Biomolecular NMR Assignments

, Volume 7, Issue 1, pp 25–29 | Cite as

1H, 13C, and 15N chemical shifts assignments for human endothelial monocyte-activating polypeptide EMAP II

  • Dmytro Lozhko
  • Jan Stanek
  • Krzysztof Kazimierczuk
  • Anna Zawadzka-Kazimierczuk
  • Wiktor Kozminski
  • Igor ZhukovEmail author
  • Alexander Kornelyuk


Endothelial and monocyte-activating polypeptide II (EMAP II) is a cytokine that plays an important role in inflammation, apoptosis and angiogenesis processes in tumour tissues. Structurally, the EMAP II is a 169 amino acid residues long C-terminal domain (residues 147–312) of auxiliary tRNA binding protein p43. In spite of existence in pdb databank of two X-ray structures there are some important aspects of EMAP II cytokine function which are still not fully understood in detail. To obtain information about 3D structure and backbone dynamic processes in solution we perform structure evaluation of human EMAP II cytokine by NMR spectroscopy. The standard approach to sequence-specific backbone assignment using 3D NMR data sets was not successful in our studies and was supplemented by recently developed 4D NMR experiments with random sampling of evolution time space. Here we report the backbone and side chain 1H, 13C, and 15N chemical shifts in solution for recombinant EMAP II cytokine together with secondary structure provided by TALOS + software.


Multidimensional NMR spectroscopy Random sampling Sequence-specific backbone assignment Side chain assignments Cytokines EMAP II 



This work was partially supported by grant N 30107131/2150 from Polish Ministry of Sciences and High Education, and FP7 EastNMR project (contract no. 228461) inside of transnational access program (for D.L. and A.K.). This work was performed as a JRA activity in FP7 BioNMR project (contract no. 261863) between Slovenian NMR Centre and Faculty of Chemistry, University of Warsaw. A.Z.-K. thanks the Foundation for Polish Science for supporting her with the MPD Programme, KK and WK thanks the Foundation for Polish Science for support with the TEAM Programme. MPD and TEAM programmes were co-financed by the EU European Regional Development.


  1. Berger AC, Tang G, Alexander HR, Libutti SK (2000) Endothelial monocyte-activating polypeptide II, a tumor-derived cytokine that plays an important role in inflammation, apoptosis, and angiogenesis. J Immunother 23:519–527CrossRefGoogle Scholar
  2. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  3. Kao J, Ryan J, Brett G, Chen J, Shen H, Fan YG, Godman G, Familletti PC, Wang F, Pan YC et al (1992) Endothelial monocyteactivating polypeptide II. A novel tumor-derived polypeptide that activates host-response mechanisms. J Biol Chem 267:20239–20247Google Scholar
  4. Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2006) Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36:157–168CrossRefGoogle Scholar
  5. Kim Y, Shin J, Li R, Cheong C, Kim K, Kim S (2000) A novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases. J Biol Chem 275:27062–27068Google Scholar
  6. Lozhko D, Zhukov I, Kornelyuk A (2011) Bacterial expression and 13C/15N isotopic labeling of EMAP II cytokine for structural studies by NMR spectroscopy. Biopolymers Cell 27:273–278CrossRefGoogle Scholar
  7. Renault L, Kerjan P, Pasqualato S, Menetrey J, Robinson JC, Kawaguchi S, Vassylyev DG, Yokoyama S, Mirande M, Cherfils J (2001) Structure of the EMAP II domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry. EMBO J 20:570–578CrossRefGoogle Scholar
  8. Reznikov AG, Chaykovskaya LV, Polyakova LI, Kornelyuk AI (2007) Antitumor effect of endothelial monocyre-activating polypeptide-II on human prostate adenocarcinoma in mouse xenograft model. Exp Oncol 29:267–271Google Scholar
  9. Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Magn Reson Spectrosc 34:93–158CrossRefGoogle Scholar
  10. Sharma D, Rajarathnam K (2000) 13C NMR chemical shifts can predict disulfide bond formation. J Biomol NMR 18:165–171CrossRefGoogle Scholar
  11. Shen Y, Bax A (2010) Prediction of Xaa–Pro peptide bond conformation from sequence and chemical shifts. J Biomol NMR 46:199–204CrossRefGoogle Scholar
  12. Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223CrossRefGoogle Scholar
  13. Stanek J, Kozminski W (2010) Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets. J Biomol NMR 47:65–77CrossRefGoogle Scholar
  14. Stanek J, Augustyniak R, Kozminski W (2012) Suppression of sampling artifacts in high-resolution four-dimensional NMR spectra using signal separation algorithm. J Magn Reson 214:91–102ADSCrossRefGoogle Scholar
  15. van Horssen R, Rens JA, Schipper D, Eggermont AM, ten Hagen TL (2006) EMAP-II facilitates TNF-R1 apoptotic signaling in endothelial cells and induces TRADD mobilization. Apoptosis 11:2137–2145CrossRefGoogle Scholar
  16. Wishart DS, Arndt D, Berjanski M, Tang P, Lin G (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucl Acid Res 36:W496–W502CrossRefGoogle Scholar
  17. Zawadzka-Kazimierczuk A, Kazimierczuk K, Kozminski W (2010) A set of 4D NMR experiments of enhanced resolution for easy resonance assignment in proteins. J Magn Reson 202:109–116ADSCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Dmytro Lozhko
    • 1
  • Jan Stanek
    • 2
  • Krzysztof Kazimierczuk
    • 2
  • Anna Zawadzka-Kazimierczuk
    • 2
  • Wiktor Kozminski
    • 2
  • Igor Zhukov
    • 3
    • 4
    • 5
    Email author
  • Alexander Kornelyuk
    • 1
  1. 1.Institute Molecular Biology and Genetics, National Academy of Sciences of UkraineKyivUkraine
  2. 2.Faculty of ChemistryUniversity of WarsawWarsawPoland
  3. 3.Slovenian NMR CentreNational Institute of ChemistryLjubljanaSlovenia
  4. 4.EN-FIST Center of ExcellenceLjubljanaSlovenia
  5. 5.Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland

Personalised recommendations