On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.

ABSTRACT: Intrinsically disordered proteins that populate the so-called "Dark Proteome" offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and

SUBMITTER: Olson MA 

PROVIDER: S-EPMC5281587 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature