Heterogeneous path ensembles for conformational transitions in semiatomistic models of adenylate kinase

Divesh Bhatt, Daniel Zuckerman

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semiatomistic protein models. The models have an all-atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single-processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semiatomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways.

Original languageEnglish (US)
Pages (from-to)3527-3539
Number of pages13
JournalJournal of Chemical Theory and Computation
Volume6
Issue number11
DOIs
StatePublished - Nov 9 2010
Externally publishedYes

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Adenylate Kinase
sampling
Sampling
central processing units
proteins
Proteins
Atoms
symmetry
atoms
simulation
interactions

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Heterogeneous path ensembles for conformational transitions in semiatomistic models of adenylate kinase. / Bhatt, Divesh; Zuckerman, Daniel.

In: Journal of Chemical Theory and Computation, Vol. 6, No. 11, 09.11.2010, p. 3527-3539.

Research output: Contribution to journalArticle

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