title: Probing dynamic protein ensembles with atomic proximity measures.
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.
authors.affiliation: Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary. szpari@chem.elte.hu
authors.forename: Zoltán
authors.initials: Z
authors.lastname: Gáspári
authors.forename: Annamária F
authors.initials: AF
authors.lastname: Angyán
authors.forename: Somdutta
authors.initials: S
authors.lastname: Dhir
authors.forename: Dino
authors.initials: D
authors.lastname: Franklin
authors.forename: András
authors.initials: A
authors.lastname: Perczel
authors.forename: Alessandro
authors.initials: A
authors.lastname: Pintar
authors.forename: Sándor
authors.initials: S
authors.lastname: Pongor
mesh_terms: D000818:Animals; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009862:Online Systems; D025341:Principal Component Analysis; D011487:Protein Conformation; D025801:Ubiquitin / Q000737:chemistry*
chemical_list: D025801:Ubiquitin