Understanding the role of arginine clusters in β-hairpin antimicrobial peptides
The work described in this thesis describes the role of arginine clusters and the importance of their position in B-hairpin antimicrobial peptides. Here, we have tried to explore the role of guanidinium groups in the studied model system Polyphemeusin-1. The thesis has been divided into four chapters. The first chapter includes the challenges associated with the antimicrobial resistance, the literature available for antimicrobial peptides and a broad view of their history, diversity, physiochemical properties and the mechanism of actions of antimicrobial peptides. From this chapter we can infer the fact the antimicrobial peptides are an important part of innate immune system and show broad spectrum activity proving them as a potential candidate for developing into therapeutics. Later, in the second chapter we have described the background study which was done to understand the arginine cluster, how we chose the model system for our study and the literature available for the model peptide Polyphemusin-1. In this chapter, we observed that all -hairpin antimicrobial peptides contain cysteine disulfide bridge. Also, all the peptides analysed showed a pattern of arginine clusters in terminal region, strand region and turn region from which we delineated our objective. In the third Chapter we have detailed all the experiments, which were performed to carry out this project. The last chapter includes the results and discussion section wherein, we have described all the detailed analysis of the experiments performed and results obtained while trying to understand the role of arginine and its position for overall potency and activity of the peptide. From this chapter we could conclude the fact that arginine in the terminal clusters plays a key role in antimicrobial activity of Polyphemusin-1 and removal of guanidinium group leads to compromise in its antimicrobial activity without compromising its interaction with the membrane. However, the peptides showed structural difference at different pH and increased structural rigidity in hydrophobic niche for which further experiments needs to be done. Summary and Outlook The arginine clusters in β-hairpin peptides play an important role for the poteny of peptides. The mutation of arginine to ornithine in which the guanidine group was lost led to compromise upon the antimicrobial activity of the Polyphemusin specially the removal of guanidinium group left the peptide with no antimicrobial activity. However, the loss of guanidinium group did not showed any major effect upon the membrane damage and membrane depolarization concluding the fact that the first interaction of the peptides with membrane is not getting affected possibly because the Polyphemusin has some internal targets which still needs to be explored.