Computational Insights into Assembly, Budding, and Maturation during HIV-1 Replication

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PROJECT SUMMARY Human immunodeficiency virus type 1 (HIV-1) is a virus that has infected and led to the deaths of millions of people since its emergence several decades ago. While modern anti-retroviral treatments (ART) have made the infection manageable for patients, negative side effects, the risk of drug resistance, and the aggregate cost due to life-long usage inspire the need for new, effective treatment strategies. One viable strategy is to disrupt the intrinsically efficient replication cycle of HIV-1. A fundamental understanding of the molecular mechanisms that regulate replication would advance this mission by revealing novel targets and new approaches for ARTs. This proposal focuses on the late stages of HIV-1 replication, which encompasses the assembly of a viral RNA dimer and other constituents, budding of the packaged components (i.e., immature virion), and activation of the virion through maturation. The group specific antigen (Gag) polyprotein is the main structural constituent, which appears to contribute important functionality during this process. For example, Gag self-assemble into an incomplete, asymmetric, and contiguous hexameric lattice; this immature lattice is found along the inner surface of the released immature virion. Proteolytic cleavage of Gag then triggers a morphological change in which the capsid protein and RNA are condensed into a fullerene core (i.e., mature lattice). Most recently, conformational changes throughout Gag have been hypothesized to act as molecular switches that act as regulatory signals. However, specific details have been difficult to experimentally characterize owing to the pleomorphic nature of virions and their associated transition states. I propose to study the molecular structure-function relationships that regulate HIV-1 assembly, budding, and maturation using a systematic, multiscale computer simulation framework. The goals of this project are to (1) predict the structure of native-like immature lattices with molecular resolution, (2) uncover molecular switches throughout Gag that regulate immature lattice assembly, and (3) determine the dynamic morphological changes during viral maturation. I will first develop a coarse-grained model of Gag to study the structure and assembly mechanisms of the immature lattice at the membrane interface in the presence of RNA. Subsequently, these coarse-grained simulations will systematically guide atomistic simulations of key protein interfaces to identify the triggering mechanisms and importance of potential molecular switches, including a noted transition of the spacer peptide 1 (SP1) domain from random coil to alpha helix for Gag oligomerization. Finally, a novel reactive coarse-grained model will be developed to identify disassembly pathways during maturation. During all phases of this project, experimentally tractable predictions will be made and tested through my collaboration with two leading experimentalists, which will enable iterative refinements to the developed models. The insights from this study will have a broad impact on virology, macromolecular assembly, and molecular biophysics.