Quantifying Geometry and Persistence of Conductance Pathways in Ion Channels and Membrane Proteins

Abstract

Geometric and topological features of proteins such as voids, pockets and channels are important for protein functions. We discuss a method for visualizing conductance pathways in ion channels and other membrane proteins based on orthogonal balls computed from alpha shapes of the protein structures, and how metric properties of channel surfaces can be mapped. In addition, we discuss how constriction sites can be computed, which may help to understand channel selectivity and specificity, with implications in developing novel therapeutic interventions.