Selective Nucleation, Polyproteins, and HIV-1

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NONTECHNICAL SUMMARYThis award supports theoretical research and education to advance understanding of the physics of proteins that are key for the assembly of virus-like particles. The search for new antiviral drugs that are effective against the human immunodeficiency viruses (HIV), which causes AIDS, focuses on ways of obstructing viral proteins that have no counterparts in normal cells. This strategy will likely minimize negative side effects. The key structural protein of HIV, known as "Gag", is an HIV protein with no counterpart in normal cells and is one of the targets for this search. Despite many years of intense research, key aspects of the way Gag functions are not understood. Gag is not only a structural protein, it also coordinates the assembly process of the HIV virus, starting with a search for HIV genetic material inside infected host cells. The large life-science literature on this topic shows that the biophysical principles of HIV assembly initiation are fundamentally different from those of "standard" viruses. Experimental studies also leave no doubt that physical interactions among Gag proteins play a key role during the selection of the HIV genetic material, yet experimental studies of Gag-Gag interactions at the level of individual proteins are very seriously hampered by the problem of protein-protein aggregation. Gag itself is more complex than proteins of analogous function in many other viruses, suggesting that the study of Gag may lead to new physical principles and insights into viral assembly. The team will carry out computer simulations of the interaction of the Gag protein with HIV genetic materials on the largest super-computers currently available. By developing a large-scale numerical simulation model of the interaction of just two or three Gag proteins with each other and with HIV genetic material, the aggregation problem is circumvented. The detailed statistical physics analysis of the dynamics and interactions of the Gag proteins, as obtained from numerical simulations, provides science with a direct route to explore the HIV genetic selection mechanism. The research program will be a training ground for young physical scientists interested in working in biological physics that has important applications for public health. A sound understanding of the fundamental limitations imposed by physics on viruses in general will help young scientists with careers in the pharmaceutical industry. A collaborative program with a community college and Cal State University, both of which serve under-represented minority students in the LA area, will provide students with the opportunity to obtain research experience that would further their career. TECHNICAL SUMMARYThis award supports theoretical and computational research and education to advance understanding of the physics of proteins that are key to the assembly of virus like particles. The team aims to carry out combined molecular dynamics (MD) and statistical mechanics studies of the very large poly-protein Gag, the main capsid protein of HIV-1. Gag is the main component of the capsid that surrounds the RNA genome molecule after formation of the virus. Originally the poly-protein was thought to play only a structural role with the different parts of Gag acting independently. More recent imaging experiments have revealed that Gag functions as an integrated unit with complex functional abilities. Its ability to select a small number of viral RNA from a large number of RNA molecules inside an infected cell, appears to rely on cooperative interactions between the domain components of Gag. Despite the large literature on the Gag protein, a physics-based model that can address the many puzzles surrounding Gag is lacking. For example, Gag can select viral RNA efficiently without a measurable free energy difference between a virus that packs viral RNA versus a virus that packs non-viral RNA. The PI aims to address this and other challenges, and investigate a statistical mechanical framework in the form of the selective nucleation hypothesis. In the selective nucleation hypothesis, long-range cooperative interactions that involve binding of RNA to Gag modulates the activation free energy barrier for the nucleation and growth of Gag clusters. The team plans to use MD simulations of Gag and Gag-Gag interactions to inform statistical physics models of nucleation and growth. The team will test hypotheses about the physics of Gag against the outcomes of MD simulations and against experiments to be carried out at The Ohio State University.The selective nucleation hypothesis depends on the sensitivity of the formation rate of the critical nucleus of a first-order transition to small changes in the activation free energy barrier in order to carry out a selection process. The statistical physics of this hypothesis is akin to that of kinetic proofreading as encountered in protein transcription and synthesis. If this hypothesis can be confirmed, then kinetic proofreading would be a unifying principle relating viral assembly to protein transcription and synthesis. Confirmation of a second hypothesis, namely that entropic allosteric signal transmission could be the principle that allows long-distance communication between the sub-components of Gag, would lead to its extension to other poly-proteins as well as to the operation of other small clusters of weakly coupled proteins, such as transcription initiation complexes. Showing that the combination of large-scale MD simulations with the principles of statistical physics can provide important insights into how a macromolecular complex as large as Gag functions could help stimulate the extension of biological physics to structurally complex systems.The research program will be a training ground for young physical scientists interested in working in biological physics that has important applications for public health. A sound understanding of the fundamental limitations imposed by physics on viruses in general will help young scientists with careers in the pharmaceutical industry. A collaborative program with a community college and Cal State University, both of which serve under-represented minority students in the LA area, will provide students with the opportunity to obtain research experience that would further their career.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.