APOBEC3F‐Vif Binding Interface Elucidated by Multiple Experimental Approaches

Background APOBEC3 family DNA cytosine deaminases provide overlapping defenses against pathogen infections. However, most viruses have elaborate evasion mechanisms such as the HIV‐1 Vif protein, which subverts cellular CBF‐beta and scaffolds the assembly of a polyubiquitin ligase complex to degrade these enzymes. Despite advances in APOBEC3 and Vif biology, a full understanding of this direct host‐pathogen conflict has been elusive. Methods We combine virus adaptation, structural, and computational studies to interrogate the APOBEC3F‐Vif interface and build a robust model for this vital host‐pathogen interaction. Results First, new structures of the Vif binding domain of APOBEC3F were solved by x‐ray crystallography. Second, a recurring compensatory amino acid substitution in HIV‐1 Vif from virus adaptation experiments provided an initial docking constraint, and microsecond molecular dynamics simulations were used to optimize interface contacts. Third, single‐cycle and spreading virus infectivity experiments were used to validate a long‐lasting electrostatic interaction predicted by molecular dynamics simulations to occur between APOBEC3F E289 and HIV‐1 Vif R15. Conclusions Our studies have yielded a comprehensive structural model for the APOBEC3F‐Vif interaction, which explains most prior genetic data. Taken together with the dynamic nature of this host‐pathogen interaction, our data suggest a “wobble model” to explain how HIV‐1 Vif has evolved to bind different APOBEC3 enzymes and, more generally, explain how pathogens may evolve to escape innate host defenses ( i.e ., a molecular explanation for the Red Queen hypothesis). Our studies also suggest that the APOBEC‐Vif interface may be a less favorable target for new antiviral drug development in comparison to other heterologous surfaces of the Vif‐CBF‐beta ubiquitin ligase complex.