Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.

ABSTRACT: Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintai

SUBMITTER: Pachov DV 

PROVIDER: S-EPMC4517867 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature