Abstract
The effect of mobility on 15N chemical shift/15N–1H dipolar coupling (PISEMA) solid state NMR experiments applied to macroscopically oriented β-barrels is assessed using molecular dynamics simulation data of the NalP autotransporter domain embedded in a DMPC bilayer. In agreement with previous findings for α-helices, the fast librational motion of the peptide planes is found to have a considerable effect on the calculated PISEMA spectra. In addition, the dependence of the chemical shift anisotropy (CSA) and dipolar coupling parameters on the calculated spectra is evaluated specifically for the β-barrel case. It is found that the precise choice of the value of the CSA parameters σ11,σ22 and σ33 has only a minor effect, whereas the choice of the CSA parameter θ shifts the position of the peaks by up to 20 ppm and changes the overall shape of the spectrum significantly. As was found for α-helices, the choice of the NH bond distance has a large effect on the dipolar coupling constant used for the calculations. Overall, it is found that the alternating β-strands in the barrel occupy distinct regions of the PISEMA spectra, forming patterns which may prove useful in peak assignment.
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Abbreviations
- CS:
-
chemical shift
- CSA:
-
chemical shift anisotropy
- CS/D:
-
15N–chemical shift/15N– 1H dipolar coupling
- D:
-
dipolar coupling
- DMPC:
-
dimyristoylphosphatidylcholine
- MD:
-
molecular dynamics
- PISA:
-
polarisation index of the slant angle
- PISEMA:
-
polarisation inversion spin exchange at the magic angle
- r.m.s:
-
root mean square.
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Bleile, D., Scott, W. & Straus, S. Can PISEMA experiments be used to extract structural parameters for mobile β-barrels?. J Biomol NMR 32, 101–111 (2005). https://doi.org/10.1007/s10858-005-5094-5
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DOI: https://doi.org/10.1007/s10858-005-5094-5