Related ArticlesRelaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex.
Proteins. 1991;10(2):117-29
Authors: Sutcliffe MJ, Dobson CM
The effect of including paramagnetic relaxation data as additional restraints in the determination of protein tertiary structures from NMR data has been explored by a systematic series of model calculations. The system used for testing the method was the 2.0 A resolution tetragonal crystal structure of hen egg white lysozyme (129 amino acid residues) and structures were generated using a version of the hybrid "distance geometry-dynamic simulated annealing" procedure. A limited set of 769 NOEs was used as restraints in all the calculations; the strengths of these were categorized into three classes on the basis of distances observed in the crystal structure. The values of 50 phi angles were also restrained on the basis of amide-alpha coupling constants calculated from the X-ray structure. Five sets of 12 structures were determined using differing sets of paramagnetic relaxation data as restraints additional to those involving the NOE and coupling constant data. The paramagnetic relaxation data were modeled on the basis of the distances of defined protons from the crystallographic binding site of Gd3+ in lysozyme. Analysis of the results showed that the relaxation data significantly improved the correspondence between the set of generated structures and the crystal structure, and that the more well defined the relaxation data, the more significant the improvement in the quality of the structures. The results suggest that the inclusion of paramagnetic relaxation restraints could be of significant value for the experimental determination of protein structures from NMR 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
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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[NMR paper] NMR structure determination of proteins supplemented by quantum chemical calculations
NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.
Related Articles NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.
J Biomol NMR. 2005 Feb;31(2):97-114
Authors: Hsiao YW, Drakenberg T, Ryde U
We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular...
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11-24-2010 11:14 PM
[NMR paper] Determination of protein rotational correlation time from NMR relaxation data at vari
Determination of protein rotational correlation time from NMR relaxation data at various solvent viscosities.
Related Articles Determination of protein rotational correlation time from NMR relaxation data at various solvent viscosities.
J Biomol NMR. 2004 Dec;30(4):431-42
Authors: Korchuganov DS, Gagnidze IE, Tkach EN, Schulga AA, Kirpichnikov MP, Arseniev AS
An accurate determination of the overall rotation of a protein plays a crucial role in the investigation of its internal motions by NMR. In the present work, an innovative approach to the...
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[NMR paper] Limits of NMR structure determination using variable target function calculations: ri
Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.
J Mol Biol. 1997 Feb 21;266(2):400-23
Authors: Pfeiffer S, Karimi-Nejad Y, Rüterjans H
Limits of NMR structure determination using multidimensional NMR spectroscopy, variable target function...
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[NMR paper] Limits of NMR structure determination using variable target function calculations: ri
Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.
J Mol Biol. 1997 Feb 21;266(2):400-23
Authors: Pfeiffer S, Karimi-Nejad Y, Rüterjans H
Limits of NMR structure determination using multidimensional NMR spectroscopy, variable target function...
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[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
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J Biomol NMR. 1991 Nov;1(4):447-56
Authors: Güntert P, Wüthrich K
A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...
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08-21-2010 11:12 PM
[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
Related Articles Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
J Biomol NMR. 1991 Nov;1(4):447-56
Authors: Güntert P, Wüthrich K
A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...
Relaxation data in NMR structure determination: model calculations for the lysozyme-G
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