NER: Geometry and Tensegrity Based Computational Modeling of Birus Assembly Pathways

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PROPOSAL NO: 0404116INSTITUTION: University of FloridaPRINCIPAL INVESTIGATOR: Sitharam , MeeraTITLE: NER: Geometry and Tensegrity Based Computational Modeling ofBirus Assembly PathwaysAbstract:Icosahedral viral shell assembly is an outstanding, poorly understood example of nanoscale self-assembly occuring in nature. Mostly identical protein monomers assemble with high rate of efficacy into a closed icosahedral shell; onset and termination are spontaneous, and assembly is robust, rapid and economical. All of these requirements are both desirable and difficult to achieve when engineering self-assembly at the nanoscale.The proposed project is to develop and test a formal, static model capable of answering focused questions about viral shell assembly pathways, based on geometric constraints and tensegrity concepts. The model development and testing crucially requires and integrates the expertise of the 3 PIs in Computer Science, Structural Biology and Mechanical Enginnering. By carefully defining and focusing on the questions of interest, the model will avoid expensive dynamics and moreover will be fully analyzable and refinable. A tractable and provably accurate computational simulation of the formal model will also be developed. Biochemical and mathematical justifications of the model assumptions and rigorous comparisons to other models will be given. The model will be validated using real data from the structure of 2 specific viruses that contain the minimal number of monomers and are carefully chosen to test various aspects of the model: the predictions of the model will be biochemically verified using known information about the viruses and experiments that are designed to be completed in the project period.