Values of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4â??8Â*Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination.
[NMR paper] On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme.
On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7388-69-wiley-full-text.png Related Articles On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme.
Chembiochem. 2020 Nov 04;:
Authors: Smith LJ, van Gunsteren WF, Hansen N
Abstract
Values of S2CH and S2NH order...
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[NMR paper] Information content of long-range NMR data for the characterization of conformational heterogeneity.
Information content of long-range NMR data for the characterization of conformational heterogeneity.
Related Articles Information content of long-range NMR data for the characterization of conformational heterogeneity.
J Biomol NMR. 2015 Jun 5;
Authors: Andra?oj? W, Berlin K, Fushman D, Luchinat C, Parigi G, Ravera E, Sgheri L
Abstract
Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational...
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Information content of long-range NMR data for the characterization of conformational heterogeneity
Information content of long-range NMR data for the characterization of conformational heterogeneity
Abstract
Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by...
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06-05-2015 01:10 AM
[NMR paper] Information-driven modeling of large macromolecular assemblies using NMR data.
Information-driven modeling of large macromolecular assemblies using NMR data.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Information-driven modeling of large macromolecular assemblies using NMR data.
J Magn Reson. 2014 Apr;241:103-14
Authors: van Ingen H, Bonvin AM
Abstract
Availability of high-resolution atomic structures is one of the prerequisites for a mechanistic understanding of biomolecular function. This atomic...
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11-18-2014 01:56 PM
[Question from NMRWiki Q&A forum] Where to find technical information on Varian and Bruker data storage formats?
Where to find technical information on Varian and Bruker data storage formats?
Hello, I would like to find detailed technical info on the binary data storage formats for Varian and Bruker. Could anyone point me to such resources?
I'm involved into a student project where NMR data will be displayed in the web browser. The first thing we'd like to explore is the possibility of processing 1D with javascript, but we first have to be able to read the original data...
I've looked through Varian manuals, but apparently the right one did not pop up in front of me :). Could you suggest -...
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07-22-2011 10:38 AM
[NMR paper] A structural mode-coupling approach to 15N NMR relaxation in proteins.
A structural mode-coupling approach to 15N NMR relaxation in proteins.
Related Articles A structural mode-coupling approach to 15N NMR relaxation in proteins.
J Am Chem Soc. 2001 Apr 4;123(13):3055-63
Authors: Tugarinov V, Liang Z, Shapiro YE, Freed JH, Meirovitch E
The two-body Slowly Relaxing Local Structure (SRLS) model was applied to (15)N NMR spin relaxation in proteins and compared with the commonly used original and extended model-free (MF) approaches. In MF, the dynamic modes are assumed to be decoupled, local ordering at the N-H sites...
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11-19-2010 08:32 PM
[NMR paper] Simulation of NMR data from oriented membrane proteins: practical information for exp
Simulation of NMR data from oriented membrane proteins: practical information for experimental design.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Simulation of NMR data from oriented membrane proteins: practical information for experimental design.
Biophys J. 1993 Oct;65(4):1460-9
Authors: Sanders CR, Schwonek JP
Several hundred solid state NMR...
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08-22-2010 03:01 AM
[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...
On the use of 3 J -coupling NMR data to derive structural information on proteins
Linear Mode
