A Chirality Calculation Algorithm for Supersecondary Protein Structural Motifs

Abstract

Coiled coils, collagen superhelices, and β-sheets belong to the supersecondary level of protein structure. Each of these classes of structural motifs is characterized by a particular chirality. However, methodology for mathematical determination of chirality of specific structures found in real proteins is currently underdeveloped. The aim of this work is to present a universal algorithm for calculating the chirality sign and value for supersecondary structure elements. In this algorithm, the basic calculation principles are the same for all three classes of structures, allowing different motifs to be compared directly. The results for a number of structures from each of the three classes are presented in tables and graphical plots. The calculated chirality signs generally agree with the predicted ones. The results also show that the chirality value is related to the number of amino acid residues in the structure and their distribution among the secondary structure elements. The relationship between amino acid composition and the chirality value is discussed using several examples. The more evident factors that determine the chirality sign and value for a particular structure are a promising subject for future research.