Selection of peptides that bind to the HLA-A2.1 molecule by molecular modelling
- Authors
- Lim, JS; Kim, S; Lee, HG; Lee, KY; Kwon, TJ; Kim, K
- Issue Date
- Feb-1996
- Publisher
- PERGAMON-ELSEVIER SCIENCE LTD
- Keywords
- computer modeling; epitope prediction; MHC binding peptide
- Citation
- MOLECULAR IMMUNOLOGY, v.33, no.2, pp 221 - 230
- Pages
- 10
- Journal Title
- MOLECULAR IMMUNOLOGY
- Volume
- 33
- Number
- 2
- Start Page
- 221
- End Page
- 230
- URI
- https://scholarworks.sookmyung.ac.kr/handle/2020.sw.sookmyung/150772
- DOI
- 10.1016/0161-5890(95)00065-8
- ISSN
- 0161-5890
- Abstract
- Cytotoxic T lymphocytes recognize antigenic peptides in association with major histocompatibility complex class I proteins. Although a large set of class I binding peptides has been described, it is not yet easy to search for potentially antigenic peptides without synthesis of a panel of peptides, and subsequent binding assays. In order to predict HLA-A2.1-restricted antigenic epitopes, a computer model of the HLA-A2.1 molecule was established using X-ray crystallography data. In this model nonameric peptide sequences were aligned. In a molecular dynamics (MD) simulation with two sets of peptides known to be presented by HLA-A2.1, it was important to know the anchor amino acid residue preference and the distance between the anchor residues. We show here that the peptides bound to the HLA-A2.1 model structure possess a side chain of C-terminal anchor residue oriented into the binding groove with different distances between the two anchor residues from 15 to 21 Angstrom. We also synthesized a set of nonamer peptides containing amino acid sequences of Hepatitis B virus protein that were selected on the basis of previously described HLA-A2.1 specific motifs. When results obtained from the MD simulation were compared with functional binding assays using the TAP-deficient cell line T2, it was evident that the MD simul
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