Related ArticlesCorrection of the NMR structure of the ETS1/DNA complex.
J Biomol NMR. 1997 Dec;10(4):317-28
Authors: Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM
The ETS family of transcription factors consists of a group of proteins that share a highly conserved 85 amino acid DNA-binding domain (DBD). This family recognizes a consensus sequence rich in purine bases with a central GGAA motif. A comparison of the published three-dimensional structures of the DBD/DNA complexes of ETS1 by NMR [Werner et al. (1995) Cell, 83, 761-771] and the related Pu.1 by X-ray crystallography [Kodandapani et al. (1996) Nature, 380, 456-460] reveals an apparent discrepancy in which the protein domains bind with opposite polarity to their target sequences. This surprising and highly unlikely result prompted us to reexamine our NMR structure. Additional NMR experiments now reveal an error in the original interpretation of the spectra defining the orientation of the ETS1-DBD on DNA. It was originally reported that the ETS1-DBD bound to DNA with a bipartite motif involving major groove recognition via a helix-turn-helix element and minor groove recognition via protein side-chain intercalation. The presence of intercalation was deduced on the basis of numerous NOEs between several amino acids in the protein and a resonance at 12.33 ppm originally assigned to a DNA imino proton. New NMR experiments now conclusively demonstrate that this resonance, which is located within the DNA imino proton region of the spectrum, arises from the hydroxyl proton of Tyr86. Realization of this error necessitated reanalysis of the intermolecular NOEs. This revealed that the orientation of the ETS1-DBD in the complex is opposite to that originally reported and that a tryptophan residue does not intercalate into the DNA. The calculation of a new ensemble of structures based on the corrected data indicates that the structure of the ETS1-DBD/DNA complex is indeed similar to the X-ray structure of the Pu.1-DBD/DNA complex.
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each...
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06-06-2011 12:53 AM
Singular spectrum analysis for an automated solvent artifact removal and baseline correction of 1D NMR spectra.
Singular spectrum analysis for an automated solvent artifact removal and baseline correction of 1D NMR spectra.
Singular spectrum analysis for an automated solvent artifact removal and baseline correction of 1D NMR spectra.
J Magn Reson. 2011 Mar 6;
Authors: De Sanctis S, Malloni WM, Kremer W, Tomé AM, Lang EW, Neidig KP, Kalbitzer HR
NMR spectroscopy in biology and medicine is generally performed in aqueous solutions, thus in (1)H NMR spectroscopy, the dominant signal often stems from the partly suppressed solvent and can be many orders of...
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04-05-2011 10:22 PM
[NMR paper] Sequence-dependent correction of random coil NMR chemical shifts.
Sequence-dependent correction of random coil NMR chemical shifts.
Related Articles Sequence-dependent correction of random coil NMR chemical shifts.
J Am Chem Soc. 2001 Apr 4;123(13):2970-8
Authors: Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ
Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil...
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11-19-2010 08:32 PM
[NMR paper] Determination of the NMR structure of the complex between U1A protein and its RNA pol
Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element.
Related Articles Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element.
J Biomol NMR. 1998 Jan;11(1):59-84
Authors: Howe PW, Allain FH, Varani G, Neuhaus D
RNA-protein recognition is critical to post-transcriptional regulation of gene expression, yet poorly understood at the molecular level. The relatively slow progress in understanding this important area of...
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11-17-2010 11:06 PM
[NMR paper] NMR structure of the Tn916 integrase-DNA complex.
NMR structure of the Tn916 integrase-DNA complex.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_nsb.gif Related Articles NMR structure of the Tn916 integrase-DNA complex.
Nat Struct Biol. 1999 Apr;6(4):366-73
Authors: Wojciak JM, Connolly KM, Clubb RT
The integrase protein catalyzes the excision and integration of the Tn916 conjugative transposon, a promiscuous genetic element that spreads antibiotic resistance in pathogenic bacteria. The solution structure of the N-terminal domain of the Tn916 integrase...
Automated solvent artifact removal and base plane correction of multidimensional NMR
Abstract Strong solvent signals lead to a disappearance of weak protein signals close to the solvent resonance frequency and to base plane variations all over the spectrum. AUREMOL-SSA provides an automated approach for solvent artifact removal from multidimensional NMR protein spectra. Its core algorithm is based on singular spectrum analysis (SSA) in the time domain and is combined with an automated base plane correction in the frequency domain. The performance of the method has been tested on synthetic and experimental spectra including two-dimensional NOESY and TOCSY spectra and a...
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08-14-2010 04:19 AM
CheckShift: automatic correction of inconsistent chemical shift referencing
CheckShift: automatic correction of inconsistent chemical shift referencing
Simon W. Ginzinger, Fabian Gerick, Murray Coles and Volker Heun
Journal of Biomolecular NMR; 2007; 39(3); pp 223-227
Abstract:
The construction of a consistent protein chemical shift database is an important step toward making more extensive use of this data in structural studies. Unfortunately, progress in this direction has been hampered by the quality of the available data, particularly with respect to chemical shift referencing, which is often either inaccurate or inconsistently annotated. Preprocessing of...
Correction of the NMR structure of the ETS1/DNA complex.
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