Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Peptide Design and Biological Activity
2.2. Simulation Details
3. Results
3.1. Accessing Peptide(s) Binding to Various Membrane with AA Modeling
3.2. Accessing Peptide(s) Binding to Gram-Negative Membrane with CG and CG2AA Modeling
3.3. Changes in Membranes Induced by Peptide Interaction
3.4. Gram-Negative Outer Membrane Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Label | No. of Peptides | Gram − | POPC | Gram + | Gram − Outer Membrane | |||||
---|---|---|---|---|---|---|---|---|---|---|
Time | No. of Lipids | Time | No. of Lipids | Time | No. of. Lipids | 2 O-Antigens | 0 O-Antigens | No. of Lipids and LPSs | ||
Time | Time | |||||||||
AA-0 | 0 | 0.5 | 192 POPE 64 POPG | - | 256 POPC | 0.5 | 146 POPG 96 Lys-PG 14 PVCL2 | 0.5 | 0.5 | Up: 50 LPS Down: 105 PVPE 30 PVPG 8 PVCL2 |
AA-1 a * | 1 | 1 | 0.5 | 1 | 0.5 | 0.1 | ||||
AA-1 b * | 1 | 1.6 | - | 1.6 | - | - | ||||
AA-2 | 2 | 1.5 | - | 1.5 | - | - | ||||
AA-12 a * | 12 | 1 | 384 POPE 128 POPG | 0.5 | 512 POPC | 1 | 292 POPG 192 Lys-PG 28 PVCL2 | - | 0.1 | |
AA-12 b * | 12 | 1 | 0.5 | 1 | 0.4 | 0.2 | ||||
CG-12 | 12 | 25 | 384 POPE 128 POPG | |||||||
CG-24 | 24 | 42.5 | ||||||||
CG2AA-12 ** | 12 | 0.5 | ||||||||
CG2AA-24 ** | 24 | 0.5 |
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Maleš, M.; Zoranić, L. Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes. Membranes 2022, 12, 891. https://doi.org/10.3390/membranes12090891
Maleš M, Zoranić L. Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes. Membranes. 2022; 12(9):891. https://doi.org/10.3390/membranes12090891
Chicago/Turabian StyleMaleš, Matko, and Larisa Zoranić. 2022. "Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes" Membranes 12, no. 9: 891. https://doi.org/10.3390/membranes12090891