Uncertainty Quantified Computational Analysis of the Energetics of Virus Capsid Assembly

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 paper presents a statistical-ensemble based approach which samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations. Furthermore, 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 concentrations and the binding free energies. We applied these protocols on the feline panleukopenia virus and the Nudaurelia capensis virus. Results from these experiments showed significant departure from those one would obtain if only the static configurations of the proteins were considered. Hence, we establish the importance of an uncertainty-aware protocol for pathway analysis, and provide a statistical framework as an important first step towards assembly pathway prediction with high statistical confidence.