Ongoing · Chowdhury Lab, BITS Pilani Hyderabad
Molecular Dynamics of Protein–Membrane Interactions
Overview
Many small proteins and peptides — from antimicrobial peptides to certain pathogen surface antigens — act in part by interacting with and destabilising host or microbial membranes. This project builds and simulates atomistic protein–membrane systems (lipid bilayers assembled with CHARMM-GUI, simulated with GROMACS) to characterise how such proteins engage a bilayer, and how membrane composition — particularly cholesterol content — modulates that interaction and any resulting membrane permeabilisation.
The computational pipeline is designed as a general capability that can be pointed at different protein–membrane systems, and is currently being developed alongside an experimental collaborator's vesicle-permeabilisation assays, translating wet-lab membrane-disruption measurements into an atomistic, mechanistic picture.
Key Highlights
- Microsecond-scale all-atom MD of protein–lipid-bilayer systems across a range of membrane compositions
- Multi-metric structural analysis: membrane thickness, lipid order, packing defects, hydration, curvature, and lipid diffusion
- Residue-level contact and motif analysis to identify membrane-engaging regions
- Designed as a direct computational complement to experimental membrane-permeabilisation assays
- General-purpose pipeline, extensible to coarse-grained and enhanced-sampling methods
Researcher
Led by Danny Muzata in the Chowdhury Lab, Dept. of Biological Sciences, BITS Pilani Hyderabad Campus, in collaboration with an experimental membrane-biophysics group.