HIV protein sequence hotspots for crosstalk with host hub proteins

Abstract

HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2). We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

Figure 1. Radar graphs visualizing predicted motifs positions on NEF and TAT.

The radar graph illustrating the computationally predicted motifs on Nef for binding to SRC (1a, 1c) and Tat for binding to EP300 (1b, 1d) at p value cut offs of 0.005 for 1a and 1b and 0.01 for 1c and 1d. The radial distance indicates amino acid residue number on the HIV protein sequence starting from the N terminal. Edges of hotspots are marked with orange lines.

Figure 2. Hotspots on HIV protein sequences.

Amino acid sequence positions of motif hotspots are shown on the horizontal axis. The vertical axis identifies the number of viral protein sequences in the alignment. Color intensity is proportional to the number of hub proteins with enriched hotspot motifs among its immediate neighbors. Regions highlighted in this figure have at least two different hub proteins associated with them.

Figure 3. Heat map for common neighbors among hub proteins considered in the study.

The number of common immediate neighbors between two hub proteins is show elements of a square matrix. Color intensity is proportional to the number of protein neighbors common to two hub proteins.

Figure 4. Hotspots on HIV protein structures.

Hotspot regions highlighted in orange on Tat (a), Rev (b), and Nef (c) proteins. PDB structures 1TBC , 2X7L , and 2NEF were used respectively. Numbers on the structures reflect the start and stop positions on the actual HIV protein sequence. Molecular graphics images were produced using the UCSF Chimera package .