Residue-residue contact prediction in the HIV-1 envelope glycoprotein complex

Reda Rawi, Khalid Kunji, Abdelali Haoudi, Halima Bensmail

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

HIV-1 Env glycoprotein complex is the key protein that mediates binding and entry of HIV-1 into human host cells. The complex entry process involves three main steps. First, the attachment, the interaction of gp120 and CD4. Second, the coreceptor binding, where gp120 binds the chemokine receptor CCR5 or CXCR4, and finally, the fusion of viral and host cell membranes. Despite the fact that several coordinate structures of HIV-1 Env in unliganded state exist (as well as in complex with CD4, CD4 mimics, or various antibodies, and of gp41 in intermediate and post-fusion state), a comprehensive understanding of structural arrangements and communication within gp120 and gp41 domains during the entry is far from complete. In this study, we applied a direct amino acid interaction detecting method to analyse the function and structure of HIV-l Env protein sequences representing all group M subtypes. We identified more than 400 coevolving residue pairs within Env, of which the majority are real contacts and proximal in the available coordinate structures, or have functional implications such as receptor binding, variable loop, gpl20-gp4l, and interdomain interactions. This work provides a new dimension of information in HIV research, important in assisting protein coordinate structure prediction and in designing new and effective entry inhibitors.

Original languageEnglish
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1709-1711
Number of pages3
ISBN (Print)9781467367981
DOIs
Publication statusPublished - 16 Dec 2015
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: 9 Nov 201512 Nov 2015

Other

OtherIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period9/11/1512/11/15

    Fingerprint

Keywords

  • Contact Prediction
  • Group M subtypes
  • HIV-1 Env

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence
  • Health Informatics
  • Biomedical Engineering

Cite this

Rawi, R., Kunji, K., Haoudi, A., & Bensmail, H. (2015). Residue-residue contact prediction in the HIV-1 envelope glycoprotein complex. In Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 1709-1711). [7359933] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359933