IMGT/Collier-de-Perles: a two-dimensional visualization tool for amino acid domain sequences

Abstract

IMGT/Collier-de-Perles is a tool that allows the user to analyze and draw two-dimensional graphical representations (or IMGT Collier de Perles) of protein domains (e.g., hydropathy plots). The IMGT/Collier-de-Perles specializes in the area of immunoglobulins (IG) or antibodies, T cell receptors (TR) and major histocompatibility (MH) of human and other vertebrate species as well as other proteins of the immunoglobulin superfamily (IgSF) and of the major histocompatibility superfamily (MhSF) and related proteins of the immune system of vertebrates and invertebrates.

Figure 1

Amino acid properties and the IMGT Collier de Perles 2D hydropathy plot. (A): The 11 IMGT physicochemical classes of the 20 common amino acids [1]. (B): IMGT Colliers de Perles of a V domain of an IG or antibody. IMGT Collier de Perles on one layer, obtained by the IMGT/Collier-de-Perles online tool [14] at the IMGT Home page, http://www.imgt.org. Four options are shown for the V domain of the heavy domain (VH) of trastuzumab, a therapeutic antibody: ‘50% hydrophobic positions’ (with that option, an amino acid at a given position is colored in blue if an hydrophobic amino acid is found at that position in 50% or more of the sequences used for establishing the statistical profile [17], ‘IGH 80% hydropathy classes’, ‘IGH 80% volume classes’, ‘IGH 80% physicochemical classes’. The CDR-IMGT lengths are [8.8.13]. The five conserved amino acid positions of a V domain 23, 41, 89, 104 and 118 (1st-CYS C23, CONSERVED-TRP W41, hydrophobic 89, 2nd-CYS C104, J-PHE or J-TRP 118, here W118) appear with red and bold letters. The six anchors (positions 26 and 39, 55 and 66, 104 and 118) which belong to the framework regions (FR-IMGT) and support the complementarity determining regions (CDR-IMGT) are in squares. (C): IMGT Collier de Perles on 2 layers and with hydrogen bonds (green lines) of the trastuzumab VH , provided by IMGT/3Dstructure-DB [26,34] (PDB code 1n8z). These hydrogen bonds are from the experimental 3D structures and are displayed by the IMGT/Collier-de-Perles tool integrated in IMGT/3Dstructure-DB [26,34]. The 3D structure representation of a V domain with its strands and loops, based on the IMGT Collier de Perles delimitations [21,22,25], is also shown.