Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

Abstract

We show how to apply the method of temperature-accelerated molecular dynamics (TAMD) in collective variables [Maragliano L, Vanden-Eijnden E (2006) Chem Phys Lett 426:168-175] to sample the conformational space of multidomain proteins in all-atom, explicitly solvated molecular dynamics simulations. The method allows the system to hyperthermally explore the free-energy surface in a set of collective variables computed at the physical temperature. As collective variables, we pick Cartesian coordinates of centers of contiguous subdomains. The method is applied to the GroEL subunit, a 55-kDa, three-domain protein, and HIV-1 gp120. For GroEL, the method induces in about 40 ns conformational changes that recapitulate the t --> r('') transition and are not observed in unaccelerated molecular dynamics: The apical domain is displaced by 30 A, with a twist of 90 degrees relative to the equatorial domain, and the root-mean-squared deviation relative to the r('') conformer is reduced from 13 to 5 A, representing fairly high predictive capability. For gp120, the method predicts both counterrotation of inner and outer domains and disruption of the so-called bridging sheet. In particular, TAMD on gp120 initially in the CD4-bound conformation visits conformations that deviate by 3.6 A from the gp120 conformer in complex with antibody F105, again reflecting good predictive capability. TAMD generates plausible all-atom models of the so-far structurally uncharacterized unliganded conformation of HIV-1 gp120, which may prove useful in the development of inhibitors and immunogens. The fictitious temperature employed also gives a rough estimate of 10 kcal/mol for the free-energy barrier between conformers in both cases.

Fig. 1.

Crystallographic backbone renderings of (A) the GroEL homotetradecamer in (i) apo (41) and (ii) nucleotide/cochaperonin (GroES)-bound (42) states, and (B) HIV-1 gp120 in the CD4/17b bound state (29). In each panel of A, one protomer is rendered depicting the equatorial (blue), intermediate (white), and apical (red) domains. In B, inner domain is blue, outer is red, and the components of the bridging sheet, β2/3 and β20/21, are white and yellow, respectively.

Fig. 2.

(A) All-atom rmsd from MD and TAMD simulations of the GroEL subunit. Uppermost panel depicts whole-subunit rmsd, and subsequent panels depict domain-aligned rmsds for apical, intermediate, and equatorial domains, respectively. Black traces correspond to traditional MD simulation; other traces colored according to fictitious temperature as labeled in the Uppermost panel. (B) ICs used to measure conformation derived from the CVs vs. simulation time. From Top to Bottom are shown the hinge angle between the equatorial and intermediate domains, the hinge angle between intermediate and apical domains, the dihedral describing the twist of the apical domain, and the angle defining the disposition of the nucleotide binding pocket. Color scheme is same as in A. Arrows along the y axis denote IC values in the crystallographic r^′′ state (42).

Fig. 3.

(A) Snapshots of the GroEL subunit from TAMD simulation at . Rightmost panel shows the crystallographic r^′′ state from the same viewpoint. (B) Whole-subunit rmsd relative to the crystallographic r^′′ state (42) for traditional MD simulation and various TAMD simulations. Color scheme follows that of Fig. 2.

Fig. 4.

(A) All-atom rmsd from MD and TAMD simulations of HIV-1 gp120. Uppermost panel depicts the whole-protein rmsd, and subsequent panels depict domain-aligned rmsds for the inner and outer domains, and bridging sheet, respectively. Black traces correspond to the traditional MD simulation and red traces to 4 ns of TAMD at , followed by 4 ns of unaccelerated MD. (B) Cartoon rendering of the HIV-1 gp120 outer domain colorized according to the difference in per-residue rms fluctuation in TAMD vs MD, with warmer colors signifying larger differences. The D-loop (“LD”), V4 loop, and CD4-binding loop are indicated.

Fig. 5.

(A) Counterrotation of inner and outer domains of HIV-1 gp120 in MD (black) and four TAMD replicas vs. simulation time. The Left-hand structure shows the initial orientation of helices α1 and α5. The Right-hand structure corresponds to the conformation at the time indicated by an asterisk. Inner domain is cyan and outer domain is red. Arrows indicate N-to-C direction of each helix. (B) rmsd relative to the F105-bound conformation of HIV-1 gp120 (30) vs. simulation time for standard MD (black) and four TAMD replicas. Left-hand structure shows an alignment of the CD4-bound conformer (inner domain cyan, outer red) and the F105 bound conformer (gray trace). Right-hand structure shows an alignment of a TAMD-generated conformational with minimal rmsd relative to the F105 conformer.