Peptide Design: Synthetic Antifreeze and Quorum Quenching Peptides and their Potential Applications

Abstract

Most peptides of biological interest are derived from native proteins. These peptides perform a range of biological activities like enzyme inhibitors, neurotransmitters, hormones etc. However, conformational flexibility and susceptibility to proteases of short peptides made up of the twenty naturally occurring amino acids make it necessary to design novel peptide structures based on the sequences of naturally occurring proteins to make them suitable for applications in any field. This thesis describes the design and synthesis of peptides with potential applications in two different fields, both of which are relevant to the NZ economy. The first part of this thesis describes studies towards the design and synthesis of antifreeze peptides (AFPs) based on naturally occurring antifreeze proteins. The AFPs described in this thesis were modelled using the peptide modelling software Sybyl and synthesized using solid phase peptide synthesis following Fmoc chemistry. Designed salt-bridges were used in an effort to enhance the secondary structure (helicity) and thereby antifreeze activity of one of the synthetic AFPs. Preliminary results from the structure elucidation (using NMR and CD) and analysis of antifreeze activity are also described. Efforts towards the design and synthesis of hyperactive AFPs are also included. AFPs can act as antagonists of the ice-nucleating proteins produced by plant pathogens like Pseudomonas syringae which result in surface frost damage to plants, particularly fruit trees including the kiwifruit. AFPs also have potential applications in the frozen food industry for preserving the texture and structure of frozen foods, thereby enhancing consumer acceptance. The second part of this thesis describes the design, synthesis and analysis of peptides with potential quorum quenching activity. Catalytic residues from the active site of quorum quenching proteins found in nature were introduced into specific positions in a well folded helix turn helix peptide reported in the literature. The designed peptides were synthesized by manual solid phase peptide synthesis following Fmoc chemistry and purified to homogeneity using High Performance Liquid Chromatography (HPLC). Ability of the synthetic peptide to act as a quorum quencher was evaluated using an enzymatic assay described in the literature using a combination of HPLC and mass spectrometry.