Exploring Viral Maturation Pathways Using Normal Mode Flexible Fitting Software
Rizzolo, Skylar M.
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The goal for this research project was to refactor a Normal Mode Flexible Fitting (NMFF) software package for use in research investigating the most energy efficient pathway between the native and mature states of a capsid, and to observe how a virus’s maturation pathway varies by a virus’s T-number. This paper details both the underlying physics of viral maturation and the normal mode analysis algorithm in order to get a better knowledge of the inter-workings of the software and its architecture and use it to perform normal mode calculations on various capsids. Along with finding maturation pathways, the software was also utilized to show how normal mode behavior can differ between all atom and Ca only representations of a capsid, thanks to a previous student’s research involving all atom models of capsids. Finally, a supplemental script was written to match, sort and extract the desired output values (the eigenmodes and their corresponding eigenvalues describing normal mode behavior) to make the output more readable for quicker and easier data analysis. Although this project itself doesn’t reveal anything earth-shattering about virus behavior, further research on how viruses undergo conformational changes could have profound impacts on the fields of chemistry, biophysics and medicine --yielding better methods for drug delivery and thus better medication-- or possibly even the answers to much larger existential questions, such as the origin of life itself.