Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses

Abstract

Quaternary structure polymorphism found in quasiequivalent virus capsids provides a static framework for studying the dynamics of protein interactions. The same protein subunits are found in different structural environments within these particles, and in some cases, the molecular switching required for the polymorphic quaternary interactions is obvious from high-resolution crystallographic studies. Employing atomic resolution structures, molecular mechanics, and continuum electrostatic methods, we have computed association energies for unique subunit interfaces of three icosahedral viruses, black beetle virus, southern bean virus, and human rhinovirus 14. To quantify the chemical determinants of quasiequivalence, the energetic contributions of individual residues forming quasiequivalent interfaces were calculated and compared. The potential significance of the differences in stabilities at quasiequivalent interfaces was then explored with the combinatorial assembly approach. The analysis shows that the unique association energies computed for each virus serve as a sensitive basis set that may determine distinct intermediates and pathways of virus capsid assembly. The pathways for the quasiequivalent viruses displayed isoenergetic oligomers at specific points, suggesting that these may determine the quaternary structure polymorphism required for the assembly of a quasiequivalent particle.