Ghosh, Suvankar2024-04-022024-04-022023ROLL NO.166106105https://gyan.iitg.ac.in/handle/123456789/2590Supervisor: Satpati, PriyadarshiThe focus of the Ph.D. thesis was to understand the mechanism of cationic antimicrobial peptide (7 and 14 amino acid residue long) binding to membrane-mimetic systems (micelle and bilayer) using classical molecular dynamics free energy simulations. The peptides were modeled and subjected to conventional classical MD simulations in the presence and absence of micelle/bilayer [micelles: SDS/DPC and bilayers: (DOPE:DOPG and POPE:POPG)/POPC as bacterial/mammalian membrane-mimic]. The structures of the free peptides in water and in complex with the membrane-mimetic systems were predicted from the conventional MD simulations and verified by our experimental collaborators. The MD structures were used as a template for estimating the energetics of peptide: micelle/bilayer binding (ΔGbind; absolute binding affinity and ΔΔG; Binding free energy difference between two peptides to the membrane-mimetic system) by employing various popular methods: Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), Steered Molecular Dynamics (SMD), Umbrella Sampling (US), and Alchemical free energy simulations (FEP, TI, BAR). The simulations of peptide binding to the simplest membrane-mimetic systems provide insight into the kinetics and establish a direct link between the calculated energetics and molecular structures.enThesis