Structural Disorder in the HIV-1 Vif Protein and Interaction-Dependent Gain of Structure

Tali      H. Reingewertz; Deborah      E. Shalev; Assaf      Friedler

Abstract

The HIV-1 Vif protein (192 residues) is required for HIV-1 infection of many target cells. Vif overcomes the anti-viral cellular defense by antagonizing the cellular cytosine deaminase APOBEC-3G through impairing APOBEC-3G production, inhibiting its enzymatic activity and targeting it for degradation. Vif interacts with several viral and cellular molecules, particularly via its C-terminal domain (residues 100-192). The structure of full-length Vif has not yet been determined. The structure of Vif and its domains was studied using computational and experimental methods. Computational predictions resulted in two suggested homology models for the full length protein. Experimental studies have shown that the Vif C-terminal domain is mainly unstructured. Residues 108-139 have mainly random coil conformation in the unbound state. This region includes an HCCH Zn2+-binding motif that also mediates Vif binding to Cul5, a protein in the E3 ubiquitin ligase complex. The C-terminal domain residues 141-192, which mediate interactions with both ElonginC and Cul5, are intrinsically disordered. This region also includes several phosphorylation sites and regions associated with the ability of Vif to undergo self-oligomerization. The unstructured nature of these regions enables them to interact with several ligands, and probably adopt various conformations as is typical for intrinsically disordered proteins. This was demonstrated by a conformational change induced by Zn2+ binding to the HCCH motif and a conformational change that the C-terminal domain underwent in the presence of dodecylphosphocholine. The only available crystal structure of Vif includes residues 140-155, which are helical when bound to the ElonginBC complex. Overall, empirical structures, predictions and other experimental data for Vif did not always indicate the same degree or type of structure for any given region. This ambiguity is likely to be the tenet of structurally unfolded proteins, which have the propensity to adopt a multitude of biologically relevant and active conformations.

Keywords: HIV-1, intrinsically disordered proteins, Vif, Zinc finger, peptides, circular dichroism, NMR, disorder prediction, APOBEC-3G