Abstract An NMR investigation of proteins with known X-ray structures is of interest in a number of endeavors. Performing these studies through nuclear magnetic resonance (NMR) requires the costly step of resonance assignment. The prevalent assignment strategy does not make use of existing structural information and requires uniform isotope labeling. Here we present a rapid and cost-effective method of assigning NMR data to an existing structureâ??either an X-ray or computationally modeled structure. The presented method, Exhaustively Permuted Assignment of RDCs (EPAR), utilizes unassigned residual dipolar coupling (RDC) data that can easily be obtained by NMR spectroscopy. The algorithm uses only the backbone Nâ??H RDCs from multiple alignment media along with the amino acid type of the RDCs. It is inspired by previous work from Zweckstetter and provides several extensions. We present results on 13 synthetic and experimental datasets from 8 different structures, including two homodimers. Using just two alignment media, EPAR achieves an average assignment accuracy greater than 80%. With three media, the average accuracy is higher than 94%. The algorithm also outputs a prediction of the assignment accuracy, which has a correlation of 0.77 to the true accuracy. This prediction score can be used to establish the needed confidence in assignment accuracy.
Content Type Journal Article
Pages 1-13
DOI 10.1007/s10858-011-9521-5
Authors
Paul Shealy, Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA
Yizhou Liu, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30603, USA
Mikhail Simin, Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA
Homayoun Valafar, Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA
Residual dipolar couplings: are multiple independent alignments always possible?
Residual dipolar couplings: are multiple independent alignments always possible?
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...
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12-26-2010 04:43 AM
[NMR paper] Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
Related Articles Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
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] Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: ne
Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination.
Related Articles Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination.
J Am Chem Soc. 2004 May 26;126(20):6232-3
Authors: Ding K, Gronenborn AM
A simple, sensitivity-enhanced experiment was devised for accurate measurement of backbone 15N-13Calpha and 1HN-13Calpha couplings in proteins. The measured residual dipolar couplings 2DHCA,...
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11-24-2010 09:51 PM
[NMR paper] Residual dipolar couplings in NMR structure analysis.
Residual dipolar couplings in NMR structure analysis.
Related Articles Residual dipolar couplings in NMR structure analysis.
Annu Rev Biophys Biomol Struct. 2004;33:387-413
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.
Residual dipolar couplings: synergy between NMR and structural genomics.
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J Biomol NMR. 2002 Jan;22(1):1-8
Authors: Al-Hashimi HM, Patel DJ
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
[NMR paper] Protein structural motif recognition via NMR residual dipolar couplings.
Protein structural motif recognition via NMR residual dipolar couplings.
Related Articles Protein structural motif recognition via NMR residual dipolar couplings.
J Am Chem Soc. 2001 Feb 14;123(6):1222-9
Authors: Andrec M, Du P, Levy RM
NMR residual dipolar couplings have great potential to provide rapid structural information for proteins in the solution state. This information even at low resolution may be used to advantage in proteomics projects that seek to annotate large numbers of gene products for entire genomes. In this paper, we...
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11-19-2010 08:32 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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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...
Backbone resonance assignment and order tensor estimation using residual dipolar couplings
Linear Mode
