title: Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits.
abstract: Traditional coarse-graining based on a reduced number of interaction sites often entails a significant sacrifice of chemical accuracy. As an alternative, we present a method for simulating large systems composed of interacting macromolecules using an energy tabulation strategy previously devised for small rigid molecules or molecular fragments [S. Lettieri and D. M. Zuckerman, J. Comput. Chem. 33, 268-275 (2012); J. Spiriti and D. M. Zuckerman, J. Chem. Theory Comput. 10, 5161-5177 (2014)]. We treat proteins as rigid and construct distance and orientation-dependent tables of the interaction energy between them. Arbitrarily detailed interactions may be incorporated into the tables, but as a proof-of-principle, we tabulate a simple α-carbon Gō-like model for interactions between dimeric subunits of the hepatitis B viral capsid. This model is significantly more structurally realistic than previous models used in capsid assembly studies. We are able to increase the speed of Monte Carlo simulations by a factor of up to 6700 compared to simulations without tables, with only minimal further loss in accuracy. To obtain further enhancement of sampling, we combine tabulation with the weighted ensemble (WE) method, in which multiple parallel simulations are occasionally replicated or pruned in order to sample targeted regions of a reaction coordinate space. In the initial study reported here, WE is able to yield pathways of the final ∼25% of the assembly process.
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15260, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Spiriti
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15260, USA.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Zuckerman
mesh_terms: D002213:Capsid / Q000737:chemistry*; D036022:Capsid Proteins / Q000737:chemistry*; D006515:Hepatitis B virus / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D021122:Protein Subunits / Q000737:chemistry*
chemical_list: D036022:Capsid Proteins; D021122:Protein Subunits