Related ArticlesResonance assignment of proteins with high shift degeneracy based on 5D spectral information encoded in G2FT NMR experiments.
J Am Chem Soc. 2005 Apr 6;127(13):4554-5
Authors: Atreya HS, Eletsky A, Szyperski T
A suite of novel (5,3)D G2FT triple resonance NMR experiments encoding highly resolved 5D spectral information is presented for sequential resonance assignment of proteins exhibiting high chemical shift degeneracy. Efficient resonance assignment is achieved by separate joint sampling of (i) chemical shifts which solely serve to provide increased resolution and (ii) shifts which also provide sequential connectivities. In these G2FT experiments, two G-matrix transformations are employed. Peaks are resolved along a first GFT dimension at both Omega(15N) + Omega(13C') and Omega(15N) - Omega(13C'), or at Omega(15N) + Omega(13Calpha) and Omega(15N) - Omega(13Calpha), to break backbone 15N,1HN chemical shift degeneracy. Sequential connectivities are established along a second GFT dimension by measuring intraresidue and sequential correlations at 2Omega(13Calpha), Omega(13Calpha + 13Cbeta), and Omega(13Calpha - 13Cbeta), or at Omega(13Calpha + 1Halpha) and Omega(13Calpha - 1Halpha), to resolve 13Calpha/beta,1Halpha chemical shift degeneracy. It is demonstrated that longitudinal proton relaxation optimization of out-and-back implementations suitable for deuterated proteins and nonlinear data sampling combined with maximum entropy reconstruction further accelerate G2FT NMR data acquisition speed. As a result, the spectral information can be obtained within hours, so that (5,3)D G2FT experiments are viable options for high-throughput structure determination in structural genomics. Applications are presented for 17 kDa alpha-helical protein YqbG and 13.5 kDa protein rps24e, targets of the Northeast Structural Genomics consortium, as well as for 9 kDa protein Z-domain. The high resolving power of the G2FT NMR experiments makes them attractive choices to study alpha-helical globular/membrane or (partially) unfolded proteins, thus promising to pave the way for NMR-based structural genomics of membrane proteins.
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase...
Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes
Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes
Abstract An approach for conveniently implementing low-power CN n ν and RN n ν symmetry-based band-selective mixing sequences for generating homo- and heteronuclear chemical shift correlation NMR spectra of low γ nuclei in biological solids is demonstrated. Efficient magnetisation transfer characteristics are achieved by selecting appropriate symmetries requiring the application of basic RF elements of relatively long duration and numerically tailoring the RF field modulation profile...
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06-20-2011 03:31 PM
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
J Comput Biol. 2011 Mar;18(3):347-63
Authors: Jang R, Gao X, Li M
Abstract In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow...
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03-10-2011 03:51 PM
Paramagnetic-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins.
Paramagnetic-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins.
Paramagnetic-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins.
J Am Chem Soc. 2011 Feb 2;
Authors: Shi L, Traaseth NJ, Verardi R, Gustavsson M, Gao J, Veglia G
Residual dipolar couplings (RDCs) are widely used as orientation-dependent NMR restraints to improve the resolution of the NMR conformational ensemble of biomacromolecules and define the...
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02-04-2011 11:34 AM
Paramagnetic-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins
Paramagnetic-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins
Lei Shi, Nathaniel J. Traaseth, Raffaello Verardi, Martin Gustavsson, Jiali Gao and Gianluigi Veglia
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja109080t/aop/images/medium/ja-2010-09080t_0003.gif
Journal of the American Chemical Society
DOI: 10.1021/ja109080t
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/Tu9H79dfKCk
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02-03-2011 06:45 AM
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2011</br>
Jie, Wen , Jihui, Wu , Pei, Zhou</br>
Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D...
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01-05-2011 11:03 AM
[NMR paper] RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins
RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
Related Articles RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
J Biomol NMR. 1999 Sep;15(1):15-26
Authors: Pons JL, Delsuc MA
The assignment of the 1H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1H...
Resonance assignment of proteins with high shift degeneracy based on 5D spectral info
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