Harsch, Tobias and Schneider, Philipp and Kieninger, Barbel and Donaubauer, Harald and Kalbitzer, Hans Robert (2017) Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis. JOURNAL OF BIOMOLECULAR NMR, 67 (2). pp. 157-164. ISSN 0925-2738, 1573-5001
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Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences >0.40 ppm for asparagine and differences >0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H-delta 21 and H-epsilon 21, respectively, at a confidence level > 95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | ; NMR stereospecific assignment; Sidechain amide protons; Chemical shift |
| Subjects: | 500 Science > 570 Life sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Dr. Hans Robert Kalbitzer |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 14 Dec 2018 13:01 |
| Last Modified: | 14 Feb 2019 15:57 |
| URI: | https://pred.uni-regensburg.de/id/eprint/420 |
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