A suite of reduced-dimensionality (13)C,(15)N,(1)H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these experiments allow one to retain the high spectral resolution required for efficient automated analysis. "Sampling limited" and "sensitivity limited" data collection regimes are defined, respectively, depending on whether the sampling of the indirect dimensions or the sensitivity of a multidimensional NMR experiments per se determines the minimally required measurement time. We show that reduced-dimensionality NMR spectroscopy is a powerful approach to avoid the "sampling limited regime"--i.e., a standard set of ten experiments proposed here allows one to effectively adapt minimal measurement times to sensitivity requirements. This is of particular interest in view of the greatly increased sensitivity of NMR spectrometers equipped with cryogenic probes. As a step toward fully automated analysis, the program AUTOASSIGN has been extended to provide sequential backbone and (13)C(beta) resonance assignments from these reduced-dimensionality NMR data.
Reduced dimensionality 3D HNCANfor unambiguous HN, CA and N assignment in proteins
Reduced dimensionality 3D HNCANfor unambiguous HN, CA and N assignment in proteins
Publication year: 2012
Source: Journal of Magnetic Resonance, Available online 8 February 2012</br>
Manoj Kumar*Rout, Pushpa*Mishra, Hanudatta S.*Atreya, Ramakrishna V.*Hosur</br>
We present here an improvisation of HNN (Panchal, Bhavesh et al. 2001)called RD 3D HNCANfor backbone (HN, CA andN) assignment inboth folded and unfolded proteins. This is a reduced dimensionality experiment which employsCAchemical shifts to improve dispersion. Distinct positive and negative peak patternsof various triplet...
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02-10-2012 09:13 AM
Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH
Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH
Abstract We present reduced dimensionality (RD) 3D HN(CA)NH for efficient sequential assignment in proteins. The experiment correlates the 15N and 1H chemical shift of a residue (â??iâ??) with those of its immediate N-terminal (i â?? 1) and C-terminal (i + 1) neighbors and provides four-dimensional chemical shift correlations rapidly with high resolution. An assignment strategy is presented which combines the correlations observed in this experiment with amino acid type information obtained from 3D ...
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01-09-2012 08:08 AM
Aliasing in reduced dimensionality NMR spectra: (3,2)D HNHA and (4,2)D HN(COCA)NH experiments as examples
Aliasing in reduced dimensionality NMR spectra: (3,2)D HNHA and (4,2)D HN(COCA)NH experiments as examples
Abstract Reduced dimensionality NMR spectra usually require very large spectral widths in the shared dimension. In this paper we show that aliasing can be introduced in reduced dimensionality NMR spectra either to decrease the acquisition time or increase the resolution of the experiments without losing information. The gains of introducing aliasing are illustrated with two examples, the (3,2)D HNHA and the (4,2)D HN(COCA)NH experiments. In both cases a reduction of the spectral...
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01-09-2011 12:46 PM
[NMR paper] NMR data collection and analysis protocol for high-throughput protein structure determination.
NMR data collection and analysis protocol for high-throughput protein structure determination.
Related Articles NMR data collection and analysis protocol for high-throughput protein structure determination.
Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10487-92
Authors: Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szyperski T
A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that...
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12-01-2010 06:56 PM
[NMR paper] High-throughput inference of protein-protein interfaces from unassigned NMR data.
High-throughput inference of protein-protein interfaces from unassigned NMR data.
Related Articles High-throughput inference of protein-protein interfaces from unassigned NMR data.
Bioinformatics. 2005 Jun;21 Suppl 1:i292-301
Authors: Mettu RR, Lilien RH, Donald BR
SUMMARY: We cast the problem of identifying protein-protein interfaces, using only unassigned NMR spectra, into a geometric clustering problem. Identifying protein-protein interfaces is critical to understanding inter- and intra-cellular communication, and NMR allows the study of...
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11-25-2010 08:21 PM
[NMR paper] High-throughput 3D structural homology detection via NMR resonance assignment.
High-throughput 3D structural homology detection via NMR resonance assignment.
Related Articles High-throughput 3D structural homology detection via NMR resonance assignment.
Proc IEEE Comput Syst Bioinform Conf. 2004;:278-89
Authors: Langmead CJ, Donald BR
One goal of the structural genomics initiative is the identification of new protein folds. Sequence-based structural homology prediction methods are an important means for prioritizing unknown proteins for structure determination. However, an important challenge remains: two highly...
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11-24-2010 09:25 PM
[NMR paper] An efficient high-throughput resonance assignment procedure for structural genomics a
An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Related Articles An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Biochemistry. 2001 Dec 11;40(49):14727-35
Authors: Bhavesh NS, Panchal SC, Hosur RV
Sequence specific resonance assignment is the primary requirement for all investigations of proteins by NMR methods. In the present postgenomic era where structural genomics and protein folding have...
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11-19-2010 08:44 PM
NMR in a crystallography-based high-throughput protein structure-determination enviro
NMR in a crystallography-based high-throughput protein structure-determination environment.
Related Articles NMR in a crystallography-based high-throughput protein structure-determination environment.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1365-6
Authors: Wüthrich K
An introduction is provided to three papers which compare corresponding protein crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG). Special mention is made of the JCSG strategy for combined use of the two...