Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones.

Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone· Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of ßand γ-turns. A study of the minimum energy conformations vis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases· A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families· Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures· The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature·

Predicted secondary structure of maltodextrin Phosphorylase from Escherichia coli as deduced using Chou-Fasman model.

Secondary structure of maltodextrin Phosphorylase from Escherichia coli has been predicted using Chou-Fasman model. The enzyme protein contains 28% α-helix, 27% ß-pleated sheets and 20% reverse β-turns. The secondary structure predicted 4 regions showing Rossman-fold super secondary structure. Two regions, one from residue 268–361 and the another from residue 606–684, having 4 consecutive strands of parallel β-pleated sheets and 3 joining α-helix, are predicted. Two regions, one from residue 379–434 and the another from residue 496–573, having 3 consecutive strands of parallel ß-pleated sheets and two joining α-helix, are predicted.

Structural and functional importance of β- turn in proteins. Studies on proline-containing peptides.

We report here two sets of results on proline-containing linear peptides, one of which brings out the role of the β-turn conformation in the structure of nascent collagen while the other points to the functional importance of the β-turn in calcium-binding proteins. Based on the data on peptides containing the -Pro-Gly- sequence, we had proposed and experimentally verified that the β-turn conformation in these peptides is a structural requirement for the enzymic hydroxylation of the proline residues in the nascent (unhydroxylated) procollagen molecule. Our recent data, presented here, on the conformation of peptides containing both the -Pro-Gly- and -Gly-Pro- sequences reveal that while the β-turn in the substrate molecule is required at the catalytic site of prolyl hydroxylase, the polyproline-II structure is necessary for effective binding at the active site of the enzyme. Thus, peptides containing either the β-turn or the polyproline-II structure alone are found to act only as inhibitors while those with the polyproline-II followed by β-turn serve as substrates of the enzyme. In another study, we have synthesized the two linear peptides: Boc-Pro-D-Ala-Ala- NHCH3 and Boc-Pro-Gly-Ala-NHCH3 each of which adopts, in solution, a structure with two consecutive β-turns, as judged from circular dichroism, infrared and nuclear magnetic resonance data. Drastic spectral changes are seen in these peptides on binding to Ca2+. Both the peptides show a distinct specificity to Ca2+ over Mg2+, Na+ and Li+. A conformational change in the peptides occurs on Ca2+ binding which brings together the carbonyl groups to coordinate with the metal ion. These results imply a functional role for the β-turn in Ca2+ - binding proteins.