Synergy between NMR, cryo-EM and large-scale MD simulations - structure and dynamics of the HIV capsid and its cellular interactors
HIV and other retroviruses use a Trojan horse style of infection, taking advantage of a cloak that shields its genome till the time is ripe to open the shield. Once HIV gets inside the cell, it takes over the cellular machinery, turning it into a factory for its own reproduction. This entails a derailment of the normal host defense pathways, rendering HIV resistant to cell-mediated destruction responses. In mature HIV-1 particles a conical-shaped capsid core encloses the viral RNA genome. Using the high-resolution NMR structure of the CA C-terminal domain (CTD) dimer and in particular the unique interface identified, it was possible to reconstruct a model for a tubular assembly of CA protein that fit extremely well into the cryoEM density map. Modeling of the hexamer-of-hexamer and pentamer-of-hexamer elements of spheroidal capsids and refinement of the cryoEM/ET model by large-scale MD simulation permitted the construction of a realistic all-atom model for the entire capsid, based on the 3D authentic core structure. A novel CTD-CTD interface at the local three-fold axis in the cryoEM map was confirmed by mutagenesis to be essential for function. Furthermore, in assembled wild-type CA, the CypA loop exhibits unprecedented motions on the nanosecond to microsecond timescales, which are significantly attenuated upon CypA binding and in the A92E and G94D CypA escape mutants. This suggests that CypA loop dynamics is a determining factor in HIV-1’s escape from CypA dependence.