Abstract RDCs for the 14 kDa protein hen egg-white lysozyme (HEWL) have been measured in eight different alignment media. The elongated shape and strongly positively charged surface of HEWL appear to limit the protein to four main alignment orientations. Furthermore, low levels of alignment and the proteinâ??s interaction with some alignment media increases the experimental error. Together with heterogeneity across the alignment media arising from constraints on temperature, pH and ionic strength for some alignment media, these data are suitable for structure refinement, but not the extraction of dynamic parameters. For an analysis of protein dynamics the data must be obtained with very low errors in at least three or five independent alignment media (depending on the method used) and so far, such data have only been reported for three small 6â??8 kDa proteins with identical folds: ubiquitin, GB1 and GB3. Our results suggest that HEWL is likely to be representative of many other medium to large sized proteins commonly studied by solution NMR. Comparisons with over 60 high-resolution crystal structures of HEWL reveal that the highest resolution structures are not necessarily always the best models for the protein structure in solution.
Content Type Journal Article
DOI 10.1007/s10858-010-9457-1
Authors
Victoria A. Higman, Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
Jonathan Boyd, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
Lorna J. Smith, Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
Christina Redfield, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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Sensitivity of NMR residual dipolar couplings to perturbations in folded and denatured staphylococcal nuclease.
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Authors: Sallum CO, Martel DM, Fournier RS, Matousek WM, Alexandrescu AT
The invariance of NMR residual dipolar couplings (RDCs) in denatured forms of staphylococcal nuclease to changes in denaturant concentration or amino acid sequence has previously been attributed...
nmrlearner
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11-25-2010 08:21 PM
[NMR paper] Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
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Eur Biophys J. 2005 Nov;34(8):1057-65
Authors: García-Mayoral MF, Pantoja-Uceda D, Santoro J, Martínez del Pozo A, Gavilanes JG, Rico M, Bruix M
(15)N-(1)H residual dipolar couplings (RDC) have been used as additional restraints to refine the solution structure of the ribotoxin alpha-sarcin. The RDC values were obtained by partial alignment of alpha-sarcin in the binary mixture...
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11-25-2010 08:21 PM
[NMR paper] Residual dipolar couplings in NMR structure analysis.
Residual dipolar couplings in NMR structure analysis.
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Authors: Lipsitz RS, Tjandra N
Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide...
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11-24-2010 09:25 PM
[NMR paper] Residual dipolar couplings: synergy between NMR and structural genomics.
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J Biomol NMR. 2002 Jan;22(1):1-8
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Structural genomics is on a quest for the structure and function of a significant fraction of gene products. Current efforts are focusing on structure determination of single-domain proteins, which can readily be targeted by X-ray crystallography, NMR spectroscopy and computational homology modeling. However,...
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11-24-2010 08:49 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
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...
stewart
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08-05-2008 02:26 AM
De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media
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Ke Ruan, Kathryn B. Briggman and Joel R. Tolman
Journal of Biomolecular NMR; 2008; 41(2) pp 61 - 76
Abstract:
The straightforward interpretation of solution state residual dipolar couplings (RDCs) in terms of internuclear vector orientations generally requires prior knowledge of the alignment tensor, which in turn is normally estimated using a structural model. We have developed a protocol which allows the requirement for prior structural knowledge to...
daniel
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Composite Alignment Media for the Measurement of Independent Sets of NMR Residual Dipolar Couplings
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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...
Residual dipolar couplings: are multiple independent alignments always possible?
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