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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| Format: | Article |
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MDPI AG
2017-10-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/22/10/1775 |
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| author | Galo E. Balatti Ernesto E. Ambroggio Gerardo D. Fidelio M. Florencia Martini Mónica Pickholz |
| author_facet | Galo E. Balatti Ernesto E. Ambroggio Gerardo D. Fidelio M. Florencia Martini Mónica Pickholz |
| author_sort | Galo E. Balatti |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-11T08:48:05Z |
| format | Article |
| id | doaj.art-5aee78fb45f1402d8a88a8d0ff1f3bf5 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-11T08:48:05Z |
| publishDate | 2017-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-5aee78fb45f1402d8a88a8d0ff1f3bf52022-12-22T01:14:06ZengMDPI AGMolecules1420-30492017-10-012210177510.3390/molecules22101775molecules22101775Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics SimulationsGalo E. Balatti0Ernesto E. Ambroggio1Gerardo D. Fidelio2M. Florencia Martini3Mónica Pickholz4Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, IFIBA, Buenos Aires C1428BFA, ArgentinaCentro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Departamento de Química Biológica “Dr. Ranwel Caputto”, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X500HUA, ArgentinaCentro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Departamento de Química Biológica “Dr. Ranwel Caputto”, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X500HUA, ArgentinaDepartamento de Farmacología, Instituto de la Química y Metabolismo del Fármaco (IQUIMIFA), Facultad de Farmacia y Bioquímica, Cátedra de Química Medicinal, CONICET-Universidad de Buenos Aires, Buenos Aires C1113AAD, ArgentinaDepartamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, IFIBA, Buenos Aires C1428BFA, ArgentinaIn 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.https://www.mdpi.com/1420-3049/22/10/1775maculatinaureinhelicoidal peptideslipid bilayersmolecular dynamicscoarse-grain |
| spellingShingle | Galo E. Balatti Ernesto E. Ambroggio Gerardo D. Fidelio M. Florencia Martini Mónica Pickholz Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations Molecules maculatin aurein helicoidal peptides lipid bilayers molecular dynamics coarse-grain |
| title | 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_short | 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 |
| topic | maculatin aurein helicoidal peptides lipid bilayers molecular dynamics coarse-grain |
| url | https://www.mdpi.com/1420-3049/22/10/1775 |
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