Publication date: Available online 21 September 2015 Source:Journal of Magnetic Resonance
Author(s): Bradley J. Harden, Subrata H. Mishra, Dominique P. Frueh
Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase. Graphical abstract
Sequential backbone assignment based on dipolar amide-to-amide correlation experiments
Sequential backbone assignment based on dipolar amide-to-amide correlation experiments
Abstract
Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an...
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05-15-2015 07:52 AM
[NMR paper] Assignment of methyl NMR resonances of a 52*kDa protein with residue-specific 4D correlation maps.
Assignment of methyl NMR resonances of a 52*kDa protein with residue-specific 4D correlation maps.
Related Articles Assignment of methyl NMR resonances of a 52*kDa protein with residue-specific 4D correlation maps.
J Biomol NMR. 2015 May 8;
Authors: Mishra SH, Frueh DP
Abstract
Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method...
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05-10-2015 03:50 AM
Assignment of methyl NMR resonances of a 52Â*kDa protein with residue-specific 4D correlation maps
Assignment of methyl NMR resonances of a 52Â*kDa protein with residue-specific 4D correlation maps
Abstract
Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to Cα and Cβ...
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05-07-2015 03:04 PM
[NMR paper] Facilitated Assignment of Large Protein NMR Signals with Covariance Sequential Spectra Using Spectral Derivatives.
Facilitated Assignment of Large Protein NMR Signals with Covariance Sequential Spectra Using Spectral Derivatives.
Facilitated Assignment of Large Protein NMR Signals with Covariance Sequential Spectra Using Spectral Derivatives.
J Am Chem Soc. 2014 Sep 16;
Authors: Harden BJ, Nichols SR, Frueh DP
Abstract
Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures...
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09-17-2014 11:54 AM
FacilitatedAssignment of Large Protein NMR Signalswith Covariance Sequential Spectra Using Spectral Derivatives
FacilitatedAssignment of Large Protein NMR Signalswith Covariance Sequential Spectra Using Spectral Derivatives
Bradley J. Harden, Scott R. Nichols and Dominique P. Frueh
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja5058407/20140916/images/medium/ja-2014-058407_0005.gif
Journal of the American Chemical Society
DOI: 10.1021/ja5058407
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/nO-MaipYTjs
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09-16-2014 08:38 PM
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
Available online 18 March 2013
Publication year: 2013
Source:Journal of Molecular Structure</br>
</br>
NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from...
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03-19-2013 12:58 AM
31P NMR correlation maps of 18O/16O chemical shift isotopic effects for phosphometabolite labeling studies
31P NMR correlation maps of 18O/16O chemical shift isotopic effects for phosphometabolite labeling studies
Abstract Intramolecular correlations among the 18O-labels of metabolic oligophosphates, mapped by J-decoupled 31P NMR 2D chemical shift correlation spectroscopy, impart stringent constraints to the 18O-isotope distributions over the whole oligophosphate moiety. The multiple deduced correlations of isotopic labels enable determination of site-specific fractional isotope enrichments and unravel the isotopologue statistics. This approach ensures accurate determination of 18O-labeling...
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06-06-2011 12:53 AM
[NMR paper] Sequential assignment of the backbone nuclei (1H, 15N and 13C) of c-H-ras p21 (1-166)
Sequential assignment of the backbone nuclei (1H, 15N and 13C) of c-H-ras p21 (1-166).GDP using a novel 4D NMR strategy.
Related Articles Sequential assignment of the backbone nuclei (1H, 15N and 13C) of c-H-ras p21 (1-166).GDP using a novel 4D NMR strategy.
J Biomol NMR. 1992 Nov;2(6):639-46
Authors: Campbell-Burk SL, Domaille PJ, Starovasnik MA, Boucher W, Laue ED
The c-H-ras p21 protein is the product of the human ras proto-oncogene, a member of a ubiquitous eukaryotic gene family which is highly conserved in evolution. These proteins play...
Effortless assignment with 4D covariance sequential correlation maps
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