Related ArticlesInfluence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.
J Struct Funct Genomics. 2003;4(2-3):179-89
Authors: Jee J, Güntert P
Reliable automated NOE assignment and structure calculation on the basis of a largely complete, assigned input chemical shift list and a list of unassigned NOESY cross peaks has recently become feasible for routine NMR protein structure calculation and has been shown to yield results that are equivalent to those of the conventional, manual approach. However, these algorithms rely on the availability of a virtually complete list of the chemical shifts. This paper investigates the influence of incomplete chemical shift assignments on the reliability of NMR structures obtained with automated NOESY cross peak assignment. The program CYANA was used for combined automated NOESY assignment with the CANDID algorithm and structure calculations with torsion angle dynamics at various degrees of completeness of the chemical shift assignment which was simulated by random omission of entries in the experimental 1H chemical shift lists that had been used for the earlier, conventional structure determinations of two proteins. Sets of structure calculations were performed choosing the omitted chemical shifts randomly among all assigned hydrogen atoms, or among aromatic hydrogen atoms. For comparison, automated NOESY assignment and structure calculations were performed with the complete experimental chemical shift but under random omission of NOESY cross peaks. When heteronuclear-resolved three-dimensional NOESY spectra are available the current CANDID algorithm yields in the absence of up to about 10% of the experimental 1H chemical shifts reliable NOE assignments and three-dimensional structures that deviate by less than 2 A from the reference structure obtained using all experimental chemical shift assignments. In contrast, the algorithm can accommodate the omission of up to 50% of the cross peaks in heteronuclear- resolved NOESY spectra without producing structures with a RMSD of more than 2 A to the reference structure. When only homonuclear NOESY spectra are available, the algorithm is slightly more susceptible to missing data and can tolerate the absence of up to about 7% of the experimental 1H chemical shifts or of up to 30% of the NOESY peaks.
[NMR paper] Influence of chemical shift tolerances on NMR structure calculations using ARIA proto
Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.
Related Articles Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.
J Biomol NMR. 2005 Jan;31(1):21-34
Authors: Fossi M, Linge J, Labudde D, Leitner D, Nilges M, Oschkinat H
Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift...
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NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived fr
NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx.
Related Articles NMR chemical shift assignments of a complex between SUMO-1 and SIM peptide derived from the C-terminus of Daxx.
Biomol NMR Assign. 2010 Oct 7;
Authors: Naik MT, Chang CC, Naik NM, Kung CC, Shih HM, Huang TH
Small Ubiquitin-like MOdifiers (SUMOs) are ubiquitin-like proteins known to covalently modify large number of cellular proteins. The mammalian SUMO family includes four paralogues, SUMO-1 through SUMO-4....
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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] 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] Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronu
Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy.
Related Articles Chemical shift assignments and secondary structure of the Grb2 SH2 domain by heteronuclear NMR spectroscopy.
J Biomol NMR. 1996 Mar;7(2):89-98
Authors: Wang YS, Frederick AF, Senior MM, Lyons BA, Black S, Kirschmeier P, Perkins LM, Wilson O
The growth factor receptor-bound protein-2 (Grb-2) is an adaptor protein that mediates signal transduction pathways. Chemical shift assignments were obtained for the SH2 domain of...
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[NMR paper] 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnes
1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and...
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...