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 â?¥0.40Â*ppm for asparagine and differences â?¥0.42Â*ppm for glutamine, the downfield shifted resonance lines can be assigned to Hδ21 and 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.
[NMR paper] Selective (15)N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy.
Selective (15)N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy.
Related Articles Selective (15)N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy.
J Biomol NMR. 2014 Jul 8;
Authors: Cao C, Chen JL, Yang Y, Huang F, Otting G, Su XC
Abstract
The side-chain amide groups of asparagine and glutamine play important roles in stabilizing the structural fold of proteins, participating in...
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07-10-2014 08:25 AM
Selective 15N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy
Selective 15N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy
Abstract
The side-chain amide groups of asparagine and glutamine play important roles in stabilizing the structural fold of proteins, participating in hydrogen-bonding networks and protein interactions. Selective 15N-labeling of side-chain amides, however, can be a challenge due to enzyme-catalyzed exchange of amide groups during protein synthesis. In the present study, we developed an efficient way of selectively...
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07-07-2014 11:50 PM
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
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04-30-2013 10:21 PM
4D Non-uniformly sampled HCBCACON and 1J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins
4D Non-uniformly sampled HCBCACON and 1J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins
Abstract A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit 13C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (Hα, and Hβ) and carbon (Cα, Cβ) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient...
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05-17-2012 08:40 AM
A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins
A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins
Abstract A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-glucose and subsaturating amounts of 2-methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1H-13C correlation spectra. Protein samples are conveniently prepared using the same media composition as the...
Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins
Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins
W. Trent Franks, Kathryn D. Kloepper, Benjamin J. Wylie and Chad M. Rienstra
Journal of Biomolecular NMR; 2007; 39(2); pp 107 - 131
Abstract:
Chemical shift assignment is the first step in all established protocols for structure determination of uniformly labeled proteins by NMR. The explosive growth in recent years of magic-angle spinning (MAS) solid-state NMR (SSNMR) applications is largely attributable to improved methods for backbone and side-chain chemical shift correlation...
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08-05-2008 01:33 PM
Chemical shift of protons?
Can someone give me the answers to the chemical shift of the protons in this compound: CH3CH2OCH2CH(CH3)COOH? Of if you can explain how to get the chemical shift it would be quite helpful as the info online does not really help me.
Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis
Linear Mode
