Conformational Analysis of Invariant Peptide Sequences in Bacterial Genomes

• Published in: Journal of molecular biology 2005-02, Vol.345 (5), p.937-955
• Main Authors: Prakash, Tulika, Ramakrishnan, C., Dash, Debasis, Brahmachari, Samir K.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacteria; Bacterial Proteins - chemistry; Conserved Sequence; Genome, Bacterial; invariant peptides; Models, Molecular; Molecular Sequence Data; peptide flip; Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; signatures: functional and chain reversal; structural determinants
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2004.11.008

The functional significance of evolutionarily conserved motifs/patterns of short regions in proteins is well documented. Although a large number of sequences are conserved, only a small fraction of these are invariant across several organisms. Here, we have examined the structural features of the functionally important peptide sequences, which have been found invariant across diverse bacterial genera. Ramachandran angles (ϕ,ψ) have been used to analyze the conformation, folding patterns and geometrical location (buried/exposed) of these invariant peptides in different crystal structures harboring these sequences. The analysis indicates that the peptides preferred a single conformation in different protein structures, with the exception of only a few longer peptides that exhibited some conformational variability. In addition, it is noticed that the variability of conformation occurs mainly due to flipping of peptide units about the virtual C α⋯C α bond. However, for a given invariant peptide, the folding patterns are found to be similar in almost all the cases. Over and above, such peptides are found to be buried in the protein core. Thus, we can safely conclude that these invariant peptides are structurally important for the proteins, since they acquire unique structures across different proteins and can act as structural determinants (SD) of the proteins. The location of these SD peptides on the protein chain indicated that most of them are clustered towards the N-terminal and middle region of the protein with the C-terminal region exhibiting low preference. Another feature that emerges out of this study is that some of these SD peptides can also play the roles of “fold boundaries” or “hinge nucleus” in the protein structure. The study indicates that these SD peptides may act as chain-reversal signatures, guiding the proteins to adopt appropriate folds. In some cases the invariant signature peptides may also act as folding nuclei (FN) of the proteins.