Brief tutorial to evaluate molecular cavities in large conformational ensembles: a K2P channel study case

Abstract

In structural bioinformatics, computational biology, or any other field where is important to assess cavities, clefts, pores, or grooves in a macromolecular system, it is imperative to perform this evaluation over a trajectory or an ensemble of structures to measure all possible structural changes produced by the atomic movements, especially in the constriction regions. This is mainly true in membrane proteins such as ions channels or transporters where the movements of the amino acid residue side chains that form the pore can significantly alter their dimensions and thus affect the protein function. In this work, we present a brief tutorial to measure the radius of the pore within macromolecules in large structural ensembles using non-commercial software widely reported in the literature.