Abstract
Most Internet online resources for investigating HIV biology contain either bioinformatics tools, protein information or sequence data. The objective of this study was to develop a comprehensive online proteomics resource that integrates bioinformatics with the latest information on HIV-1 protein structure, gene expression, post-transcriptional/post-translational modification, functional activity, and protein-macromolecule interactions. The BioAfrica HIV-1 Proteomics Resource is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites. The HIV-1 Protein Data-mining Tool includes a set of 27 group M (subtypes A through K) reference sequences that can be used to assess the influence of genetic variation on immunological and functional domains of the protein. The BLAST Structure Tool identifies proteins with similar, experimentally determined topologies, and the Tools Directory provides a categorized list of websites and relevant software programs. This combined database and software repository is designed to facilitate the capture, retrieval and analysis of HIV-1 protein data, and to convert it into clinically useful information relating to the pathogenesis, transmission and therapeutic response of different HIV-1 variants. The HIV-1 Proteomics Resource is readily accessible through the BioAfrica website at:
Highlights
The HIV-1 genome contains only 9 genes, it is capable of generating more than 19 gene products
To facilitate studies of the biological consequences of genetic variation, we have developed an integrated, user-friendly proteomics resource that integrates common approaches to HIV-1 protein analysis (Figure 1)
Studies have shown that resistance mutations in the protease of subtype B are associated with impaired proteolytic processing and decreased enzymatic activity, and that compensatory mutations at Gag and Gag-Pol cleavage sites can partially overcome these defects [8]. These findings suggest that variation at protease cleavage sites may play an important role, in regulation of the viral life cycle, and in disease progression and response to therapy
Summary
The HIV-1 genome contains only 9 genes, it is capable of generating more than 19 gene products. (iFDSnGcivagheteuansm-brtemiaergasaitne2litcioOnErgnvset)eTprrrioeveoisse,le,wantn,htdaDetRioHoemnIfVeao-rin1fesBnB/ciFoLeoAsldSfarsTni/cMdSa'toRsrteuHifcsIot,VumG-r1emenPTeornoomdoteilc,doaLmRnodeicaastdhtRienoegnPss,or)Po,urtrhoecoetem,HisnihIc-VMos-wT1acioPnrorgoolmsitseDoalfieisrveceucClmteolearIanjyovtr(eafgrocaeorcmStBiotepegnosisn,senePnecrtrtismsi:oatanhnr,edythaHAendIdVHv-aSI1Vnec-P1eordonPdtreaoortymeine Schematic representation of BioAfrica's HIV-1 Proteomics Resource, showing its five major components: the HIV-1 Proteome (General Overview, Domains/Folds/Motifs, Genomic Location, Protein-Macromolecule Interactions, Primary and Secondary Database Entries, and References and Recommended Readings), the HIV-1 Protease Cleavage Sites section, the HIV-1 Protein Data-mining Tool, the HIV-1 BLAST Structure Tool, and the Proteomics Tools Directory (for Beginners and Advanced investigators). The advanced webpage displays a list of more than 200 links to different websites and web-servers These data sources contain a variety of TFbahigseeusirnerter8oledvuacntofroyr ltishteinagnoalfypsirsootefoHmIVicsproetseoiunrdceatsafohrttHp:I/V/biroeasferaicrac.hmcrhco.asce.zna/tporogitveeoamgicesn/epraoltoeovemrivcisetwooolsf.ohtnmlinl e tools and dataThe introductory listing of proteomics resources for HIV research chosen to give a general overview of online tools and databases relevant for the analysis of HIV protein data http://bioafrica.mrc.ac.za/proteomics/proteomicstools.html. Information ranging from specialized protein sequence databases to software programs capable of performing rigid body protein-protein molecular docking simulations
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