Conformational Studies of Biologically Active Peptides

In this work conformational studies have been performed on peptides from four different systems in an attempt to gain knowledge about their biological function. Circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy in combination with distance geometry and restrained molecular dynamics simulations were the methods used. A detailed conformational study of a cyclic peptide designed to adopt a predetermined conformation in order to mimic the active site of a serine protease was performed. The spatial arrangement of the catalytically active residues was shown not to fulfil the requirement of forming a catalytic triad. In addition, a high temperature molecular dynamics simulation was carried out starting from the designed structure without experimental restraints to explore the correlation with experiment and with the aim of demonstrating the usefulness of simulation as a predictive technique to guide design. In this simulation the experimentally determined conformation was visited after less than a nanosecond. The drug DDAVP, an analogue of the naturally occurring peptide hormone vasopressin, with high and specific activity was subjected to detailed conformational analysis. The analogue was shown to adopt a significant population of a preferred backbone conformation in aqueous solution. Refinement of the peptide with time-averaged distance restraints gave a good picture of the inherent flexibility in the peptide. A possible explanation for the high activity of DDAVP could be that its active conformation is favored already in its unbound sate. Glycopeptides capable of generating carbohydrate-specific immune response could be an important new group of potential peptide vaccines. Conformational studies of glycopeptides which have been demonstrated to induce a carbohydrate-specific immune response showed that the immune response is not affected by any specific conformations induced by the glycosylation of the peptide. Another group of peptides with the potential to become useful vaccines is fragments from Escherichia coli pilus subunit proteins. Infectious bacteria express filamentous polymeric protein structures called pili on their surfaces. A key event in the assembly of these pili is the formation of complexes between pilus subunit proteins and the periplasmic chaperone PapD. Peptides corresponding to the C-terminal part of these pilus subunit proteins also bind to PapD with varying binding-affinities. In this work the peptide with the highest affinity was shown to possess different conformational preferences in comparison to the other pilus subunit peptides. The peptide predominately exists in an extended conformation with low propensity to adopt an a-helical structure. This suggests that analogues with the proper restriction of the conformational space may work as improved inhibitors of complex formation between the chaperone PapD and pilus subunit proteins. In addition, using transferred NOE and heteronuclear NMR techniques it was shown that short peptides from a specific subunit protein are bound by the chaperone PapD in extended conformations. This result serves as a complement to a recent crystal structure of a subunit peptide in complex with PapD where dimerization occurred as a consequence of crystal packing