Structural assessment of glycyl mutations in invariantly conserved motifs

Abstract

Motifs that are evolutionarily conserved in proteins are crucial to their structure and function. In one of our earlier studies, we demonstrated that the conserved motifs occurring invariantly across several organisms could act as structural determinants of the proteins. We observed the abundance of glycyl residues in these invariantly conserved motifs. The role of glycyl residues in highly conserved motifs has not been studied extensively. Thus, it would be interesting to examine the structural perturbations induced by mutation in these conserved glycyl sites. In this work, we selected a representative set of invariant signature (IS) peptides for which both the PDB structure and mutation information was available. We thoroughly analyzed the conformational features of the glycyl sites and their local interactions with the surrounding residues. Using Ramachandran angles, we showed that the glycyl residues occurring in these IS peptides, which have undergone mutation, occurred more often in the L-disallowed as compared with the L-allowed region of the Ramachandran plot. Short range contacts around the mutation site were analyzed to study the steric effects. With the results obtained from our analysis, we hypothesize that any change of activity arising because of such mutations must be attributed to the long-range interaction(s) of the new residue if the glycyl residue in the IS peptide occurred in the L-allowed region of the Ramachandran plot. However, the mutation of those conserved glycyl residues that occurred in the L-disallowed region of the Ramachandran plot might lead to an altered activity of the protein as a result of an altered conformation of the backbone in the immediate vicinity of the glycyl residue, in addition to long range effects arising from the long side chains of the new residue. Thus, the loss of activity because of mutation in the conserved glycyl site might either relate to long range interactions or to local perturbations around the site depending upon the conformational preference of the glycyl residue.

Preferred left-handed conformations of glycyls with pathogenic variants protect against aggregation

“…The analysis showed significantly lower evolutionary divergence rates of L-disallowed Gly as compared to L- allowed ones at both pathogenic and benign sites, though relatively greater at pathogenic sites (Figure 2A, Table S1). This was consistent with the earlier reports wherein the Gly present in the conserved regions of proteins tended to exhibit L-disallowed conformation 24 .…”

“…Mutation of Gly to L-Ala, but not to D-Ala, leads to loss of structural and functional attributes of protein 23 . Prakash et al 24 has shown that the glycyl residues occurring in the evolutionarily invariant peptides in bacteria tend to be buried and were moderately more frequent in the L-disallowed regions. More recently, Lakshmi et al has claimed that the small size of the Gly, regardless of L-allowed or L-disallowed conformation, could likely have guided their evolutionary selection in conserved protein families 25 .…”

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted February 10, 2024. ; https://doi.org/10.1101/2024.02.09.579738 doi: bioRxiv preprint loss of structural and functional attributes of protein 23 . Prakash et al 24 has shown that the glycyl residues occurring in the evolutionarily invariant peptides in bacteria tend to be buried and were moderately more frequent in the L-disallowed regions. More recently, Lakshmi et al has claimed that the small size of the Gly, regardless of L-allowed or L-disallowed conformation, could likely have guided their evolutionary selection in conserved protein families 25 .…”