Further evidence for the relationship of HIV-1 gp120 V3 loops with Ig superfamily members: similarity with the putative CDR3 region of T-cell receptor δ-chains

Abstract

Twenty-five V3 loops of envelope gp 120 extracted from 30 HIV-1 isolates were compared with T-cell receptor (TCR) subunits variable (V) portions using pairwise alignments of 11-residue peptides. The results indicate that, in comparison with random sequences, the analyzed V3 loops, unlike control (unrelated) sequences, display highly significant local similarity with TCR V δ (p ≈ 10 −20). However, pattern-matching searches were performed on a much larger number of V3 loops (484). In particular, selective pattern TR ∗∗∗ NT ∗ K ∗ I is shared by V δ from human T-cell line KT19E and 230 HIV-1 V3 loops (N-terminal portion). Pattern RA ∗ YT ∗∗∗ I ∗ G is common for V δ chain isolated from T-cell line DS6 of an immunodeficient patient and 69 V3 loops (C-terminal portion). The presented δ-chain portions of sequence similarity with the V3 loops overlap the putative complementarity-determining region (CDR3), thus possibly indicating functional similarity too.