Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase

We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic 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...

Full description

Saved in:
Bibliographic Details
Published in:Journal of chemical theory and computation 2010-10, Vol.6 (11), p.3527-3539
Main Authors: Bhatt, Divesh, Zuckerman, Daniel M
Format: Article
Language:English
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic 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 semi-atomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways.
ISSN:1549-9618
1549-9626
DOI:10.1021/ct100406t