Related ArticlesJoint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.
J Biomol NMR. 2001 Nov;21(3):235-48
Authors: Raves ML, Doreleijer JF, Vis H, Vorgias CE, Wilson KS, Kaptei R
Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus stearothermophilus (HUBst). The procedure was aimed at investigating the compatibility of the two data sets and at identifying conflicting information. Wherever important differences were found, such as peptide flips in the main-chain conformation, the data were further analyzed to find the cause. The NMR data showed some errors arising either from the manual interpretation of the spectra or from the incorrect account for spin diffusion. The most important artefact inherent to the X-ray data is the crystal packing of the molecules: the effects range from the limitation of the freedom of the flexible parts of the HUBst molecule to possibly one of the peptide flips.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...
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High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
J Biomol NMR. 2011 Sep 22;
Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...
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09-23-2011 05:30 PM
[NMR paper] Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
Related Articles Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
Structure. 2004 Jul;12(7):1165-76
Authors: Chao JA, Williamson JR
L30e, a Saccharomyces cervisiae ribosomal protein, regulates its own expression by binding to a purine-rich asymmetric internal loop located in both its pre-mRNA and mature mRNA. A crystal structure of an MBP-L30e fusion protein in complex with an RNA containing the pre-mRNA regulatory site was solved at 3.24 A. Interestingly, the...
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11-24-2010 09:51 PM
[NMR paper] Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data
Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations.
J Mol Biol. 1995 Apr 7;247(4):689-700
Authors: van Tilborg MA, Bonvin AM, Hård K, Davis AL, Maler B, Boelens R, Yamamoto KR, Kaptein R
The solution structure of the glucocorticoid...
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[NMR paper] A systematic comparison of three structure determination methods from NMR data: depen
A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
Related Articles A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
J Biomol NMR. 1992 Jul;2(4):373-88
Authors: Liu Y, Zhao D, Altman R, Jardetzky O
We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints, (2) their assumed precision, (3) the method of structure calculation...
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08-21-2010 11:41 PM
[NMR paper] Motional effects on NMR structural data. Comparison of spinach and Escherichia coli a
Motional effects on NMR structural data. Comparison of spinach and Escherichia coli acyl carrier proteins.
Related Articles Motional effects on NMR structural data. Comparison of spinach and Escherichia coli acyl carrier proteins.
Biochem Pharmacol. 1990 Jul 1;40(1):7-13
Authors: Kim Y, Ohlrogge JB, Prestegard JH
Proteins in solution need not exist in a single rigid structure but can exist in a dynamic equilibrium among structural forms. The problems that this poses for structure determination using nuclear Overhauser effect data from...
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[NMR paper] Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Related Articles Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Proteins. 1990;8(4):377-85
Authors: Kim Y, Prestegard JH
Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling...
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[NMR paper] A branch and bound algorithm for protein structure refinement from sparse NMR data se
A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
J Mol Biol. 1999 Jan 29;285(4):1691-710
Authors: Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE
We describe new methods for predicting protein tertiary structures to low resolution given the specification of secondary structure and a...