Probing dynamic protein ensembles with atomic proximity measures

Zoltán Gáspári, Annamária F. Ángyán, Somdutta Dhir, Dino Franklin, András Perczel, Alessandro Pintar, Sándor Pongor

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)515-522
Number of pages8
JournalCurrent Protein and Peptide Science
Volume11
Issue number7
DOIs
Publication statusPublished - Dec 1 2010

Keywords

  • Atom depth
  • Protein NMR
  • Protein structural ensemble
  • Protein structure comparison
  • Solvent exposition

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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