Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations
In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG) model within the MARTINI force field; we...
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2017
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14203049_v22_n10_p_Balatti http://hdl.handle.net/20.500.12110/paper_14203049_v22_n10_p_Balatti |
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paper:paper_14203049_v22_n10_p_Balatti2023-06-08T16:13:34Z Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations Aurein Coarse-grain Helicoidal peptides Lipid bilayers Maculatin Molecular dynamics 1-palmitoyl-2-oleoylphosphatidylcholine amphibian protein antimicrobial cationic peptide aurein 1.2 peptide maculatin-1.1 protein, Litoria phosphatidylcholine chemistry computer simulation conformation lipid bilayer metabolism molecular dynamics molecular model Amphibian Proteins Antimicrobial Cationic Peptides Computer Simulation Lipid Bilayers Models, Molecular Molecular Conformation Molecular Dynamics Simulation Phosphatidylcholines In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG) model within the MARTINI force field; we simulated the peptide–lipid system from three different initial configurations: (a) peptides in water in the presence of a pre-equilibrated lipid bilayer; (b) peptides inside the hydrophobic core of the membrane; and (c) random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide–lipid ratios. The exploration of the possible lipid–peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies. © 2017 by the authors. 2017 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14203049_v22_n10_p_Balatti http://hdl.handle.net/20.500.12110/paper_14203049_v22_n10_p_Balatti |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Aurein Coarse-grain Helicoidal peptides Lipid bilayers Maculatin Molecular dynamics 1-palmitoyl-2-oleoylphosphatidylcholine amphibian protein antimicrobial cationic peptide aurein 1.2 peptide maculatin-1.1 protein, Litoria phosphatidylcholine chemistry computer simulation conformation lipid bilayer metabolism molecular dynamics molecular model Amphibian Proteins Antimicrobial Cationic Peptides Computer Simulation Lipid Bilayers Models, Molecular Molecular Conformation Molecular Dynamics Simulation Phosphatidylcholines |
| spellingShingle |
Aurein Coarse-grain Helicoidal peptides Lipid bilayers Maculatin Molecular dynamics 1-palmitoyl-2-oleoylphosphatidylcholine amphibian protein antimicrobial cationic peptide aurein 1.2 peptide maculatin-1.1 protein, Litoria phosphatidylcholine chemistry computer simulation conformation lipid bilayer metabolism molecular dynamics molecular model Amphibian Proteins Antimicrobial Cationic Peptides Computer Simulation Lipid Bilayers Models, Molecular Molecular Conformation Molecular Dynamics Simulation Phosphatidylcholines Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations |
| topic_facet |
Aurein Coarse-grain Helicoidal peptides Lipid bilayers Maculatin Molecular dynamics 1-palmitoyl-2-oleoylphosphatidylcholine amphibian protein antimicrobial cationic peptide aurein 1.2 peptide maculatin-1.1 protein, Litoria phosphatidylcholine chemistry computer simulation conformation lipid bilayer metabolism molecular dynamics molecular model Amphibian Proteins Antimicrobial Cationic Peptides Computer Simulation Lipid Bilayers Models, Molecular Molecular Conformation Molecular Dynamics Simulation Phosphatidylcholines |
| description |
In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG) model within the MARTINI force field; we simulated the peptide–lipid system from three different initial configurations: (a) peptides in water in the presence of a pre-equilibrated lipid bilayer; (b) peptides inside the hydrophobic core of the membrane; and (c) random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide–lipid ratios. The exploration of the possible lipid–peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies. © 2017 by the authors. |
| title |
Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations |
| title_short |
Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations |
| title_full |
Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations |
| title_fullStr |
Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations |
| title_full_unstemmed |
Differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations |
| title_sort |
differential interaction of antimicrobial peptides with lipid structures studied by coarse-grained molecular dynamics simulations |
| publishDate |
2017 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14203049_v22_n10_p_Balatti http://hdl.handle.net/20.500.12110/paper_14203049_v22_n10_p_Balatti |
| _version_ |
1768542470840254464 |