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Antimicrobial peptides (AMP) inactivate microorganisms by forming pores in cell membrane. Since their mechanism of action differs from that of antibiotics, they could be very useful for combating drug resistant microbes, for treatment of microbial infections and also for prevention. Elucidation of mechanism of pore formation will help in the design of synthetic AMP for specific microorganism.

Pore formation in DMPC liposomes by AMP melittin, its mutants G1I (higher hydrophobicity) and I17K (higher net charge) and Cecropin P1 as monitored by leakage of fluorescent dye calcein, encapsulated within DMPC liposomes indicated that the leakage rates and the extent of leakage were in the order Cecropin P1 > melittin > G1I > I17K. Pore formation in cell membrane of Listeria monocytogenes and E. coli by melittin and cecropin P1 and resulting antimicrobial activity were demonstrated by transmission electron microscopy (TEM) and plate count. Immobilization of cecropin P1 onto silica nanoparticles with a Maleimide-PEG-NHS Ester linker resulted in a decreased antimicrobial activity against E. coli because of its loss of secondary structure as characterized by Fourier Transform Infrared Spectroscopy (FTIR) and Circular Dichroism (CD). Size distribution and TEM of liposomes exposed to peptides of different concentrations indicated pore formation with accompanied stretching of liposomes at low peptide concentrations. At higher concentration, however, cecropin P1 aggregates and solubilizes lipids thus suggesting a carpet mechanism of pore formation.

Molecular dynamics (MD) simulation of melittin interacting with DOPC/DOPG mixed bilayer indicated a critical peptide/lipid ratio for penetration of melittin from the surface as well as for water channel formation for transmembrane peptides in lipid bilayer. The phospholipid density profile across the bilayer indicated a toroidal pore structure. A mathematical model for the evaluation of energy barrier for formation of pore consisting of peptide aggregates of different size interspersed with phospholipid head was proposed which considers detailed pore structure as well as intermolecular interactions. Estimated free energy barriers for insertion of melittin into an ideal paraboloid pores of different sizes were compared with those evaluated by potential mean force calculations. A mathematical model was proposed for the rates of formation of pores by AMP by adsorption and surface diffusion. The rate of dissociation of peptides from pores was evaluated by first passage time analysis. The model was employed for the prediction of rates of nucleation of pores.