(742f) Structure and Dynamics of Human Beta Defensin Interacting with Bacterial Lipid Membranes
AIChE Annual Meeting
2020
2020 Virtual AIChE Annual Meeting
Engineering Sciences and Fundamentals
Modeling of Lipid Membranes and Membrane Proteins
Friday, November 20, 2020 - 9:15am to 9:30am
Firstly, we set up simulations on hBD-3 monomer and hBD-1 dimer binding with both gram-positive and gram-negative bacterial lipid membranes with CHARMM-GUI software and ran for at least 50 ns each in wildtype form by using NAMD program and CHARMM forcefields. The compositions of Gram-positive and Gram-negative bacterial lipid membranes that were used to set up the simulations consist of 4 types of lipids: palmitoyloleoyl phosphatidylglycerol (POPG), palmitoyloleoyl phosphatidylethanolamine (POPE), 1,2-dioleoyal-3-trimethylammonium-propane (DOTAP) and tetraoleyl cardiolipin (TOCL), with different molar ratios. The Gram-positive lipid membrane was set up with 60% POPG, 14% POPE, 15% DOTAP and 10% TOCL. Gram-negative lipid membrane was set up with 20% POPG, 70% POPE, and 10% TOCL. Then we analyzed hBD on the bacterial membrane simulation trajectories by calculating Root Mean Square Deviation (RMSD), Root mean square fluctuation (RMSF), the number of hydrogen bonds of hBD-1 and hBD-3 with lipids using VMD program.
It is found that hBD-1 has more structure change than hBD-3. It is also found that hBD-3 forms more hydrogen bonds with the Gram-negative and Gram-positive membranes than those of hBD-1, and hBD-3 has more stable binding on bacterial membranes than hBD-1. The result can help to explain the binding and activity discrepancy of hBDs during bacterial eliminating.