A universal residue numbering scheme for the Immunoglobulin-fold (Ig-fold) to study Ig-Proteomes and Ig-Interactomes

Abstract

The Immunoglobulin fold (Ig-fold) is found in proteins from all domains of life and represents the most populous fold in the human genome, with current estimates ranging from 2 to 3% of protein coding regions. That proportion is much higher in the surfaceome where Ig and Ig-like domains orchestrate cell-cell recognition, adhesion and signaling. The ability of Ig-domains to reliably fold and self-assemble through highly specific interfaces represents a remarkable property of these domains, making them key elements of molecular interaction systems: the immune system, the nervous system, the vascular system and the muscular system. We define a universal residue numbering scheme, common to all domains sharing the Ig-fold in order to study the wide spectrum of Ig-domain variants constituting the Ig-proteome and Ig-Ig interactomes at the heart of thesesystems. The “IgStrand numbering scheme” enables the identification of Ig structural proteomes and interactomes in and between any species, and comparative structural, functional, and evolutionary analyses. We review how Ig-domains are classified today as topological and structural variants and highlight the“Ig-fold irreducible structural signature”shared by all of them. The IgStrand numbering scheme lays the foundation for the systematic annotation of structural proteomes by detecting and accurately labeling Ig-, Ig-like and Ig-extended domains in proteins, which are poorly annotated in current databases and opens the door to accurate machine learning. Importantly it sheds light on the robustIg protein folding algorithmused by nature to form beta sandwich supersecondary structures. The numbering scheme powers an algorithm implemented in the interactive structural analysis software iCn3D to systematically recognize Ig-domains, annotate them and perform detailed analyses comparing any domain sharing the Ig-fold in sequence, topology and structure, regardless of their diverse topologies. The scheme provides a robust fold detection and labeling mechanism that reveals unsuspected structural homologies among protein structures beyond currently identified Ig- and Ig-like domain variants. Indeed, multiple folds classified independently contain a common structural signature, in particular jelly-rolls. Examples of folds that harbor an “Ig-extended” architecture are given. Applications in protein engineering should be straightforward.

Unusual traits shape the architecture of the Ig ancestor molecule

“…Shown are the 2D maps for a series of Ig-sets representative of the evolution the Ig-domain in the animal kingdom. Colors correspond to the Ig Protodomain reduced rainbow color spectrum 14 with four strands colors blue, green, yellow, orange for ABCC' and DEFG and a fith color red for the C" strand, if present. Using this color scheme, a sheet ABED will be blue-green-green-blue; a sheet GFCC' will be orange-yellow-yellow-orange.…”