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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Updated: Jul 21, 2026

Prediction of HIV-1 Coreceptor Usage (Tropism) by Sequence Analysis using a Genotypic Approach
07:06

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Published on: December 1, 2011

Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix

J R Schafer1, B M Jesdale, J A George

  • 1TB/HIV Research Laboratory, International Health Institute, Brown University, Providence, RI 02912, USA.

Vaccine
|October 31, 1998
PubMed
Summary

This study identified new human leucocyte antigen (HLA) ligands from HIV-1 proteins that are conserved across strains. These findings may help develop vaccines that induce cross-reactive cytotoxic T lymphocytes (CTLs).

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Area of Science:

  • Immunology
  • Virology
  • Bioinformatics

Background:

  • Identifying conserved human immunodeficiency virus type 1 (HIV-1) epitopes is crucial for developing effective vaccines.
  • Human leucocyte antigen (HLA) ligands are key targets for cytotoxic T lymphocytes (CTLs) in viral infections.

Purpose of the Study:

  • To identify novel, highly conserved HIV-1 ligands for HLA-A2 and HLA-B27.
  • To evaluate the utility of EpiMatrix for predicting conserved HIV-1 CTL epitopes.

Main Methods:

  • Bioinformatic prediction of potential HLA ligands using EpiMatrix.
  • Selection of 26 conserved HIV-1 peptides for experimental validation.
  • Peptide binding assays utilizing the T2 stabilization assay.

Main Results:

  • Ten new major histocompatibility complex (MHC) ligands were identified from the screened HIV-1 peptides.
  • EpiMatrix accurately predicted peptides likely to bind to HLA-A2 and HLA-B27.
  • Positive control peptides demonstrated expected binding, validating the assay.

Conclusions:

  • EpiMatrix is an effective tool for screening HIV-1 sequences to find conserved, MHC-binding regions.
  • The identified ligands represent potential targets for inducing cross-reactive CTL responses against HIV-1.
  • This approach may facilitate the development of broadly protective HIV-1 vaccines.