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Comparison of predicted scaffold-compatible sequence variation in the triple-hairpin structure of human immunodeficiency virus type 1 gp41 with patient data

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dc.contributor.author Boutonnet, N. en_US
dc.contributor.author Janssens, W. en_US
dc.contributor.author Boutton, C. en_US
dc.contributor.author Verschelde, J. L. en_US
dc.contributor.author Heyndrickx, L. en_US
dc.contributor.author Beirnaert, E. en_US
dc.contributor.author van der Groen, G. en_US
dc.contributor.author Lasters, I. en_US
dc.date.accessioned 2007-12-06T14:46:31Z
dc.date.available 2007-12-06T14:46:31Z
dc.date.issued 2002 en_US
dc.identifier.issn 0022-538X en_US
dc.identifier.doi http://dx.doi.org/10.1128/JVI.76.15.7595-7606.2002
dc.identifier.other ITG-M2A en_US
dc.identifier.other ITG-M5A en_US
dc.identifier.other ITG-M6B en_US
dc.identifier.other ITG-MLA en_US
dc.identifier.other MICRO en_US
dc.identifier.other U-VIROL en_US
dc.identifier.other JIF en_US
dc.identifier.other DOI en_US
dc.identifier.other ABSTRACT en_US
dc.identifier.uri http://hdl.handle.net/10390/1681
dc.description.abstract It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-gp41), involved in HIV entry into the target cell, exists in at least two conformations, a pre-hairpin intermediate and a fusion-active hairpin structure. To obtain more information on the structure-sequence relationship in e-gp41, we performed in silico a full single-amino-acid substitution analysis, resulting in a Fold Compatible Database (FCD) for each conformation. The FCD contains for each residue position in a given protein a list of values assessing the energetic compatibility (ECO) of each of the 20 natural amino acids at that position. Our results suggest that FCD predictions are in good agreement with the sequence variation observed for well-validated e-gp41 sequences. The data show that at a minECO threshold value of 5 kcal/mol, about 90% of the observed patient sequence variation is encompassed by the FCD predictions. Some inconsistent FCD predictions at N-helix positions packing against residues of the C helix suggest that packing of both peptides may involve some flexibility and may be attributed to an altered orientation of the C-helical domain versus the N-helical region. The permissiveness of sequence variation in the C helices is in agreement with FCD predictions. Comparison of N-core and triple-hairpin FCDs suggests that the N helices may impose more constraints on sequence variation than the C helices. Although the observed sequences of e-gp41 contain many multiple mutations, our method, which is based on single-point mutations, can predict the natural sequence variability of e-gp41 very well. en_US
dc.language English en_US
dc.subject HIV-1 en_US
dc.subject Virology en_US
dc.subject Glycoproteins en_US
dc.subject gp41 en_US
dc.subject Sequence variation en_US
dc.title Comparison of predicted scaffold-compatible sequence variation in the triple-hairpin structure of human immunodeficiency virus type 1 gp41 with patient data en_US
dc.type Article en_US
dc.citation.jtitle Journal of Virology en_US
dc.citation.volume 76 en_US
dc.citation.pages 7595-7606 en_US
dc.identifier.pmid http://www.ncbi.nlm.nih.gov/pubmed/12097573
dc.citation.jabbreviation J Virol en_US


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