Sequence alignment of primary and laboratory Nef alleles used in this study.

Abstract

<p>Nef cDNA clones representative of all major non-recombinant HIV-1 clades were selected from the NIH HIV-1 sequence database as described in the text. The first letter in each clone ID (bold) indicates the subtype assignment. This Clustal W alignment also includes Nef-SF2 (top), which has been studied extensively in our laboratory in terms of Hck activation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-Briggs1" target="_blank">[41]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-Lerner1" target="_blank">[43]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-Trible1" target="_blank">[44]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-Choi1" target="_blank">[50]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-EmertSedlak1" target="_blank">[53]</a>, as well as Nef-ELI, which fails to activate Hck or other SFKs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-Trible1" target="_blank">[44]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-Choi1" target="_blank">[50]</a>. Key residues in the SF2 sequence that are essential for SH3 binding are shown in red, and include the PxxPxR motif and hydrophobic pocket residues F90, W113, and Y/F120. In Nef-ELI, Y120 is replaced with isoleucine (highlighted in yellow); this single substitution accounts for loss of SH3 engagement and Hck activation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032561#pone.0032561-Choi1" target="_blank">[50]</a>. Residues involved in Nef dimerization include K/R105, L112, Y115, F121, and D123 (blue). Flanking N- and C-terminal Nef sequences are more variable and have been omitted for clarity.</p