Multiscale modeling of mechanisms for viral capsid assembly and polymorphism

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DESCRIPTION (provided by applicant): During the replication of many viruses, hundreds to thousands of protein subunits assemble around the viral nucleic acid to form a protein shell called a capsid. Within their host organism, most viruses form one particular structure with astonishing fidelity; yet, recent experiments demonstrate that capsids can assemble with different sizes and morphologies to accommodate nucleic acids, inorganic nanoparticles, and polyanions with different sizes. This project will use computational models to determine the features of viral proteins and their cargoes that enable assembly to be so precise and yet so adaptable. We develop simplified representations of viral proteins and cargoes that range from rigid spheres to fluctuating polymers to model nucleic acids. With these models we will develop experimentally testable predictions for the mechanisms by which viral proteins dynamically encapsidate these objects, and which factors direct the assembly process towards a particular size and morphology. These coarse-grained models of the overall assembly process will be validated and guided by atomic-resolution simulations that examine the dynamic conformations of viral proteins.