Probing Dynamic Protein Ensembles with Atomic Proximity Measures

Zoltan      Gaspari; Annamaria      F. Angyan; Somdutta      Dhir; Dino      Franklin; Andras      Perczel; Alessandro      Pintar; Sandor      Pongor

Abstract

The emerging role of internal dynamics in protein fold and function requires new avenues of structure analysis. We analyzed the dynamically restrained conformational ensemble of ubiquitin generated from residual dipolar coupling data, in terms of protruding and buried atoms as well as interatomic distances, using four proximity-based algorithms, CX, DPX, PRIDE and PRIDE-NMR (http://hydra.icgeb.trieste.it/protein/). We found that Ubiquitin, this relatively rigid molecule has a highly diverse dynamic ensemble. The environment of protruding atoms is highly variable across conformers, on the other hand, only a part of buried atoms tends to fluctuate. The variability of the ensemble cautions against the use of single conformers when explaining functional phenomena. We also give a detailed evaluation of PRIDE-NMR on a wide dataset and discuss its usage in the light of the features of available NMR distance restraint sets in public databases.

Keywords: Protein structural ensemble, protein NMR, atom depth, solvent exposition, protein structure comparison, Probing, Atomic Proximity Measures, ubiquitin, proximity-based algorithms, CX, DPX, PRIDE, protein-protein interactions, PRIDE-NMR, 1P88, 1VND, 1SP2, fold recognition tests, SCOP database