Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

Abstract

High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.

Fig. 1.

The best folded structure (red) from REMD with 0.46 Å C_α-rmsd (1.59 Å heavy-atom rmsd) compared with the x-ray crystal structure of HP35 (purple, Protein Data Bank ID code 1YRF). Both terminal residues were excluded from rmsd calculations.

Fig. 2.

The folding population landscapes of HP35 from REMD and CMD at 300 K, 340 K, and 360 K. The axes are the C_α-rmsds of segments A and B.

Fig. 3.

The folding free-energy landscape of HP35 at 300 K from REMD. Representative structures of the four states are shown on the figure, including the folded state (F), denatured state (D), major intermediate state (I₁), and minor intermediate state (I₂).

Fig. 4.

Thermodynamic properties obtained from REMD simulations. (Top) Free-energy profiles of HP35 from REMD at 300 K based on C_α-rmsd of the two segments A and B. (Middle) Population of the denatured state as a function of temperature. (Bottom) Heat capacity as a function of temperature. The first 50 ns of the simulation trajectories were excluded from the analysis. The error bars of the heat capacity were obtained by dividing the trajectories into two blocks (50–125 ns and 125–200 ns).

Fig. 5.

The folding population landscape of HP35 projected to the first two principle components. Representative structures of the three highly populated regions are shown on the right.

Fig. 6.

C_α-rmsd (Left) and population (Right) of the no.1 clusters at different temperatures. The first 50 ns of the simulation trajectories were excluded from the clustering analysis. Hierarchical clustering scheme was adopted and pairwise C_α-rmsd of 2.5 Å was chosen as the cutoff for clustering. The clusters were ranked by the populations at the specific temperature.