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 relative orientation of multidomain proteins and protein complexes. However, the interpretation of RDCs is complicated by the intrinsic degeneracy of analytical solutions and protein dynamics that lead to ill-defined orientations of the structural domains (ghost orientations). Here, we illustrate how restraints from paramagnetic relaxation enhancement (PRE) experiments lift the orientational ambiguity of multidomain membrane proteins solubilized in detergent micelles. We tested this approach on monomeric phospholamban (PLN), a 52-residue membrane protein, which is composed of two helical domains connected by a flexible loop. We show that the combination of classical solution NMR restraints (NOEs and dihedral angles) with RDC and PRE constraints resolves topological ambiguities, improving the convergence of the PLN structural ensemble and giving the depth of insertion of the protein within the micelle. The combination of RDCs with PREs will be necessary for improving the accuracy and precision of membrane protein conformational ensembles, where three-dimensional structures are dictated by interactions with the membrane-mimicking environment rather than compact tertiary folds common in globular proteins.
PMID: 21287984 [PubMed - as supplied by publisher]
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...
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09-30-2011 05:59 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
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[NMR paper] Resonance assignment of proteins with high shift degeneracy based on 5D spectral info
Resonance assignment of proteins with high shift degeneracy based on 5D spectral information encoded in G2FT NMR experiments.
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11-25-2010 08:21 PM
[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.
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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] Assignment of 1H, 15N, and backbone 13C resonances in detergent-solubilized M13 coat
Assignment of 1H, 15N, and backbone 13C resonances in detergent-solubilized M13 coat protein via multinuclear multidimensional NMR: a model for the coat protein monomer.
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Biochemistry. 1993 Aug 17;32(32):8322-8
Authors: van de Ven FJ, van Os JW, Aelen JM, Wymenga SS, Remerowski ML, Konings RN, Hilbers CW
The major coat protein (gVIIIp) of bacteriophage M13...
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[NMR paper] Assignment of amide 1H and 15N NMR resonances in detergent-solubilized M13 coat prote
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Biochemistry. 1992 Jun 16;31(23):5284-97
Authors: Henry GD, Sykes BD
The major coat protein of the filamentous coliphage M13 is a 50-residue integral membrane protein. Detergent-solubilized M13 coat protein is a promising candidate for structure determination by nuclear magnetic...
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08-21-2010 11:41 PM
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
F. Gabel, B. Simon, M. Nilges, M. Petoukhov, D. Svergun and M. Sattler
Journal of Biomolecular NMR; 2008; 41(4); pp 199-208
Abstract:
We present the implementation of a target function based on Small Angle Scattering data (Gabel et al. Eur Biophys J 35(4):313–327, 2006) into the Crystallography and NMR Systems (CNS) and demonstrate its utility in NMR structure calculations by simultaneous application of small angle scattering (SAS) and residual dipolar coupling (RDC)...