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 conformational plasticity 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 changes relationships. 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 an updated and improved version that expands it use to quantify changes in cavity features, like volume and flexibility, due to protein structural distortions performed on predefined biologically relevant directions, for example, directions of largest contribution to protein fluctuations (principal component analysis [PCA modes]) obtained by MD simulations or ensembles of NMR structures, collective NMA modes or any other direction of motion associated with specific conformational changes. A web page has been developed where its facilities are explained in detail. First, we show that ANA can be useful to explore gradual changes of cavity volume and flexibility associated with protein ligand binding. Secondly, we perform a comparison study of the extent of variability between protein backbone structural distortions, and changes in cavity volumes and flexibilities evaluated for an ensemble of NMR active and 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.

Post‐translational modification sites are present in hydrophilic cavities of alpha‐synuclein, tau, FUS, and TDP‐43 fibrils: A molecular dynamics study

“…Fibril cavities were detected using the Analysis of Null Areas 2's (ANA2) 36 pocket discovery feature on the last 25 ns of simulation which we then used to build the cavity amino acid content heatmap shown in Figure S5A and Table T2 in Data S1. Using the detected cavity residues, ANA2 was used to calculate volumes by sampling five equally spaced timepoints of the last 25 ns production run (75–100 ns of simulation) in triplicate.…”

“…15 Here, we expanded our simulations to three new recombinant aSyn fibril structures: H50Q (PDB: 6PES) and E46K (PDB: 6UFR) mutant fibrils, and the WT aSyn polymorph 2b (PDB: 6SST). As shown in Figure 1, we detected hydrophilic cavities in the new aSyn polymorphs (Figure 1F-H) as indicated by the volumes in gray, green, and red, which were identified using the last 25 ns of simulation with the Analysis of Null Areas (ANA2) package developed by Barletta et al 36…”