In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts

Abstract

Tetherin, an interferon-induced host protein encoded by the bone marrow stromal antigen 2 (BST2/CD317/HM1.24) gene, is involved in obstructing the release of many retroviruses and other enveloped viruses by cross-linking the budding virus particles to the cell surface. This activity is antagonized in the case of human immunodeficiency virus (HIV)-1 wherein its accessory protein Viral Protein U (Vpu) interacts with tetherin, causing its downregulation from the cell surface. Vpu and tetherin connect through their transmembrane (TM) domains, culminating into events leading to tetherin degradation by recruitment of β-TrCP2. However, mutations in the TM domains of both proteins are reported to act as a resistance mechanism to Vpu countermeasure impacting tetherin's sensitivity towards Vpu but retaining its antiviral activity. Our study illustrates the binding aspects of blood-derived, brain-derived, and consensus HIV-1 Vpu with tetherin through protein-protein docking. The analysis of the bound complexes confirms the blood-derived Vpu-tetherin complex to have the best binding affinity as compared to other two. The mutations in tetherin and Vpu are devised computationally and are subjected to protein-protein interactions. The complexes are tested for their binding affinities, residue connections, hydrophobic forces, and, finally, the effect of mutation on their interactions. The single point mutations in tetherin at positions L23Y, L24T, and P40T, and triple mutations at {L22S, F44Y, L37I} and {L23T, L37T, T45I}, while single point mutations in Vpu at positions A19H and W23Y and triplet of mutations at {V10K, A11L, A19T}, {V14T, I18T, I26S}, and {A11T, V14L, A15T} have revealed no polar contacts with minimal hydrophobic interactions between Vpu and tetherin, resulting in reduced binding affinity. Additionally, we have explored the aggregation potential of tetherin and its association with the brain-derived Vpu protein. This work is a possible step toward an understanding of Vpu-tetherin interactions.

Keywords: HIV-1 Vpu; aggregation potential; tetherin; transmembrane interactions.

Figure 1

Representation of identity (*) and conserved substitutions (:) between human immunodeficiency virus (HIV)-1 Viral Protein U (Vpu) sequences from blood and brain isolates and the consensus Vpu sequence.

Figure 2

The hydrophobic interactions within 5 Å for wild-type blood-derived Vpu–tetherin complex, wild-type brain-derived Vpu–tetherin complex, and wild-type consensus Vpu–tetherin complex.

Figure 3

(A) Blood-derived Vpu–tetherin complex with interfacial contact residues of Vpu in blue, interfacial residues of tetherin in red, and non-contact residues in grey. (B) Residues forming hydrophobic interactions (labeled in yellow) between blood-derived Vpu and tetherin.

Figure 4

(A) Brain-derived Vpu–tetherin complex with interfacial contact residues of Vpu in blue, interfacial residues of tetherin in red, and non-contact residues in grey. (B) Residues forming hydrophobic interactions (labeled in yellow) between brain-derived Vpu and tetherin.

Figure 5

(A) Consensus Vpu–tetherin complex with interfacial contact residues of Vpu in blue, interfacial residues of tetherin red, and non-contact residues in grey. (B) Residues forming hydrophobic interactions (labeled in yellow) between consensus Vpu and tetherin.

Figure 6

The hydrophobic interactions within 5 Å for tetherin mutants having reduced binding affinities and minimal hydrophobic connections.

Figure 7

The hydrophobic interactions within 5 Å for Vpu mutants having reduced binding affinities and minimal hydrophobic connections.

Figure 8

(A) Pairing results in PASTA2.0 for tetherin. (B) Aggregation and disorder profile of tetherin-derived in PASTA2.0.

Figure 9

Beta aggregation and Helix aggregation plots generated in TANGO highlighting regions 22—38 and 168—179 to have high aggregation probability.