Multiscale computer simulation of the immature HIV-1 virion

Abstract

Multiscale computer simulations, employing a combination of experimental data and coarse-graining methods, are used to explore the structure of the immature HIV-1 virion. A coarse-grained (CG) representation is developed for the virion membrane shell and Gag polypeptides using molecular level information. Building on the results from electron cryotomography experiments, the simulations under certain conditions reveal the existence of an incomplete p6 hexameric lattice formed from hexameric bundles of the Gag CA domains. In particular, the formation and stability of the immature Gag lattice at the CG level requires enhanced interfacial interactions of the CA protein C-terminal domains (CTDs). An exact mapping of the CG representation back to the molecular level then allows for detailed atomistic molecular dynamics studies to confirm the existence of these enhanced CA(CTD) interactions and to probe their possible origin. The multiscale simulations further provide insight into potential CA(CTD) mutations that may disrupt or modify the Gag immature lattice assembly process in the immature HIV-1 virion.

Figure 1

A schematic of the Gag/membrane CG model. (Left panel) Domain decomposition of the Gag and PS/PC membrane. (Small spheres) Linker sites. Detailed atomic-level information was used to parameterize the MA, CA, and NC/RNA domains. Close-contact CG sites 34, 35, 40, 42, 43, and 44 in the CA_CTD domain are highlighted. (Right panel) Initial virion structure; 2034 Gags, each in bundles of six, were replicated in a 125-nm diameter virion. The initial p6 hexagonal lattice spacing was 10 nm, with the Gags relatively uniformly spaced.

Figure 2

Final CG simulation snapshots of shells of the enhanced (left column) and nonenhanced (right column) virion simulations at 273 K. In descending order from the top of the image the different domains are shown, lipids, MA, CA, and then the SP1/NC and RNA site. Only the CA domain with enhanced interactions exhibits p6 hexagonal order.

Figure 3

CG simulation snapshots of the CA domain p6 hexagonal order: (A) from 273 K WT simulation, (B) WT result at 308 K, and (C) K158A/D197A double mutant at 308 K. Transparent blue (darker) regions depict the CA_NTD domain while yellow (lighter) regions correspond to the CA_CTD domain. The predominance of yellow (lighter) regions in panel C is due to the CA_NTD domains occupying the interstitial space between the hexameric bundles in the double mutant.

Figure 4

Potential of mean force (PMF) U(r) for the residues from all-atom MD simulations that correspond to the enhanced interaction CG sites. The black curve is for the WT at 273 K (with a molecular snapshot in the lower-right of the image) with the shaded error bars giving the fluctuations due to the three different constraints (free, N-terminal α-carbon frozen, N- and C-terminal α-carbon frozen). The PMF at 308 K was well within the error bars. The shaded (red online) curve is for the K158A/D197A double mutant at 308 K (a similar PMF was found at 273 K) with a snapshot in the upper left. In each of the molecular structure snapshots, the residues corresponding to CG sites 35 and 42 are highlighted. The inner ring connects CG site 42 on adjacent CA domains, giving a qualitative estimate of the size of the hexamer bundle pore in the CA_NTD domain. The line between CG sites 35 and 42 shows the interaction between CC sites on adjacent domains. In the K158A/D197A double mutant, the mutated residues are shown by the dots (D197A dark shaded, purple online and K158A light shaded, cyan online).