Related ArticlesGeneral framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation.
J Am Chem Soc. 2002 Apr 24;124(16):4522-34
Authors: Prompers JJ, Brüschweiler R
A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin interactions responsible for spin relaxation. The covariance matrix, which is evaluated using a molecular dynamics (MD) simulation, is diagonalized yielding reorientational eigenmodes and amplitudes that reveal detailed information about correlated protein dynamics. The eigenvalue distribution allows one to quantitatively assess whether overall and internal motions are statistically separable. To each eigenmode belongs a correlation time that can be adjusted to optimally reproduce experimental relaxation parameters. A key feature of the method is that it does not require separability of overall tumbling and internal motions, which makes it applicable to a wide range of systems, such as folded, partially folded, and unfolded biomolecular systems and other macromolecules in solution. The approach was applied to NMR relaxation data of ubiquitin collected at multiple magnetic fields in the native form and in the partially folded A-state using MD trajectories with lengths of 6 and 70 ns. The relaxation data of native ubiquitin are well reproduced after adjustment of the correlation times of the 10 largest eigenmodes. For this state, a high degree of separability between internal and overall motions is present as is reflected in large amplitude and collectivity gaps between internal and overall reorientational modes. In contrast, no such separability exists for the A-state. Residual overall tumbling motion involving the N-terminal beta-sheet and the central helix is observed for two of the largest modes only. By adjusting the correlation times of the 10 largest modes, a high degree of consistency between the experimental relaxation data and the iRED model is reached for this highly flexible biomolecule.
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
Top Curr Chem. 2011 Sep 28;
Authors: Chen K, Tjandra N
Abstract
The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole-dipole interaction vectors within a common reference frame. Its measurement requires a...
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09-30-2011 06:00 AM
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
Top Curr Chem. 2011 Sep 28;
Authors: Chen K, Tjandra N
Abstract
The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole-dipole interaction vectors within a common reference frame. Its measurement requires a...
nmrlearner
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0
09-30-2011 05:59 AM
[NMR paper] Studying excited states of proteins by NMR spectroscopy.
Studying excited states of proteins by NMR spectroscopy.
Related Articles Studying excited states of proteins by NMR spectroscopy.
Nat Struct Biol. 2001 Nov;8(11):932-5
Authors: Mulder FA, Mittermaier A, Hon B, Dahlquist FW, Kay LE
Protein structure is inherently dynamic, with function often predicated on excursions from low to higher energy conformations. For example, X-ray studies of a cavity mutant of T4 lysozyme, L99A, show that the cavity is sterically inaccessible to ligand, yet the protein is able to bind substituted benzenes rapidly....
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11-19-2010 08:44 PM
[NMR paper] Chemical ligation of folded recombinant proteins: segmental isotopic labeling of doma
Chemical ligation of folded recombinant proteins: segmental isotopic labeling of domains for NMR studies.
Related Articles Chemical ligation of folded recombinant proteins: segmental isotopic labeling of domains for NMR studies.
Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):388-93
Authors: Xu R, Ayers B, Cowburn D, Muir TW
A convenient in vitro chemical ligation strategy has been developed that allows folded recombinant proteins to be joined together. This strategy permits segmental, selective isotopic labeling of the product. The src homology...
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11-18-2010 07:05 PM
[NMR paper] Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of
Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol.
J Mol Biol. 1996 Apr 5;257(3):669-83
Authors: Buck M, Schwalbe H, Dobson CM
15N NMR relaxation measurements have been used to study the dynamic...
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08-22-2010 02:27 PM
[NMR paper] A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TO
A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TOCSY triple resonance experiments.
Related Articles A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TOCSY triple resonance experiments.
J Biomol NMR. 1993 Mar;3(2):225-31
Authors: Logan TM, Olejniczak ET, Xu RX, Fesik SW
A general approach for assigning the resonances of uniformly 15N- and 13C-labeled proteins in their unfolded state is presented. The assignment approach takes advantage of the spectral dispersion of the amide...
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08-21-2010 11:53 PM
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
2H NMR Spin Relaxation for studying RNA dynamics
A Suite of 2H NMR Spin Relaxation Experiments for the Measurement of RNA Dynamics
Pramodh Vallurupalli and Lewis E. Kay, J. Am. Chem. Soc.; 2005; 127 (18) pp 6893 - 6901
ABSTRACT:
A suite of (2)H-based spin relaxation NMR experiments is presented for the measurement of molecular dynamics in a site-specific manner in uniformly (13)C, randomly fractionally deuterated ( approximately 50%) RNA molecules. The experiments quantify (2)H R(1) and R(2) relaxation rates that can subsequently be analyzed to obtain information about dynamics on a pico- to nanosecond time scale. Sensitivity...