteins. This method is based on a simplified representation of a protein molecule in which the backbone of the alpha-helix is represented by a cylinder and the side chains of the amino acids by hard spheres. The energy function includes hydrophobic, electrostatic and Van der Waals' interactions. This method is used to compute low energy packings of an assembly of the alpha-helices of a globin molecule. The effect of mutations, deletions and insertions of a single amino acid resulting in drastic distortion of the spatial structure of sperm whale myoglobin was studied. The results demonstrated that these events can produce a breakdown of the spatial structure of the protein molecule.