Related ArticlesAn empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation.
J Am Chem Soc. 2004 Jun 16;126(23):7281-92
Authors: Grishaev A, Bax A
A new multidimensional potential is described that encodes for the relative spatial arrangement of the peptidyl backbone units as observed within a large database of high-resolution X-ray structures. The detailed description afforded by such an analysis provides an opportunity to study the atomic details of hydrogen bonding in proteins. The specification of the corresponding potential of mean force (PMF) is based on a defined set of physical principles and optimized to yield the maximum advantage when applied to protein structure refinement. The observed intricate differences between hydrogen-bonding geometries within various patterns of secondary structure allow application of the PMF to both validation of protein structures and their refinement. A pronounced improvement of several aspects of structural quality is observed following the application of such a potential to a variety of NMR-derived models, including a noticeable decrease in backbone coordinate root-mean-square deviation relative to the X-ray structures and a considerable improvement in the Ramachandran map statistics.
[NMR paper] 1H NMR investigation of the distal hydrogen bonding network and ligand tilt in the cy
1H NMR investigation of the distal hydrogen bonding network and ligand tilt in the cyanomet complex of oxygen-avid Ascaris suum hemoglobin.
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J Biol Chem. 1999 Nov 5;274(45):31819-26
Authors: Xia Z, Zhang W, Nguyen BD, Mar GN, Kloek AP, Goldberg DE
The O(2)-avid hemoglobin from the parasitic nematode Ascaris suum exhibits one of the slowest known O(2) off rates. Solution (1)H NMR has been...
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Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy
Abstract We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual 15Nâ??T 1 timescales). We observed chemical exchange for 6...
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10-27-2010 08:51 AM
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.
Related Articles Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.
J Biomol NMR. 2010 Oct 20;
Authors: Del Amo JM, Fink U, Reif B
We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that...
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[NMR paper] NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the D
NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with target RNA fragments with site-specific uridine substitutions.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-oxfordjournals_final_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with...
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[NMR paper] NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the D
NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with target RNA fragments with site-specific uridine substitutions.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-oxfordjournals_final_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with...
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[NMR paper] Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA meth
Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR.
Biochemistry. 1996 Jul 23;35(29):9335-48
Authors: Habazettl J, Myers LC, Yuan F, Verdine GL, Wagner G
The 10kDa amino-terminal fragment of...
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Hydrogen-bonding potential to refine NMR structure
An Empirical Backbone-Backbone Hydrogen-Bonding Potential in Proteins and Its Applications to NMR Structure Refinement and Validation
Alexander Grishaev and Ad Bax
J. Am. Chem. Soc.; 2004; 126(23) pp 7281 - 7292
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Abstract:
A new multidimensional potential is described that encodes for the relative spatial arrangement of the peptidyl backbone units as observed within a large database of high-resolution X-ray structures. The detailed description afforded by such an analysis provides an opportunity to study...
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06-29-2005 04:16 AM
Mars - automatic backbone assignment of proteins
Link to the program
Mars - robust automatic backbone assignment of proteins.
Jung YS, Zweckstetter M. J Biomol NMR. 2004 Sep;30(1):11-23.
Abstract:
MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar...
An empirical backbone-backbone hydrogen-bonding potential in proteins and its applica
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