Abstract
While chemical shift prediction has played an important role in aspects of protein NMR that include identification of secondary structure, generation of torsion angle constraints for structure determination, and assignment of resonances in spectra of intrinsically disordered proteins, interest has arisen more recently in using it in alternate assignment strategies for crosspeaks in 1H–15N HSQC spectra of sparsely labeled proteins. One such approach involves correlation of crosspeaks in the spectrum of the native protein with those observed in the spectrum of the denatured protein, followed by assignment of the peaks in the latter spectrum. As in the case of disordered proteins, predicted chemical shifts can aid in these assignments. Some previously developed empirical formulas for chemical shift prediction have depended on basis data sets of 20 pentapeptides. In each case the central residue was varied among the 20 amino common acids, with the flanking residues held constant throughout the given series. However, previous choices of solvent conditions and flanking residues make the parameters in these formulas less than ideal for general application to denatured proteins. Here, we report 1H and 15N shifts for a set of alanine based pentapeptides under the low pH urea denaturing conditions that are more appropriate for sparse label assignments. New parameters have been derived and a Perl script was created to facilitate comparison with other parameter sets. A small, but significant, improvement in shift predictions for denatured ubiquitin is demonstrated.
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Acknowledgments
This work was supported by grants from the NIH to the Resource for Integrated Glycotechnology at the University of Georgia (P41 RR005351-23 and P41 GM103390-23), to JHP for research support (R01 GM061268-09), from the NIH to J. L. Urbauer from the Shared Instrumentation Program for upgrading an NMR console (S10RR027097-01A1) and to DL from the Shared Instrumentation Program for the purchase of the peptide synthesizer (1S10 RR027155-01).
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Prestegard, J.H., Sahu, S.C., Nkari, W.K. et al. Chemical shift prediction for denatured proteins. J Biomol NMR 55, 201–209 (2013). https://doi.org/10.1007/s10858-012-9702-x
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DOI: https://doi.org/10.1007/s10858-012-9702-x