Abstract
The work in this thesis can be divided into two sections, namely the study of delicious peptide, a food flavour and the antimicrobial peptide lactofenicin B. The main interest in these compounds is in terms of structure and conformation adopted in solution and how this relates to their mode of action. Delicious peptide was studied initially by 1H NMR spectroscopy for evidence of a specific solution structure. Results show that delicious peptide does not adopt a regular conformation in solution. Molecular dynamics simulations of this peptide show the flexibility of the peptide structure in solution. Quenched molecular dynamics simulations were used to search for low energy conformers of the peptide. The results suggest that the flavour of the peptide is produced by interaction of basic and acidic regions in the peptide. The work was extended to examine delicious peptide analogues with similar flavour characteristics. The results obtained suggest that similar interactions of basic and acidic regions occur for these peptides to produce a savoury flavour. The antimicrobial peptide Lactofemcin B was synthesised by Fmoc poly-amide synthesis. Problems with the synthesis occurred due to the protecting groups used for the five arginine residues present in the sequence. Predictive modelling studies on Lactofenicin B peptide, derived from bovine lactofenicin protein suggest that the peptide adopts a region of alpha-helical conformation in solution. The flexibility of the peptide was studied by molecular dynamics in solution and simulations of other environmental conditions were carried out by variation of electrostatic interactions using dielectric constants for membrane, TFE and water environments. The results suggest the beta-helical conformation is most stable in an environment such as trifluoroethanol, the peptide showing more flexibility in aqueous solution. Experimental results for the peptide confirm the flexibility of the peptide in solution. CD results show that lactofenicin B has no specific conformation in solution, although an beta-helical conformation is adopted in trifluoroethanol. The peptide also adopts a beta-sheet conformation in low concentrations of SDS micelle and therefore its conformation is dependant on environmental conditions. NMR studies show that the peptide, although flexible in solution, shows short-range NOE interactions that suggest a local beta-helical conformation may be present. However the overall conformation for the peptide is a flexible one.