Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility

Abstract

Dynamics of protein cavities associated with protein fluctuations and conformationalplasticity is essential for their biological function. NMR ensembles, molecular dynamics (MD) simulations, and normal mode analysis (NMA) provide appropriate frameworks to explore functionally relevant protein dynamics and cavity changesrelationships. Within this context, we have recently developed analysis of null areas(ANA), an efficient method to calculate cavity volumes. ANA is based on a combination of algorithms that guarantees its robustness against numerical differentiations.This is a unique feature with respect to other methods. Herein, we present anupdated and improved version that expands it use to quantify changes in cavity features, like volume and flexibility, due to protein structural distortions performed onpredefined biologically relevant directions, for example, directions of largest contribution to protein fluctuations (principal component analysis [PCA modes]) obtained byMD simulations or ensembles of NMR structures, collective NMA modes or anyother direction of motion associated with specific conformational changes. A webpage has been developed where its facilities are explained in detail. First, we showthat ANA can be useful to explore gradual changes of cavity volume and flexibilityassociated with protein ligand binding. Secondly, we perform a comparison study ofthe extent of variability between protein backbone structural distortions, andchanges in cavity volumes and flexibilities evaluated for an ensemble of NMR activeand inactive conformers of the epidermal growth factor receptor structures. Finally,we compare changes in size and flexibility between sets of NMR structures for different homologous chains of dynein.