Viral Capsid Assembly: A Quantified Uncertainty Approach

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Nathan ClementC Bajaj

Abstract

Most of the existing research in assembly pathway prediction/analysis of viral capsids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This assumption does not take into account the conformational changes of the constituent proteins as well as minor changes to the binding interfaces that continue throughout the assembly process until stabilization. This article presents a statistical-ensemble-based approach that samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations. Further, instead of using larger capsomers (trimers, pentamers) as building blocks, we allow all possible subassemblies to bind in all possible combinations. We represent the resulting assembly graph in two different ways: First, we use the Wilcoxon signed-rank measure to compare the distributions of binding free energy computed on the sampled conformations to predict likely pathways. Second, we represent chemical equilibrium aspects of the transitions as a Bayesian Factor graph where both associations and dissociations are modeled based on concentr...Continue Reading

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Citations

Jun 10, 2018·BMC Systems Biology·Marcus Thomas, Russell Schwartz
Feb 11, 2020·Computer Methods in Applied Mechanics and Engineering·Huan LeiNathan A Baker

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Software Mentioned

HingeProt
MolEnergy
PMEOPA
DeclareMathSizes

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