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http://hdl.handle.net/10603/503806
Title: | Mechanism of Antimicrobial Peptide Binding to Membrane-mimetic Systems: Insight from Molecular Dynamics Simulations |
Researcher: | Ghosh, Suvankar |
Guide(s): | Satpati, Priyadarshi |
Keywords: | Biotechnology and Applied Microbiology Life Sciences Microbiology |
University: | Indian Institute of Technology Guwahati |
Completed Date: | 2023 |
Abstract: | "The 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." |
URI: | http://hdl.handle.net/10603/503806 |
Appears in Departments: | DEPARTMENT OF BIOSCIENCES AND BIOENGINEERING |
Files in This Item:
File | Description | Size | Format | |
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01_fulltext.pdf | Attached File | 7.54 MB | Adobe PDF | View/Open |
04_abstract.pdf | 118.32 kB | Adobe PDF | View/Open | |
80_recommendation.pdf | 395.73 kB | Adobe PDF | View/Open |
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