Interchanges of spatially neighbouring residues in structurally conserved environments

Abstract

The question of whether interchanges of spatially neighboring residues are coupled, or whether they change independently of each other, has been addressed repeatedly over the last few years. Utilizing a residue order-independent structural comparison tool, we investigated interchanges of spatially adjacent residue pairs in conserved 3D environments in globally dissimilar protein structures. We define spatially adjacent pairs to be non-local neighboring residues which are in spatial contact, though separated along the backbone, to exclude backbone effects. A dataset of unrelated structures is extensively compared, constructing a matrix of all 400 x 400 interchanges of residue pairs. Our study indicates that (i) interchanges of residues which are spatial neighbors are indepedent of each other. With the exception of a few pairs, the pattern of interchanges of pairs of adjacent residues resembles that expected from interchanges of single residues. However, clustering residues of similar characteristics, serves to enhance secondary trends. Hence, (ii) clustering the hydrophobic, aliphatic and, separately, the aromatic, and comparing them with the charged, and the polar, indicates that hydrophobic pairs are favorably replaced by hydrophobic, and charged/polar by charged/polar. The most strongly conserved are the charged. Interestingly, the type of charge (like or opposite) plays no role. Interchanges between the hydrophobic and hydrophilic classes are unfavorable. (iii) Clustering by volume indicates that the most highly conserved are the (Small, Small) pairs. The least favorable are interchanges of the type (Small, Small) ⇆ (Large, Large). Interchanges of the type (Large, Small) ⇆ (Large, Large) are less favorable than (Large, Small) ⇆ (Small, Small). Compensatory interchanges of the type (Large, Small) ⇆ (Small, Large) are unfavorable. (iv) Inspection of the trends in the interchanges of the clustered small residues versus clustered large rigid, and separately versus clustered large flexible, illustrates clear differences. Consistently, within all hydrophobic, large and small, the flexible aliphatic differ from the more rigid aromatic. The flexible aliphatic residue pairs are unfavorably replaced by other residue types. Furthermore, (v) the unique properties of the aromatics, conferred by the electronic configuration of their benzene rings, are transformed into clear trends. Replacements of polar residues by aromatics, while unfavorable, are nevertheless consistently more favorable than into aliphatics. We address these issues and their direct implications to protein design and to fold recognition.