Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis

Icosahedral viruses are under a micrometer in diameter, their infectious genome encapsulated by a shell assembled by a multiscale process, starting from an integer multiple of 60 viral capsid or coat protein (VP) monomers. We predict and validate inter-atomic hotspot interactions between VP monomers that are important for the assembly of 3 types of icosahedral viral capsids: Adeno Associated Virus serotype 2 (AAV2) and Minute Virus of Mice (MVM), both T = 1 single stranded DNA viruses, and Bromo Mosaic Virus (BMV), a T = 3 single stranded RNA virus. Experimental validation is by in-vitro, site-directed mutagenesis data found in literature. We combine ab-initio predictions at two scales: at the interface-scale, we predict the importance (cruciality) of an interaction for successful subassembly across each interface between symmetry-related VP monomers; and at the capsid-scale, we predict the cruciality of an interface for successful capsid assembly. At the interface-scale, we measure cruciality by changes in the capsid free-energy landscape partition function when an interaction is removed. The partition function computation uses atlases of interface subassembly landscapes, rapidly generated by a novel geometric method and curated opensource software EASAL (efficient atlasing and search of assembly landscapes). At the capsid-scale, cruciality of an interface for successful assembly of the capsid is based on combinatorial entropy. Our study goes all the way from resource-light, multiscale computational predictions of crucial hotspot inter-atomic interactions to validation using data on site-directed mutagenesis’ effect on capsid assembly. By reliably and rapidly narrowing down target interactions, (no more than 1.5 hours per interface on a laptop with Intel Core i5-2500K @ 3.2 Ghz CPU and 8GB of RAM) our predictions can inform and reduce time-consuming in-vitro and in-vivo experiments, or more computationally intensive in-silico analyses.Author summary: Viruses, found in all classes of living orgaisms, can be beneficial as well as harmful to their hosts. Understanding their mechanism of assembly is critical to understanding how we can inhibit or enhance their life cycle process. Icosahedral viral capsids, as elucidated by Caspar and Klug, are self-assembled from nearly identical viral capsid or coat-protein (VP) monomers spontaneously and rapidly, with high efficacy and accuracy, a process sometimes facilitated by other biomolecules. Understanding virus assembly requires identifying crucial VP-VP hotspot interactions whose removal would disrupt the process. We combine a novel geometric method for rapidly atlasing free energy landscapes with a symmetry-based combinatorial method to give a two-scale prediction of hotspot interactions. We validate the predictions for 3 types of viruses, using in-vitro, site-directed mutagenesis’ disruptive effects on capsid assembly, found in literature, noting that the biophysical assays for AAV2 were carried out by the Mavis Agbandje-Mckenna’s lab contemporaneously with the development of our computational model and prediction. Our predictions are reproducible using our curated opensource software EASAL (efficient atlasing and search of assembly landscapes). To the best of our knowledge, prevailing methods for statistical mechanical prediction of hotspot interactions use a single scale, are knowledge-based, are computationally intensive, or have not been validated by in-vitro site directed mutagenesis results.