Equilibrium kinetic network of the villin headpiece in implicit solvent.

ABSTRACT: We applied the single-replica multiple-state transition-interface sampling method to elucidate the equilibrium kinetic network of the 35-residue-fragment (HP-35) villin headpiece in implicit water at room temperature. Starting from the native Protein Data Bank structure, nine (meta)stable states of the system were identified, from which the kinetic network was built by sampling pathways between these states. Application of transition path theory allowed analysis of the (un)folding mechanism. The resulting (un)folding rates agree well with experiments. This work demonstrates that high (un)folding barriers can now be studied.

SUBMITTER: Du W 

PROVIDER: S-EPMC4302211 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature