Simulation of oriented NMR spectra : Combining molecular dynamics and chemical shift tensor calculations
© 2023 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.
| Veröffentlicht in: | Magnetic resonance in chemistry : MRC. - 1985. - 62(2024), 3 vom: 17. Feb., Seite 125-144 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2024
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| Zugriff auf das übergeordnete Werk: | Magnetic resonance in chemistry : MRC |
| Schlagworte: | Journal Article 15N chemical shift tensors D-amino acids MDOC PISEMA chemical shift constraints dipolar 1H-15N couplings gramicidin A molecular dynamics order parameters |
| Zusammenfassung: | © 2023 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd. Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned α-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like α-helices, or the signal pattern is disturbed by molecular motion. Here, we present a new method that combines molecular dynamics simulation with tensorial orientational constraints (MDOC) and chemical shift tensor calculations for the simulation and interpretation of PISEMA-like spectra. The calculations include the spectra arising from non α-helical molecules and molecules with non-uniform intrinsic mobility. In a first step, dipolar or quadrupolar interaction tensors drive molecular rotations and reorientations to obtain the proper mean values as observed in corresponding NMR experiments. In a second step, the coordinate snapshots of the MDOC simulations are geometry optimized with the isotropic 15 N chemical shifts as constraints using Bond Polarization Theory (BPT) to provide reliable 15 N CS tensor data. The averaged dipolar 1 H-15 N couplings and the δzz tensor components can then be combined to simulate PISEMA patterns. We apply this method to the ß-helical peptide gramicidin A (gA) and demonstrate that this method enables the assignment of most PISEMA resonances. In addition, MDOC simulations provide local order parameters for the calculated sites. These local order parameters reveal large differences in backbone mobility between L- and D-amino acids of gA |
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| Beschreibung: | Date Revised 11.02.2024 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
| ISSN: | 1097-458X |
| DOI: | 10.1002/mrc.5403 |