Related ArticlesEZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data.
J Biomol NMR. 2013 Sep 11;
Authors: Zuiderweg ER, Bagai I, Rossi P, Bertelsen EB
Abstract
For several of the proteins in the BioMagResBank larger than 200 residues, 60*% or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6*×*10(260) possible assignments. In "EZ-ASSIGN", the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281-298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592-610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335-344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested.
PMID: 24022834 [PubMed - as supplied by publisher]
[NMR paper] Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
J Biomol NMR. 2013 Aug 14;
Authors: Bellstedt P, Seiboth T, Häfner S, Kutscha H, Ramachandran R, Görlach M
Abstract
NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though...
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Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins
Influence of 1H chemical shift assignments of the interface residues on structure determinations of homodimeric proteins
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
Yi-Jan Lin, Donata K. Kirchner, Peter Güntert</br>
Homodimeric proteins pose a difficulty for NMR structure determination because the degeneracy of the chemical shifts in the two identical monomers implies an ambiguity in all assignments of distance restraints. For homodimeric proteins, residues involved in the interface between two monomers provide essential intermolecular NOEs. The...
[NMR paper] 1H,15N,13C-triple resonance NMR of very large systems at 900 MHz.
1H,15N,13C-triple resonance NMR of very large systems at 900 MHz.
Related Articles 1H,15N,13C-triple resonance NMR of very large systems at 900 MHz.
J Magn Reson. 2003 Aug;163(2):360-8
Authors: Chung J, Kroon G
We provide quantitative signal to noise data and feasibility study at 900 MHz for 1H-15N-13C triple resonance backbone assignment pulse sequences obtained from a medium sized 2H, 13C, 15N labeled protein slowed down in glycerol-water solution to mimic relaxation and spectroscopic properties of a much larger protein system with...
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[NMR paper] 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct
1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
J Biomol NMR. 1997 Feb;9(2):167-80
Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C
1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia...
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[NMR paper] Heteronuclear 3D NMR and isotopic labeling of calmodulin. Towards the complete assign
Heteronuclear 3D NMR and isotopic labeling of calmodulin. Towards the complete assignment of the 1H NMR spectrum.
Related Articles Heteronuclear 3D NMR and isotopic labeling of calmodulin. Towards the complete assignment of the 1H NMR spectrum.
Biochem Pharmacol. 1990 Jul 1;40(1):153-60
Authors: Ikura M, Marion D, Kay LE, Shih H, Krinks M, Klee CB, Bax A
New methods are described that permit detailed analysis of the NMR spectra of calmodulin, an alpha-helical protein with a molecular weight of 16.7 kD. Two complementary approaches have been...
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[NMR paper] Solid-state NMR triple-resonance backbone assignments in a protein.
Solid-state NMR triple-resonance backbone assignments in a protein.
Related Articles Solid-state NMR triple-resonance backbone assignments in a protein.
J Biomol NMR. 1999 Apr;13(4):337-42
Authors: Tan WM, Gu Z, Zeri AC, Opella SJ
Triple-resonance solid-state NMR spectroscopy is demonstrated to sequentially assign the 13C' and 15N amide backbone resonances of adjacent residues in an oriented protein sample. The observed 13C' chemical shift frequency provides an orientational constraint complementary to those measured from the 1H and 15N amide...
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A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data.
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