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 nonisotropic orientation, through a direct or indirect magnetic field alignment, of the protein in solution. There has been recent progress in the developments of alignment methods to allow the measurement of RDC and of methods to analyze the resulting data. In this chapter we briefly go through the mathematical expressions for the RDC and common descriptions of the alignment tensor, which may be represented using either Saupe order or the principal order matrix. Then we review the latest developments in alignment media. In particular we looked at the lipid-compatible media that allow the measurement of RDCs for membrane proteins. Other methods including conservative surface residue mutation have been invented to obtain up to five orthogonal alignment tensors that provide a potential for de novo structure and dynamics study using RDCs exclusively. We then discuss approximations assumed in RDC interpretations and different views on dynamics uncovered from the RDC method. In addition to routine usage of RDCs in refining a single structure, novel applications such as ensemble refinement against RDCs have been implemented to represent protein structure and dynamics in solution. The RDC application also extends to the study of protein-substrate interaction as well as to solving quaternary structure of oligomer in equilibrium with a monomer, opening an avenue for RDCs in high-order protein structure determination.
PMID: 21952837 [PubMed - as supplied by publisher]
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
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 05:59 AM
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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09-17-2011 10:20 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.
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
[NMR paper] Detecting protein kinase recognition modes of calmodulin by residual dipolar coupling
Detecting protein kinase recognition modes of calmodulin by residual dipolar couplings in solution NMR.
Related Articles Detecting protein kinase recognition modes of calmodulin by residual dipolar couplings in solution NMR.
Biochemistry. 2002 Oct 29;41(43):12899-906
Authors: Mal TK, Skrynnikov NR, Yap KL, Kay LE, Ikura M
Calmodulin-regulated serine/threonine kinases (CaM kinases) play crucial roles in Ca2+-dependent signaling transduction pathways in eukaryotes. Despite having a similar overall molecular architecture of catalytic and...
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11-24-2010 08:58 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
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...