Can PISEMA experiments be used to extract structural parameters for mobile beta-barrels?
The effect of mobility on 15N chemical shift/15N-(1)H dipolar coupling (PISEMA) solid state NMR experiments applied to macroscopically oriented beta-barrels is assessed using molecular dynamics simulation data of the NalP autotransporter domain embedded in a DMPC bilayer. In agreement with previous findings for alpha-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 beta-barrel case. It is found that the precise choice of the value of the CSA parameters sigma11, sigma22 and sigma33 has only a minor effect, whereas the choice of the CSA parameter theta shifts the position of the peaks by up to 20 ppm and changes the overall shape of the spectrum significantly. As was found for alpha-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 beta-strands in the barrel occupy distinct regions of the PISEMA spectra, forming patterns which may prove useful in peak assignment.
Bleile
Dustin W
DW
Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., V6T 1Z1, Canada.
Scott
Walter R P
WR
Straus
Suzana K
SK
D006859:Hydrogen; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D009584:Nitrogen; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D006859:Hydrogen; D009584:Nitrogen