Related ArticlesThe fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.
J Magn Reson. 2005 Apr;173(2):310-6
Authors: Meiler J, Baker D
We illustrate how moderate resolution protein structures can be rapidly obtained by interlinking computational prediction methodologies with un- or partially assigned NMR data. To facilitate the application of our recently described method of ranking and subsequent refining alternative structural models using unassigned NMR data [Proc. Natl. Acad. Sci. USA 100 (2003) 15404] for such "structural genomics"-type experiments it is combined with protein models from several prediction techniques, enhanced to utilize partial assignments, and applied on a protein with an unknown structure and fold. From the original NMR spectra obtained for the 140 residue fumarate sensor DcuS, 1100 1H, 13C, and 15N chemical shift signals, 3000 1H-1H NOESY cross peak intensities, and 209 backbone residual dipolar couplings were extracted and used to rank models produced by de novo structure prediction and comparative modeling methods. The ranking proceeds in two steps: first, an optimal assignment of the NMR peaks to atoms is found for each model independently, and second, the models are ranked based on the consistency between the NMR data and the model assuming these optimal assignments. The low-resolution model selected using this ranking procedure had the correct overall fold and a global backbone RMSD of 6.0 angstrom, and was subsequently refined to 3.7 angstrom RMSD. With the incorporation of a small number of NOE and residual dipolar coupling constraints available very early in the traditional spectral assignment process, a model with an RMSD of 2.8 angstrom could rapidly be built. The ability to generate moderate resolution models within days of NMR data collection should facilitate large scale NMR structure determination efforts.
Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins
Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins
Abstract It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results. Here we present a suite of time- and sensitivity optimized NMR experiments for rapid measurement of up to six RDCs per residue. Including such an RDC data set, measured in less...
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[NMR paper] Rapid assessment of protein structural stability and fold validation via NMR.
Rapid assessment of protein structural stability and fold validation via NMR.
Related Articles Rapid assessment of protein structural stability and fold validation via NMR.
Methods Enzymol. 2005;394:142-75
Authors: Hoffmann B, Eichmüller C, Steinhauser O, Konrat R
In structural proteomics, it is necessary to efficiently screen in a high-throughput manner for the presence of stable structures in proteins that can be subjected to subsequent structure determination by X-ray or NMR spectroscopy. Here we illustrate that the (1)H chemical...
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[NMR paper] Rapid protein fold determination using unassigned NMR data.
Rapid protein fold determination using unassigned NMR data.
Related Articles Rapid protein fold determination using unassigned NMR data.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9
Authors: Meiler J, Baker D
Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs),...
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[NMR paper] The NMR structure of the sensory domain of the membranous two-component fumarate sens
The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli.
The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli.
J Biol Chem. 2003 Oct 3;278(40):39185-8
Authors: Pappalardo L, Janausch IG, Vijayan V, Zientz E, Junker J, Peti W, Zweckstetter M, Unden G, Griesinger C
The structure of the water-soluble, periplasmic domain of the fumarate sensor DcuS (DcuS-pd) has been determined...
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, resid
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes.
J Comput Chem. 2010 Aug 30;
Authors: Latek D, Kolinski A
Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low-cost global protein fold determination. Here, we present...
The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining pro
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