title: 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.
authors.affiliation: G. N. Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi 110007, India.
authors.forename: Tulika
authors.initials: T
authors.lastname: Prakash
authors.forename: Kuljeet Singh
authors.initials: KS
authors.lastname: Sandhu
authors.forename: Nitin Kumar
authors.initials: NK
authors.lastname: Singh
authors.forename: Yasha
authors.initials: Y
authors.lastname: Bhasin
authors.forename: C
authors.initials: C
authors.lastname: Ramakrishnan
authors.forename: Samir K
authors.initials: SK
authors.lastname: Brahmachari
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004926:Escherichia coli; D005998:Glycine / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D010963:Plasmodium falciparum; D011387:Prokaryotic Cells; D017510:Protein Folding; D016944:Sulfolobus; D014734:Vibrio cholerae
chemical_list: D001426:Bacterial Proteins; D005998:Glycine