Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope.

Abstract

The secondary structure of proteins results from both local and long-range interactions, the latter being primarily backbone hydrogen bonding. In this chapter, based on our recent work, we suggest that the striking regularity of secondary structure can be described, in a semi-analytical manner, in terms of Kubo cluster cumulants (corresponding to the expansion of the protein's potential of mean force) that originate from the coupling between the backbone-local and backbone-electrostatic interactions. This finding is illustrated by the analysis of the Protein Data Bank statistics. Examples demonstrating the importance of the coupling terms in coarse-grained treatment of proteins are also presented.