<p>A novel approach is proposed for modeling of structurally variable regions in proteins. In this approach, a prerequisite sequence-structure alignment is examined for regions where the target sequence is not covered by the structural template. These regions, extended with a number of residues from adjacent stem regions, are submitted to fold recognition. The alignments produced by fold recognition are integrated into the initial alignment to create a multiple alignment where gaps in the main structural template are covered by local structural templates. This multiple alignment is used to create a protein model by existing protein modeling techniques.</p><p>Several alternative parameters are evaluated using a set of ten proteins. One set of parameters is selected and evaluated using another set of 31 proteins. The most promising result is for loop regions not located at the C- or N-terminal of a protein, where the method produces an average RMSD 12% lower than the loop modeling provided with the program MODELLER. This improvement is shown to be statistically significant.</p>

A novel approach is proposed for modeling of structurally variable regions in proteins. In this approach, a prerequisite sequence-structure alignment is examined for regions where the target sequence is not covered by the structural template. These regions, extended with a number of residues from adjacent stem regions, are submitted to fold recognition. The alignments produced by fold recognition are integrated into the initial alignment to create a multiple alignment where gaps in the main structural template are covered by local structural templates. This multiple alignment is used to create a protein model by existing protein modeling techniques. Several alternative parameters are evaluated using a set of ten proteins. One set of parameters is selected and evaluated using another set of 31 proteins. The most promising result is for loop regions not located at the C- or N-terminal of a protein, where the method produces an average RMSD 12% lower than the loop modeling provided with the program MODELLER. This improvement is shown to be statistically significant.

Le VIH infecte les cellules par fusion de sa membrane avec la membrane de la cellule cible. Cette fusion est effectuée par les glycoprotéines de l'enveloppe (Env) qui sont synthétisées en tant que précurseur, gp160, qui est ensuite clivé en gp120 et gp41. La protéine gp41 est la partie transmembranaire du complexe de l'enveloppe et l’ancre à la particule virale alors que la gp120 assure la liaison au récepteur cellulaire CD4 et corécepteur CCR5 ou CXCR4. Ces interactions successives induisent des changements de conformation d’Env qui alimentent le processus d'entrée du virus conduisant finalement à l'insertion du peptide de fusion de la gp41 dans la membrane de la cellule cible. La sous-unité extérieure gp120 contient cinq régions variables (V1 à V5), dont trois (V1, V2 et V3) étant capables d’empêcher l’adoption spontanée de la conformation liée à CD4. Cependant, le rôle de régions variables V4 et V5 vis-à-vis de ces changements de conformation reste inconnu. Pour étudier leur effet, des mutants de l'isolat primaire de clade B YU2, comprenant une délétion de la V5 ou une mutation au niveau de tous les sites potentiels de N-glycosylation de la V4 (PNGS), ont été générés. L'effet des mutations sur la conformation des glycoprotéines d'enveloppe a été analysé par immunoprécipitation et résonance de plasmon de surface avec des anticorps dont la liaison dépend de la conformation adopté par la gp120. Ni le retrait des PNGS de la V4 ni la délétion de V5 n’a affecté les changements conformationnels d’Env tels que mesurés par ces techniques, ce qui suggère que les régions variables V1, V2 et V3 sont les principaux acteurs dans la prévention de l’adoption de la conformation lié de CD4 d’Env. / HIV infects cells by fusing its membrane with the membrane of the target cell. This fusion is performed by the envelope glycoproteins (Env) which are synthesized as a precursor, gp160, which is later cleaved into gp120 and gp41. The transmembrane protein gp41 anchors the envelope complex to the viral particle whereas the gp120 ensures the binding to the cell receptor CD4 and coreceptor CCR5 or CXCR4. These sequential interactions trigger conformational changes on Env that fuel the viral entry process ultimately leading to the insertion of the gp41-derived-fusion peptide into the target cell membrane. The exterior subunit gp120 contains five variable regions (V1 to V5), of which three (V1, V2 and V3) have been shown to restrain the spontaneous sampling of the CD4-bound conformation by gp120. However, the role of variable regions V4 and V5 in these conformational changes remains unknown. To investigate their effect, mutants of the clade B YU2 primary isolate, comprising a deletion of the V5 or mutating all V4 potential N-linked glycosylation sites (PNGS), have been generated. The effect of mutations on the conformation of the envelope glycoproteins was analyzed by immunoprecipitation with conformation-dependent antibodies and surface plasmon resonance. Neither the removal of the V4 PNGS nor the removal of V5 affected Env conformational changes as measured by these techniques. Thus, suggesting that variable regions V1, V2 and V3 are the major players in preventing Env from spontaneously snapping into the CD4-bound conformation.