Identification of Bacterial Membrane Selectivity of Romo1-Derived Antimicrobial Peptide AMPR-22 via Molecular Dynamics
Abstract
:1. Introduction
2. Results
2.1. Construction of the Representative AMPR-11 or AMPR-22 Structure via Molecular Dynamics
2.2. AMPR-11 and AMPR-22 Interact with Bacterial Inner/Outer Membranes Specifically over Eukaryotic Plasma Membranes
2.3. AMPR-22 Permeabilizes Bacterial Membrane Mimicking Large Unilamellar Vesicles (LUVs) by Selectively Binding to Cardiolipin or Lipid A
2.4. AMPR-22 Selectively Binds to Carbapenem-Resistant P. aeruginosa (CRPA) in Bacteremia-Mimic Conditions
3. Discussion
4. Materials and Methods
4.1. Molecular Modeling and Molecular Dynamic Simulation
4.2. Chemicals and Peptides
4.3. Bacterial Strains
4.4. Liposome Adhesion Assay
4.5. Liposome Permeabilization Assay
4.6. The Interaction of AMPR-22 with Bacteria or RBCs
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Force Field | Membranes | Lipid Composition | PLR | Time | Iterations |
---|---|---|---|---|---|
CHARMM36m | Bacterial OM | Outer leaflet: Lipid A = 32 | 1/128 | 10 ns | 100 |
Inner leaflet: PPPE:PVPG = 71:25 | |||||
Bacterial IM | PPPE:PVPG:PVCL2 = 47:12:3 | 1/124 | 10 ns | 100 | |
Eukaryotic PM | POPC:POPE:SM:CHOL = 22:11:11:18 | 1/124 | 10 ns | 100 | |
Bacterial IM | PPPE:PVPG:PVCL2 = 47:12:3 | 1/124 | 1 µs | 3 | |
Martini22p | Bacterial IM | POPE:POPG:CDL2 = 705:180:45 | 9/1860 | 1 ms | 3 |
Membrane Models | Lipid in Outer Leaflet | Ratio | Total Hydrogen Bonds with AMPR-22 | Lipid Preference (%) |
---|---|---|---|---|
Bacterial OM | Lipid A | 32 | 26,716 | 100 |
Bacterial IM | PPPE | 47 | 15,884 | 16.32 |
PVPG | 12 | 7193 | 28.94 | |
PVCL2 | 3 | 3401 | 54.74 | |
Eukaryotic PM | POPC | 22 | 1458 | 41.20 |
POPE | 11 | 753 | 42.56 | |
SM | 11 | 280 | 15.83 | |
CHOL | 18 | 12 | 0.41 |
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Kim, H.; Yoo, Y.D.; Lee, G.Y. Identification of Bacterial Membrane Selectivity of Romo1-Derived Antimicrobial Peptide AMPR-22 via Molecular Dynamics. Int. J. Mol. Sci. 2022, 23, 7404. https://doi.org/10.3390/ijms23137404
Kim H, Yoo YD, Lee GY. Identification of Bacterial Membrane Selectivity of Romo1-Derived Antimicrobial Peptide AMPR-22 via Molecular Dynamics. International Journal of Molecular Sciences. 2022; 23(13):7404. https://doi.org/10.3390/ijms23137404
Chicago/Turabian StyleKim, Hana, Young Do Yoo, and Gi Young Lee. 2022. "Identification of Bacterial Membrane Selectivity of Romo1-Derived Antimicrobial Peptide AMPR-22 via Molecular Dynamics" International Journal of Molecular Sciences 23, no. 13: 7404. https://doi.org/10.3390/ijms23137404
APA StyleKim, H., Yoo, Y. D., & Lee, G. Y. (2022). Identification of Bacterial Membrane Selectivity of Romo1-Derived Antimicrobial Peptide AMPR-22 via Molecular Dynamics. International Journal of Molecular Sciences, 23(13), 7404. https://doi.org/10.3390/ijms23137404