Background: The de novo design of peptides and proteins has recently surfaced as an approach for investigating protein structure and function. This approach vitally tests our knowledge of protein folding and function, while also laying the groundwork for the fabrication of proteins with properties not precedented in nature. The success of these studies relies heavily on the ability to design relatively short peptides that can espouse stable secondary structures. To this end, substitution with alpha, beta-dehydroamino acids, especially alpha, beta-dehydrophenylalanine (Delta Phe) comes in use for spawning well-defined structural motifs. Introduction of Delta Phe induces beta-bends in small and 3(10)-helices in longer peptide sequences.
Results: The present report is an investigation of the effect of incorporating two glycines in the middle of a DeltaPhe containing undecapeptide. A de novo designed undecapeptide, Ac-Gly1-Ala2-Delta Phe3-Leu4-Gly5-Delta Phe6-Leu7-Gly8-Delta Phe9-Ala10-Gly11-NH2, was synthesized and characterized using X-ray diffraction and Circular Dichroism spectroscopic methods. Crystallographic studies suggest that, despite the presence of L-amino acid (L-Ala and L-Leu) residues in the middle of the sequence, the peptide adopts a 3(10)-helical conformation of ambidextrous screw sense, one of them a left-handed (A) and the other a right-handed (B) 3(10)-helix with A and B being antiparallel to each other. However, CD studies reveal that the undecapeptide exclusively adopts a right-handed 3(10)-helical conformation. In the crystal packing, three different interhelical interfaces, Leu-Leu, Gly-Gly and Delta Phe-Delta Phe are observed between the helices A and B. A network of C-H...O hydrogen bonds are observed at Delta Phe-Delta Phe and Gly-Gly interhelical interfaces. An important feature observed is the occurrence of glycine zipper motif at Gly-Gly interface. At this interface, the geometric pattern of interhelical interactions seems to resemble those observed between helices in transmembrane (TM) proteins.
Conclusion: The present design strategy can thus be exploited in future work on de novo design of helical bundles of higher order and compaction utilizing Delta Phe residues along with GXXG motif.