Differential geometry of proteins: Helical approximations

Abstract

We regard a protein molecule as a geometric object, and in a first approximation represent it as a regular parametrized space curve passing through its alpha-carbon atoms (the backbone). In an earlier paper we argued that the regular patterns of secondary structures of proteins (morphons) correspond to geodesics on minimal surfaces. In this paper we discuss methods of recognizing these morphons on space curves that represent the protein backbone conformation. The mathematical tool we employ is the differential geometry of curves and surfaces. We introduce a natural approximation of backbone space curves in terms of helical approximating elements and present a computer algorithm to implement the approximation. Simple recognition criteria are given for the various morphons of proteins. These are incorporated into our helical approximation algorithm, together with more non-local criteria for the recognition of beta-sheet topologies. The method and the algorithm are illustrated with several examples of representative proteins. Generalizations of the helical approximation method are considered and their possible implications for protein energetics are sketched.