On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

ABSTRACT: FSD-1, a designed small ultrafast folder with a ββα fold, has been actively studied in the last few years as a model system for studying protein folding mechanisms and for testing of the accuracy of computational models. The suitability of this protein to describe the folding of naturally occurring α/β proteins has recently been challenged based on the observation that the melting transition is very broad, with ill-resolved baselines. Using molecular dynamics simulations with the AMBER protein force field (ff96) coupled with the implicit solvent model (IGB = 5), we shed new light into the nature of this transition and resolve the experimental controversies. We show that the melting transition corresponds to the melting of the protein as a whole, and not solely to the helix-coil transition.

SUBMITTER: Wu C 

PROVIDER: S-EPMC2987907 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature