HIV Protein-Interaction Database

Documenting the interaction of human immunodeficiency virus type 1 (HIV-1) proteins with those of the host cell is crucial to our understanding of the processes of HIV-1 replication and pathogenesis. To meet this need, the Division of Acquired Immunodeficiency Syndrome (DAIDS) of the National Institute of Allergy and Infectious Diseases (NIAID), in collaboration with the Southern Research Institute and NCBI, has begun compiling a comprehensive “HIV Protein-Interaction Database” to provide a concise summary of documented interactions between HIV-1 proteins and host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV or AIDS. For each documented protein-protein interaction the following information is collected, if available:

Protein Reference Sequence accession numbers.
Entrez Gene ID numbers.
The Amino acids from each protein that are known to be involved in the interaction.
A Brief description of the protein-protein interaction.
Keywords to support searching for interactions.
PubMed identification numbers for all journal articles describing the interaction.

The HIV Protein-Interaction Database may be searched through an online interface at:

www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/index.html

Clicking on a link for an HIV-1 protein in the “Reports and downloads” section of the page displays its interaction report.

Interaction reports for HIV-1 proteins are displayed in a 4-column format beginning from the left with the HIV-1 protein name, linked to the LocusLink report for the gene, and continuing with phrases taken from the literature indicating, in the second column, a type of interaction, and, in the third column, a description of the interaction partner. The fourth column displays links to LocusLink and Entrez Gene reports for the interaction partner. Interaction reports can be filtered in a number of ways by phrases appearing in the reports using pull down phrase lists. Full or filtered reports may be downloaded as text in a tab-delimited format that includes fields for the name of the subject HIV-1 protein, its RefSeq accession number, the interaction phrase, the description of the interaction partner, the partner’s RefSeq accession number, the title of the publication reporting the interaction, and its PubMed identifier. For example, the first line in the tab-delimited file produced by filtering the interaction report for the “tat” protein by the interaction “upregulates” is shown in Figure 1.

Figure 1: First line in the tab-delimited file produced by filtering the interaction fro the "tat" protein by the interaction "upregulates".

Interaction reports are currently available for 7 of the 9 proteins produced by HIV-1 including, gag, pol, rev, tat, vif, vpr, and vpu. Reports for the remaining proteins nef and env, will be completed soon. All protein-protein interactions documented in the HIV Protein-Interaction Database are listed in Entrez Gene reports in the “HIV-1 protein interactions” section.

—DW