Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors
Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides,...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-10-01
|
| Series: | Antibiotics |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-6382/10/10/1265 |
| _version_ | 1797515538723766272 |
|---|---|
| author | Jiří Czernek Jiří Brus |
| author_facet | Jiří Czernek Jiří Brus |
| author_sort | Jiří Czernek |
| collection | DOAJ |
| description | Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, such as ALM, in lipid bilayers. Here, it is demonstrated how an analysis of the SSNMR measurements can benefit from fully periodic calculations, which employ the plane-wave density-functional theory (PW DFT) of the solid-phase geometry and related spectral parameters of ALM. The PW DFT calculations are used to obtain the structure of desolvated crystalline ALM and predict the NMR chemical shift tensors (CSTs) of its nuclei. A variation in the CSTs of the amidic nitrogens and carbonyl carbons along the ALM backbone is evaluated and included in simulations of the orientation-dependent anisotropic <sup>15</sup>N and <sup>13</sup>C chemical shift components. In this way, the influence of the site-specific structural effects on the experimentally determined orientation of ALM is shown in models of cell membranes. |
| first_indexed | 2024-03-10T06:46:50Z |
| format | Article |
| id | doaj.art-f9162c458f5e43d9927ad1e9af1ae1dc |
| institution | Directory Open Access Journal |
| issn | 2079-6382 |
| language | English |
| last_indexed | 2024-03-10T06:46:50Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj.art-f9162c458f5e43d9927ad1e9af1ae1dc2023-11-22T17:14:44ZengMDPI AGAntibiotics2079-63822021-10-011010126510.3390/antibiotics10101265Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift TensorsJiří Czernek0Jiří Brus1Institute of Macromolecular Chemistry, Czech Academy of Sciences, 16206 Prague, Czech RepublicInstitute of Macromolecular Chemistry, Czech Academy of Sciences, 16206 Prague, Czech RepublicAlamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, such as ALM, in lipid bilayers. Here, it is demonstrated how an analysis of the SSNMR measurements can benefit from fully periodic calculations, which employ the plane-wave density-functional theory (PW DFT) of the solid-phase geometry and related spectral parameters of ALM. The PW DFT calculations are used to obtain the structure of desolvated crystalline ALM and predict the NMR chemical shift tensors (CSTs) of its nuclei. A variation in the CSTs of the amidic nitrogens and carbonyl carbons along the ALM backbone is evaluated and included in simulations of the orientation-dependent anisotropic <sup>15</sup>N and <sup>13</sup>C chemical shift components. In this way, the influence of the site-specific structural effects on the experimentally determined orientation of ALM is shown in models of cell membranes.https://www.mdpi.com/2079-6382/10/10/1265antimicrobial peptidesalamethicinsolid-state NMRDFT |
| spellingShingle | Jiří Czernek Jiří Brus Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors Antibiotics antimicrobial peptides alamethicin solid-state NMR DFT |
| title | Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors |
| title_full | Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors |
| title_fullStr | Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors |
| title_full_unstemmed | Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors |
| title_short | Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors |
| title_sort | modeling the structure of crystalline alamethicin and its nmr chemical shift tensors |
| topic | antimicrobial peptides alamethicin solid-state NMR DFT |
| url | https://www.mdpi.com/2079-6382/10/10/1265 |
| work_keys_str_mv | AT jiriczernek modelingthestructureofcrystallinealamethicinanditsnmrchemicalshifttensors AT jiribrus modelingthestructureofcrystallinealamethicinanditsnmrchemicalshifttensors |