Empirical correlation between protein backbone (15)N and (13)C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

Wang, L., Markley, J. L. (May 2009) Empirical correlation between protein backbone (15)N and (13)C secondary chemical shifts and its application to nitrogen chemical shift re-referencing. J Biomol NMR, 44 (2). p. 95. ISSN 1573-5001 (Electronic)

URL: http://www.ncbi.nlm.nih.gov/pubmed/19436955
DOI: 10.1007/s10858-009-9324-0

Abstract

The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting (13)C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to (15)N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary (15)N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta (13)C chemical shifts are available (their difference is referencing error-free), the (15)N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have delta (15)N values mis-referenced by over 0.7 ppm and over 25% of them have delta (1)H(N) values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone (15)N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.

Item Type: Paper
Uncontrolled Keywords: Validation of chemical shifts Carbon-13 chemical shift Proton chemical shift Nitrogen-15 chemical shift LACS
Subjects: Investigative techniques and equipment
Investigative techniques and equipment > spectroscopy > magnetic resonance spectroscopy
Investigative techniques and equipment > spectroscopy
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: 13 May 2009
Date Deposited: 21 Feb 2013 15:35
Last Modified: 21 Feb 2013 15:35
PMCID: PMC2782637
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27367

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