Atomistic Characterization of the HIV Capsid from Molecular Dynamics Simulations

Abstract

The HIV capsid is large, containing about 1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure. The large size and lack of symmetry pose a huge challenge to studying the chemical details of the HIV capsid. Simulations of 64 million atoms for over 1 micro­ second allow us to conduct a comprehensive study of the physical properties of the entire HIV capsid including electrostatic potential, all­atom normal modes, as well as the effects of the solvent (ions and water) on the capsid. The results from the simulations reveal critical details of the capsid protein with important implications for assembly, uncoating and nuclear import.