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 than 24 h on a single aligned protein sample, greatly improves convergence of the Rosetta-NMR protocol, allowing for overnight fold calculation of small proteins. We demonstrate the performance of our fast fold calculation approach for ubiquitin as a test case, and for two RNA-binding domains of the plant protein HYL1. Structure calculations based on simulated RDC data highlight the importance of an accurate and precise set of several complementary RDCs as additional input restraints for high-quality de novo structure determination.
Content Type Journal Article
Category Article
Pages 1-10
DOI 10.1007/s10858-011-9567-4
Authors
Rodolfo M. Rasia, Institut de Biologie Structurale, Jean-Pierre Ebel CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex, France
Ewen Lescop, Institut de Biologie Structurale, Jean-Pierre Ebel CNRS/CEA/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex, France
Simultaneous measurement of 1Hâ??15N and Methyl 1Hmâ??13Cm residual dipolar couplings in large proteins
Simultaneous measurement of 1Hâ??15N and Methyl 1Hmâ??13Cm residual dipolar couplings in large proteins
Abstract A two-dimensional TROSY-based SIM-13Cmâ??1Hm/1Hâ??15N NMR experiment for simultaneous measurements of methyl 1 D CH and backbone amide 1 D NH residual dipolar couplings (RDC) in {U-; Ileδ1-; Leu,Val-}-labeled samples of large proteins is described. Significant variation in the alignment tensor of the 82-kDa enzyme Malate synthase G is observed as a function of only slight changes in experimental conditions. The SIM-13Cmâ??1Hm/1Hâ??15N data sets provide convenient means...
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09-30-2011 08:01 PM
Measurement of 1Hâ??15N and 1Hâ??13C residual dipolar couplings in nucleic acids from TROSY intensities
Measurement of 1Hâ??15N and 1Hâ??13C residual dipolar couplings in nucleic acids from TROSY intensities
Abstract Analogous to the recently introduced ARTSY method for measurement of one-bond 1Hâ??15N residual dipolar couplings (RDCs) in large perdeuterated proteins, we introduce methods for measurement of base 13Câ??1H and 15Nâ??1H RDCs in protonated nucleic acids. Measurements are based on quantitative analysis of intensities in 1Hâ??15N and 13Câ??1H TROSY-HSQC spectra, and are illustrated for a 71-nucleotide adenine riboswitch. Results compare favorably with those of conventional...
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[NMR paper] The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining pro
The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.
Related Articles The 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...
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11-25-2010 08:21 PM
[NMR paper] Controlling residual dipolar couplings in high-resolution NMR of proteins by strain i
Controlling residual dipolar couplings in high-resolution NMR of proteins by strain induced alignment in a gel.
Related Articles Controlling residual dipolar couplings in high-resolution NMR of proteins by strain induced alignment in a gel.
J Biomol NMR. 2001 Oct;21(2):141-51
Authors: Ishii Y, Markus MA, Tycko R
Water-soluble biological macromolecules can be weakly aligned by dissolution in a strained, hydrated gel such as cross-linked polyacrylamide, an effect termed 'strain-induced alignment in a gel' (SAG). SAG induces nonzero nuclear...
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11-19-2010 08:44 PM
Facile measurement of 1Hâ??15N residual dipolar couplings in larger perdeuterated pro
Abstract We present a simple method, ARTSY, for extracting 1JNH couplings and 1Hâ??15N RDCs from an interleaved set of two-dimensional 1Hâ??15N TROSY-HSQC spectra, based on the principle of quantitative J correlation. The primary advantage of the ARTSY method over other methods is the ability to measure couplings without scaling peak positions or altering the narrow line widths characteristic of TROSY spectra. Accuracy of the method is demonstrated for the model system GB3. Application to the catalytic core domain of HIV integrase, a 36 kDa homodimer with unfavorable spectral...
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08-14-2010 04:19 AM
MQ-HNCO-TROSY for the measurement of scalar and residual dipolar couplings in larger
Abstract We describe a novel pulse sequence, MQ-HNCO-TROSY, for the measurement of scalar and residual dipolar couplings between amide proton and nitrogen in larger proteins. The experiment utilizes the whole 2TN polarization transfer delay for labeling of 15N chemical shift in a constant time manner, which efficiently doubles the attainable resolution in 15N dimension with respect to the conventional HNCO-TROSY experiment. In addition, the accordion principle is employed for measuring (J + D)NHs, and the multiplet components are selected with the generalized version of the TROSY scheme...
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Theoretical framework for NMR residual dipolar couplings in unfolded proteins
Theoretical framework for NMR residual dipolar couplings in unfolded proteins
O. I. Obolensky, Kai Schlepckow, Harald Schwalbe and A. V. Solov’yov
Journal of Biomolecular NMR; 2007; 39(1) pp 1-16
Abstract:
A theoretical framework for the prediction of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) in unfolded proteins under weakly aligning conditions is presented. The unfolded polypeptide chain is modeled as a random flight chain while the alignment medium is represented by a set of regularly arranged obstacles. For the case of bicelles oriented perpendicular to...
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08-05-2008 02:26 AM
Composite Alignment Media for the Measurement of Independent Sets of NMR Residual Dipolar Couplings
Composite Alignment Media for the Measurement of Independent Sets of NMR Residual Dipolar Couplings
Ke Ruan and Joel R. Tolman
J. Am. Chem. Soc.; 2005; 127(43) pp 15032 - 15033;
Abstract:
The measurement of independent sets of NMR residual dipolar couplings (RDCs) in multiple alignment media can provide a detailed view of biomolecular structure and dynamics, yet remains experimentally challenging. It is demonstrated here that independent sets of RDCs can be measured for ubiquitin using just a single alignment medium composed of aligned bacteriophage Pf1 particles embedded in a...
Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins
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