MOLECULAR DYNAMICS SIMULATIONS OF AN ENTIRE HIV VIRION*

The HIV viral particle contains all the necessary components to infect a human cell. The so-called virion is made of glycoproteins, lipids, the Gag polyprotein, viral RNA and other essential proteins. After budding, several biological process occur inside the virion, including a major re-arrangement of the virion's cargo commonly referred as maturation. Here, we present the steps performed towards the construction of an atomistic model of a mature and immature virion. Our model includes all major components, including glycosylated proteins, twenty-four lipid types and capsid protein. Our effort constitutes one of the major efforts to construct a realistic HIV virion at atomic resolution. In addition, we discuss the techniques developed to prepare the system and the steps required to simulate and analyze our atomistic HIV virion model, which contains over 800 million atoms.