Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures.

ABSTRACT: A novel method for the refinement of misfolded protein structures is proposed in which the properties of the solvent environment are oscillated in order to mimic some aspects of the role of molecular chaperones play in protein folding in vivo. Specifically, the hydrophobicity of the solvent is cycled by repetitively altering the partial charges on solvent molecules (water) during a molecular dynamics simulation. During periods when the hydrophobicity of the solvent is increased, intramolecular hydrogen bonding and secondary structure formation are promoted. During periods of increased solvent polarity, poorly packed regions of secondary structures are destabilized, promoting structural rearrangement. By cycling between these two extremes, the aim is to minimize the formation of long-lived

SUBMITTER: Fan H 

PROVIDER: S-EPMC2280060 | biostudies-literature | 2004 Apr

REPOSITORIES: biostudies-literature