Simulation of an Ensemble of Conformational Transitions in a United-Residue Model of Calmodulin

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76 Scopus citations

Abstract

Conformational transitions in proteins provide the mechanism for enacting many critical biological functions at the molecular level. Unfortunately, a full description of the ensemble of dynamical pathways in proteins has been out of reach for both experimental and computational techniques. Here, we demonstrate that a simple residue-level computer model of calmodulin's N-terminal lobe yields a statistically converged ensemble of dynamic conformational transitions using ordinary Monte Carlo simulation, without guiding forces, in a few months time on a single desktop computer. The ensemble reveals clear pathway heterogeneity, and additionally provides detailed information on intermediate structures. The model uses static structural information from two Protein Data Bank files as the sole empirical input, whereas the dynamical results are generated from ordinary simulation.

Original languageEnglish (US)
Pages (from-to)5127-5137
Number of pages11
JournalJournal of Physical Chemistry B
Volume108
Issue number16
DOIs
StatePublished - Apr 22 2004

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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