Structural and evolutionary tunnels of pairwise residue-interaction symmetries connect different structural classes of proteins

TL;DR

This study uncovers universal patterns of residue-residue interaction symmetries in proteins, identifying specific interaction 'tunnels' that are favored or disfavored across structural classes, revealing their role in protein structural organization.

Contribution

It introduces the concept of structural and evolutionary tunnels, highlighting their universal presence and significance in protein symmetry and organization across different classes.

Findings

Certain residue interactions are universally favored or disfavored by structural and evolutionary constraints.

Overlaps exist among acceptable and unacceptable interaction tunnels, indicating shared underlying principles.

The MET-MET tunnel is most unacceptable, while ASP-LEU is most acceptable across proteins.

Abstract

Studying all non-redundant proteins in 76 most-commonly found structural domains, the present work attempts to decipher latent patterns that characterize acceptable and unacceptable symmetries in residue-residue interactions in functional proteins. We report that cutting across the structural classes, a select set of pairwise interactions are universally favored by geometrical and evolutionary constraints, termed 'acceptable' structural and evolutionary tunnels, respectively. An equally small subset of residue-residue interactions, the 'unacceptable' structural and evolutionary tunnels, is found to be universally disliked by structural and evolutionary constraints. Non-trivial overlapping is detected among acceptable structural and evolutionary tunnels, as also among unacceptable structural and evolutionary tunnels. A subset of tunnels is found to have equal relative importance, structurally and evolutionarily, in different structural classes. The MET-MET tunnel is detected to be universally most unacceptable by both structural and evolutionary constraints, whereas the ASP-LEU tunnel was found to be the closest approximation to be universally most acceptable. Residual populations in structural and evolutionary tunnels are found to be independent of stereochemical properties of individual residues. It is argued with examples that tunnels are emergent features that connect extent of symmetry in residue-residue interactions to the level of quaternary structural organization.