Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and comparison with solution X-ray scattering.

ABSTRACT: While coarse-grained (CG) simulations provide an efficient approach to identify small- and large-scale motions important to protein conformational transitions, coupling with appropriate experimental validation is essential. Here, by comparing small-angle X-ray scattering (SAXS) predictions from CG simulation ensembles of adenylate kinase (AK) with a range of energetic parameters, we demonstrate that AK is flexible in solution in the absence of ligand and that a small population of the closed form exists without ligand. In addition, by analyzing variation of scattering patterns within CG simulation ensembles, we reveal that rigid-body motion of the LID domain corresponds to a dominant scattering feature. Thus, we have developed a novel approach for three-dimensional structural interpretatio

SUBMITTER: Daily MD 

PROVIDER: S-EPMC3375699 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature