Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions

Abstract

For HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However, only 5% of the Gag polyproteins, termed Gag-Pol, carry this protease domain, and they are embedded within the structured lattice. The mechanism of Gag-Pol dimerization is unknown. Here, we use spatial stochastic computer simulations of the immature Gag lattice as derived from experimental structures, showing that dynamics of the lattice on the membrane is unavoidable due to the missing 1/3 of the spherical protein coat. These dynamics allow for Gag-Pol molecules carrying the protease domains to detach and reattach at new places within the lattice. Surprisingly, dimerization timescales of minutes or less are achievable for realistic binding energies and rates despite retaining most of the large-scale lattice structure. We derive a formula allowing extrapolation of timescales as a function of interaction free energy and binding rate, thus predicting how additional stabilization of the lattice would impact dimerization times. We further show that during assembly, dimerization of Gag-Pol is highly likely and therefore must be actively suppressed to prevent early activation. By direct comparison to recent biochemical measurements within budded virions, we find that only moderately stable hexamer contacts (-12kBT<∆G<-8kBT) retain both the dynamics and lattice structures that are consistent with experiment. These dynamics are likely essential for proper maturation, and our models quantify and predict lattice dynamics and protease dimerization timescales that define a key step in understanding formation of infectious viruses.

TomoNet: A streamlined cryoET software pipeline with automatic particle picking on flexible lattices

“…All VLP lattices with various sizes and shapes were captured even with irregular shapes (Figure 7e and Supplementary Movie 2), demonstrated TomoNet’s particle picking ability on flexible lattices. Lattice defects on each VLP were also identified consistent with previous studies 48 , enhancing the understanding of lattice assembly mechanisms 49 .…”

“…Lattice defects on each VLP were also identified consistent with previous studies 48 , enhancing the understanding of lattice assembly mechanisms 49 .…”

TomoNet: A streamlined cryogenic electron tomography software pipeline with automatic particle picking on flexible lattices

“…Hui Wang et al shapes were captured even with irregular shapes (Figure 7e and Supplementary Material S2), demonstrating TomoNet's particle-picking ability on flexible lattices. Lattice defects on each VLP were also identified consistent with previous studies, 52 enhancing the understanding of lattice assembly mechanisms. 53…”