Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association.

ABSTRACT: Some frequently encountered deficiencies in all-atom molecular simulations, such as nonspecific protein-protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest possible change, by modifying the short-range protein-water pair interactions, and leaving all the water-water and protein-protein parameters unchanged. We find that a modest strengthening of protein-water interactions is sufficient to recover the correct dimensions of intrinsically disordered or unfolded proteins, as determined by direct comparison with small-angle X-ray scattering (SAXS) and Förster resonance energy transfer (FRET) dat

SUBMITTER: Best RB 

PROVIDER: S-EPMC4230380 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature