Structural Insights into the Two Sequential Folding Transition States of the PB1 Domain of NBR1 from Phi Value Analysis and Biased Molecular Dynamics Simulations

摘要

The PB1 domain of NBR1 folds via a single pathway mechanism involving two sequential energy barriers separated by a high-energy intermediate. The structural ensemble representing each of the two transition states (TS1 and TS2) has been calculated using experimental Phi values and biased molecular dynamics simulations. Both TS1 and TS2 represent compact states (beta(TS1) = 0.71, and beta(TS2) = 0.93) but are defined by quite different distributions of Phi values, degrees of structural heterogeneity, and nativelike secondary structure. TS1 forms a heterogeneous ensemble of dynamic structures, representing a global collapse of the polypeptide chain around a set of weak nativelike contacts. In contrast, TS2 has a high proportion of nativelike secondary structure, which is reflected in an extensive distribution of high Phi values. Two snapshots along the folding pathway of the PB1 domain reveal insights into the malleability, the solvent accessibility, and the timing of nativelike core packing that stabilizes the folded state.