Determination of the folding transition states of barnase by using PhiI-value-restrained simulations validated by double mutant PhiIJ-values.

ABSTRACT: The protein barnase folds from the denatured state into its native conformation via a high-energy intermediate. Using PhiI-values determined experimentally from single-point mutations as restraints in all-atom molecular dynamics simulations, we have determined ensembles of structures corresponding to the transition states for the formation of the folding intermediate and its conversion into the native state. We have also introduced a stringent validation of the approach used to calculate such structures by predicting interaction PhiIJ-values determined experimentally from a series of double-mutant cycles. The ensembles that we have obtained illustrate the heterogeneity in the nucleation-condensation process by which barnase folds. Obligatory steps of this process include the sequential for

SUBMITTER: Salvatella X 

PROVIDER: S-EPMC1194897 | biostudies-literature | 2005 Aug

REPOSITORIES: biostudies-literature