Common structural transitions in explicit-solvent simulations of villin headpiece folding

Abstract

Molecular dynamics simulations of protein folding can provide very high-resolution data on the folding process; however, due to computational challenges most studies of protein folding have been limited to small peptides, or made use of approximations such as Gō potentials or implicit solvent models. We have performed a set of molecular dynamics simulations totaling >50 micros on the villin headpiece subdomain, one of the most stable and fastest-folding naturally occurring proteins, in explicit solvent. We find that the wild-type villin headpiece reliably folds to a native conformation on timescales similar to experimentally observed folding, but that a fast folding double-norleucine mutant shows significantly more heterogeneous behavior. Along with other recent simulation studies, we note the occurrence of nonnative structures intermediates, which may yield a nativelike signal in the fluorescence measurements typically used to study villin folding. Based on the wild-type simulations, we propose alternative approaches to measure the formation of the native state.

Figure 1

Progress of the WT folding simulations. (a) C_α-RMSD and Q_res relative to the 1YRF crystal structure; running averages over 30 ns are shown in red, and the range defined by the mean ± two standard deviations from simulation WT-NAT as blue bars. (b) Secondary structure throughout the WT folding trajectories. The secondary structure of the crystal structure is shown at left.

Figure 2

C_α-RMSD to the crystal structure throughout the NLE folding trajectories. The mean ± 2 standard deviations of values from simulation NLE-NAT are shown as dotted lines, and an average over 30 ns is shown as a red line.

Figure 3

Proposed experimental metrics for villin folding. (a) Clusters 1 and 2 from simulation WT-FOLD1. Hydrophobic, polar, basic, and acidic side chains are shown in white, green, blue, and red, respectively. (b) Density plot showing the formation of the D44-K48 salt bridges throughout the WT simulations; for each 6-ns segment, the fraction of frames with a formed salt bridge (<3.5 Å heavy atom distance) is shown. Dashed cyan, yellow, and magenta lines indicate the opening transition, formation of native structure, and final frame, respectively, in each trajectory. (c) Solvent-exposed surface area of the side chain of F58, averaged over 60 ns.