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Sparsely-sampled, high-resolution 4-D omit spectra for detection and assignment of intermolecular NOEs of protein complexes

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Abstract

Unambiguous detection and assignment of intermolecular NOEs are essential for structure determination of protein complexes by NMR. Such information has traditionally been obtained with 3-D half-filtered experiments, where scalar coupling-based purging of intramolecular signals allows for selective detection of intermolecular NOEs. However, due to the large variation of 1JHC scalar couplings and limited chemical shift dispersion in the indirect proton dimension, it is difficult to obtain reliable and complete assignments of interfacial NOEs. Here, we demonstrate a strategy that combines selective labeling and high-resolution 4-D NOE spectroscopy with sparse sampling for reliable identification and assignment of intermolecular NOEs. Spectral subtraction of component-labeled complexes from a uniformly-labeled protein complex yields an “omit” spectrum containing positive intermolecular NOEs with little signal degeneracy. Such a strategy can be broadly applied to unbiased detection, assignment and presentation of intermolecular NOEs of protein complexes.

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References

  • Bhat TN (1988) Calculation of an OMIT map. J Appl Cryst 21:279–281

    Article  MathSciNet  Google Scholar 

  • Bienko M, Green CM, Crosetto N, Rudolf F, Zapart G, Coull B, Kannouche P, Wider G, Peter M, Lehmann AR et al (2005) Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science 310:1821–1824. doi:10.1126/science.1120615

    Article  ADS  Google Scholar 

  • Bomar MG, D’Souza S, Bienko M, Dikic I, Walker GC, Zhou P (2010) Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1. Mol Cell 37:408–417. doi:10.1016/j.molcel.2009.12.038

    Article  Google Scholar 

  • Boudko SP, Strelkov SV, Engel J, Stetefeld J (2004) Design and crystal structure of bacteriophage T4 mini-fibritin NCCF. J Mol Biol 339:927–935. doi:10.1016/j.jmb.2004.04.001

    Article  Google Scholar 

  • Breeze AL (2000) Isotope-filtered NMR methods for the study of biomolecular structure and interactions. Prog Nucl Magn Reson Spectrosc 36:323–372

    Article  Google Scholar 

  • Burschowsky D, Rudolf F, Rabut G, Herrmann T, Peter M, Wider G (2011) Structural analysis of the conserved ubiquitin-binding motifs (UBMs) of the translesion polymerase iota in complex with ubiquitin. J Biol Chem 286:1364–1373. doi:10.1074/jbc.M110.135038

    Article  Google Scholar 

  • Coggins BE, Zhou P (2008) High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN. J Biomol NMR 42:225–239. doi:10.1007/s10858-008-9275-x

    Article  Google Scholar 

  • Coggins BE, Venters RA, Zhou P (2010) Radial sampling for fast NMR: concepts and practices over three decades. Prog Nucl Magn Reson Spectrosc 57:381–419. doi:10.1016/j.pnmrs.2010.07.001

    Article  Google Scholar 

  • Coggins BE, Werner-Allen JW, Yan A, Zhou P (2012) Rapid protein global fold determination using ultrasparse sampling, high-dynamic range artifact suppression, and time-shared NOESY. J Am Chem Soc 134:18619–18630. doi:10.1021/ja307445y

    Article  Google Scholar 

  • Cui G, Benirschke RC, Tuan HF, Juranic N, Macura S, Botuyan MV, Mer G (2010) Structural basis of ubiquitin recognition by translesion synthesis DNA polymerase iota. Biochemistry 49:10198–10207. doi:10.1021/bi101303t

    Article  Google Scholar 

  • Güntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378

    Google Scholar 

  • Guthe S, Kapinos L, Moglich A, Meier S, Grzesiek S, Kiefhaber T (2004) Very fast folding and association of a trimerization domain from bacteriophage T4 fibritin. J Mol Biol 337:905–915. doi:10.1016/j.jmb.2004.02.020

    Article  Google Scholar 

  • Hiller S, Ibraghimov I, Wagner G, Orekhov VY (2009) Coupled decomposition of four-dimensional NOESY spectra. J Am Chem Soc 131:12970–12978. doi:10.1021/ja902012x

    Article  Google Scholar 

  • Hoch JC, Stern AS (2001) Maximum entropy reconstruction, spectrum analysis and deconvolution in multidimensional nuclear magnetic resonance. Methods Enzymol 338:159–178

    Article  Google Scholar 

  • Hyberts SG, Frueh DP, Arthanari H, Wagner G (2009) FM reconstruction of non-uniformly sampled protein NMR data at higher dimensions and optimization by distillation. J Biomol NMR 45:283–294. doi:10.1007/s10858-009-9368-1

    Article  Google Scholar 

  • Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Kozminski W (2010) Random sampling in multidimensional NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 57:420–434. doi:10.1016/j.pnmrs.2010.07.002

    Article  Google Scholar 

  • Nudelman I, Akabayov SR, Scherf T, Anglister J (2011) Observation of intermolecular interactions in large protein complexes by 2D-double difference nuclear overhauser enhancement spectroscopy: application to the 44 kDa interferon-receptor complex. J Am Chem Soc 133:14755–14764. doi:10.1021/ja205480v

    Article  Google Scholar 

  • Otting G, Wuthrich K (1990) Heteronuclear filters in two-dimensional [1H,1H]-NMR spectroscopy: combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions. Q Rev Biophys 23:39–96

    Article  Google Scholar 

  • Stuart AC, Borzilleri KA, Withka JM, Palmer AG 3rd (1999) Compensating for variations in 1H–13C scalar coupling constants in isotope-filtered NMR experiments. J Am Chem Soc 121:5346–5347

    Article  Google Scholar 

  • Tao Y, Strelkov SV, Mesyanzhinov VV, Rossmann MG (1997) Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain. Structure 5:789–798

    Article  Google Scholar 

  • Tugarinov V, Kay LE, Ibraghimov I, Orekhov VY (2005) High-resolution four-dimensional 1H–13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J Am Chem Soc 127:2767–2775

    Article  Google Scholar 

  • Wen J, Zhou P, Wu J (2012) Efficient acquisition of high-resolution 4-D diagonal-suppressed methyl-methyl NOESY for large proteins. J Magn Reson 218:128–132. doi:10.1016/j.jmr.2012.02.021

    Article  ADS  Google Scholar 

  • Werner-Allen JW, Coggins BE, Zhou P (2010) Fast acquisition of high resolution 4-D amide-amide NOESY with diagonal suppression, sparse sampling and FFT-CLEAN. J Magn Reson 204:173–178. doi:10.1016/j.jmr.2010.02.017

    Article  ADS  Google Scholar 

  • Zwahlen C, Legault P, Vincent SJF, Greenblatt J, Konrat R, Kay LE (1997) Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage N-peptide/boxB RNA complex. J Am Chem Soc 119:6711–6721

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported in part by the National Institutes of Health/National Institute of Allergy and Infectious Diseases (AI055588) to P. Z.

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Correspondence to Pei Zhou.

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Wang, S., Zhou, P. Sparsely-sampled, high-resolution 4-D omit spectra for detection and assignment of intermolecular NOEs of protein complexes. J Biomol NMR 59, 51–56 (2014). https://doi.org/10.1007/s10858-014-9834-2

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  • DOI: https://doi.org/10.1007/s10858-014-9834-2

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