Flexibility of the HIV Vif-A3F binding interaction.

Abstract

Viral infectivity factor (Vif) is an intrinsically disordered protein used by HIV-1 to hijack an immune cell's natural defenses to prevent viral DNA degradation. Vif binds to an E3 ubiquitin ligase complex composed of Elongin B (EloB), Elongin C (EloC), CBF-ß and Cullin 5 (Cul5). In the ligase complex, Vif acts as a substrate binding protein for the APOBEC3 proteins (A3s), allowing for their ubiquitination and subsequent proteasomal degradation. Without A3s, HIV-1 can continue to spread to other cells. A3F is a member of the A3's family and is targeted by Vif for ubiquitination. With the use of the crystal structure of A3F bound to Vif and CBF-ß, molecular dynamic simulations were used to identify the specific residue interactions in the Vif-A3F binding domain that stabilize the conformations sampled by the complex. We are studying how the interface changes over time and how stable it is. Contrasting the interactions between A3F and Vif residues in the crystal from the simulation data can help better understand how Vif is affecting A3F. Through contact maps, interactions between specific A3F and Vif residues were identified. Principle component analysis (PCA) was run, and the preliminary results showed that the VCBC complex with A3F bound was less flexible than the complex by itself. Future work includes analysis of allosteric effects to examine how binding A3F can cause changes in conformation and dynamics of the overall protein complex. Understanding the molecular basis of Vif's affinity towards A3F will allow for the development of treatments that can target and interrupt Vif-A3F binding, rendering Vif and the rest of the virus useless.