title: Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis.
abstract: 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 Hδ21and Hε21, 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.
authors.affiliation: Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Harsch
authors.affiliation: Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Schneider
authors.affiliation: Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
authors.forename: Bärbel
authors.initials: B
authors.lastname: Kieninger
authors.affiliation: Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
authors.forename: Harald
authors.initials: H
authors.lastname: Donaubauer
authors.affiliation: Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany. hans-robert.kalbitzer@biologie.uni-regensburg.de.
authors.forename: Hans Robert
authors.identifier: 0000-0002-6514-2355
authors.initials: HR
authors.lastname: Kalbitzer
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D001216:Asparagine / Q000737:chemistry*; D005973:Glutamine / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D012984:Software
chemical_list: D000577:Amides; D011506:Proteins; D011522:Protons; D005973:Glutamine; D001216:Asparagine
keywords: Chemical shift; NMR stereospecific assignment; Sidechain amide protons