Modelling nucleic acid compaction inside viruses and self-assembly of viral capsids

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Some double-stranded DNA viruses pack their genomes under pressures of up to ~50 atm and sustain external deformations better than hard plastics. This project focuses on theoretical aspects of DNA and RNA compaction inside viral shells and on physical-chemical properties of capsid self-assembly, both from static and dynamical perspective. In the static part, the emphasis is on electrostatic effects that dominate the close-range DNA-DNA forces and are known to significantly contribute to capsomer-capsomer association energies for a number of viruses. State-of-the-art theories of DNA-DNA electrostatic interactions and polyelectrolyte adsorption onto oppositely charged surfaces will be implemented to describe the compaction of semiflexible DNA and flexible RNA chains inside the capsids. The detailed molecular structures of viral capsid proteins from the Protein and Viper Data Banks are going to be analyzed in order to rationalize the inter-capsomer interactions and their implications for the shell shape and elastic properties of the capsids. The dynamical part of the project is focused on unraveling the implications of crowded molecular environments of the cell cytoplasm on the kinetics of the capsid self-assembly process. Here, the innovative theories of generalized diffusional processes under confinement are going to be implemented. This proposal will lead to a better understanding of physical mechanisms behind DNA/RNA packing in confined geometries inside viruses and of driving forces for capsid self-assembly by relating the fine structural details of nucleic acids and viral capsomer proteins on the nano-scale to measurable macroscopic properties of entire viruses.