Journal of the Korean Magnetic Resonance Society (한국자기공명학회논문지)

Korean Magnetic Resonance Society (한국자기공명학회)
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Advanced techniques of solution nuclear magnetic resonance spectroscopy for structural investigation of protein-protein interaction

  • Sugiki, Toshihiko (Institute for Protein Research, Osaka University) ;
  • Lee, Young-Ho (Protein Structure Group, Division of Bioconvergence Analysis, Korea Basic Science Institute)
  • Received : 2018.10.31
  • Accepted : 2018.11.24
  • Published : 2018.12.20
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Abstract

Investigation of the protein-protein interaction mode at atomic resolution is essential for understanding on the underlying functional mechanisms of proteins as well as for discovering druggable compounds blocking deleteriou interprotein interactions. Solution NMR spectroscopy provides accurate and precise information on intermolecular interactions even for weak and transient interactions, and it is also markedly useful for examining the change in the conformation and dynamics of target proteins upon binding events. In this mini-review, we comprehensively describe three unique and powerful methods of solution NMR spectroscopy, paramagnetic relaxation enhancement (PRE), pseudo-contact shift (PCS), and residual dipolar coupling (RDC), for the study on protein-protein interactions.

Keywords

JGGMB2_2018_v22n4_76_f0001.png 이미지

Figure 1. Illustration of paramagnetic effect-based NMR methods for investigation of protein-protein interactions. Effects of paramagnetic relaxation enhancement (PRE) (A) and pseudo-contact shift (PCS) (B) are shown. The alteration of the intensity (A) and chemical shift (B) of NMR signals of isotopically-labeled protein are analysed. PRE causes attenuation of the signal intensity depending on the distance, and PCS induces chemical shift changes depending on the distance and angle from the immobilized paramagnetic center (small red sphere). The region in which PRE and PCS, which affects the NMR signal, is highlighted with gray spheres with dotted line and four ellipses, respectively. Black spheres with numbering (in the target proteins) indicate the location of the residues, which are corresponding to the NMR spectra.

JGGMB2_2018_v22n4_76_f0002.png 이미지

Figure 2. Schematic illustration of residual dipolar coupling (RDC) experiments. (A) Orientation of the dipole-dipole vector in the target protein in the cartesian space is determined. (B) Schematic representation of the two-dimensional 1H-15N spectrum for RDC. The “Aligned” and “Isotropic” (reference experiment) show peak splitting in the presence and absence of orienting media, respectively. JHN and D indicate the constants of J-coupling and RDC, respectively. The asterisk indicates the chemical shift alteration in the midpoint of the split signals (denoted as small circles), which results from the PCS effect when the alignment is achieved by lanthanide ions.

References

  1. G. Otting, Annu. Rev. Biophys. 39, 387 (2010) https://doi.org/10.1146/annurev.biophys.093008.131321
  2. G. M. Clore and J. Iwahara, Chem. Rev. 109, 4108 (2009) https://doi.org/10.1021/cr900033p
  3. S. R. Tzeng, M. T. Pai, and C.G. Kalodimos, Methods Mol. Biol. 831, 133 (2012)
  4. Y. Yang, F. Huang, T. Huber, and X. C. Su, J. Biomol. NMR 64, 103 (2016) https://doi.org/10.1007/s10858-016-0011-7
  5. J. Wohnert, K. Franz, M. Nitz, B. Imperiali, and H. Schwalbe, J. Am. Chem. Soc. 125, 13338 (2003) https://doi.org/10.1021/ja036022d
  6. M. Hass and M. Ubbink, Curr. Opin. Struct. Biol. 24, 45 (2014) https://doi.org/10.1016/j.sbi.2013.11.010
  7. W. Liu, M. Overhand, and M. Ubbink, Coord. Chem. Rev. 273, 2 (2014)
  8. T. Saio, M. Yokochi, H. Kumeta, and F. Inagaki, J. Biomol. NMR 46, 271 (2010) https://doi.org/10.1007/s10858-010-9401-4
  9. P. H. Keizers and M. Ubbink, Prog. Nucl. Magn. Reson. Spectrosc. 58, 88 (2011) https://doi.org/10.1016/j.pnmrs.2010.08.001
  10. C. Tang, J. Iwahara, and G. M. Clore, Nature 444, 383 (2006) https://doi.org/10.1038/nature05201
  11. J. Iwahara and G. M. Clore, Nature 440, 1227 (2006) https://doi.org/10.1038/nature04673
  12. K. van de Water, N. van Nuland, and A. Volkov, Chem. Sci. 5, 4227 (2014) https://doi.org/10.1039/C4SC01232A
  13. Q. Xing, P. Huang, J. Yang, J. Sun, Z. Gong, X. Dong, D. Guo, S. Chen, Y. Yang, Y. Wang, M. Yang, M. Yi, Y. Ding, M. Liu, W. Zhang, and C. Tang, Angew. Chem. Int. Ed. 53, 11501 (2014) https://doi.org/10.1002/anie.201405976
  14. Z. Liu, Z. Gong, X. Dong, and C. Tang, Biochimi. Biophys. Acta 1864, 115 (2016) https://doi.org/10.1016/j.bbapap.2015.04.009
  15. G. M. Clore and A. Gronenborn, J. Magn. Reson. 53, 423 (1983)
  16. M. Prudencio, J. Rohovec, J. A. Peters, E. Tocheva, M. J. Boulanger, M. E. Murphy, H. J. Hupkes, W. Kosters, A. Impagliazzo, and M. Ubbink, Chemistry 10, 3252 (2004) https://doi.org/10.1002/chem.200306019
  17. F. Rodriguez-Castaneda, P. Haberz, A. Leonov, and C. Griesinger, Magn. Reson. Chem. 44, S10 (2006) https://doi.org/10.1002/mrc.1811
  18. T. Saio, K. Ogura, M. Yokochi, Y. Kobashigawa, and F. Inagaki, J. Biomol. NMR 44, 157 (2009) https://doi.org/10.1007/s10858-009-9325-z
  19. K. Furuita, S. Kataoka, T. Sugiki, Y. Hattori, N. Kobayashi, T. Ikegami, K. Shiozaki, T. Fujiwara, and C. Kojima, J. Biomol. NMR 61, 55 (2015) https://doi.org/10.1007/s10858-014-9882-7
  20. M. Ikura, G. M. Clore, A. Gronenborn, G. Zhu, C. Klee, and A. Bax, Science 256, 632 (1992) https://doi.org/10.1126/science.1585175
  21. N. Silvaggi, L. Martin, H. Schwalbe, B. Imperiali, and K. Allen, J. Am. Chem. Soc. 129, 7114 (2007) https://doi.org/10.1021/ja070481n
  22. P. Keizers, A. Saragliadis, Y. Hiruma, M. Overhand, and M. Ubbink, J. Am. Chem. Soc. 130, 14802 (2008) https://doi.org/10.1021/ja8054832
  23. N. Tjandra and A. Bax, Science 278, 1111 (1997) https://doi.org/10.1126/science.278.5340.1111
  24. M. Fischer, J. Losonczi, J. Weaver, and J. Prestegard, Biochemistry 38, 9013 (1999) https://doi.org/10.1021/bi9905213
  25. A. Bax and N. Tjandra, J. Biomol. NMR 10, 289 (1997) https://doi.org/10.1023/A:1018308717741
  26. M. Ruckert and G. Otting, J. Am. Chem. Soc. 122, 7793 (2000) https://doi.org/10.1021/ja001068h
  27. M. R. Hansen, L. Mueller, and A. Pardi, Nat. Struct. Biol. 5, 1065 (1998) https://doi.org/10.1038/4176
  28. M. Zweckstetter and A. Bax, J. Biomol. NMR 20, 365 (2001) https://doi.org/10.1023/A:1011263920003
  29. J. Chou, S. Gaemers, B. Howder, J. Louis, and A. Bax, J. Biomol. NMR 21, 377 (2001) https://doi.org/10.1023/A:1013336502594
  30. M. Ottiger and A. Bax, J. Biomol. NMR 12, 361 (1998) https://doi.org/10.1023/A:1008366116644
  31. M. Ottiger and A. Bax, J. Biomol. NMR 13, 187 (1999) https://doi.org/10.1023/A:1008395916985
  32. M. Ottiger, F. Delaglio, and A. Bax, J. Magn. Reson. 131, 373 (1998) https://doi.org/10.1006/jmre.1998.1361
  33. M. Ottiger, F. Delaglio, J. Marquardt, N. Tjandra, and A. Bax, J. Magn. Reson. 134, 365 (1998) https://doi.org/10.1006/jmre.1998.1546
  34. M. Zweckstetter, Nat. Protoc. 3, 679 (2008) https://doi.org/10.1038/nprot.2008.36
  35. E. Schmidt and P. Guntert, J. Am. Chem. Soc. 134, 12817 (2012) https://doi.org/10.1021/ja305091n
  36. C. Schmidt, S. Irausquin, and H. Valafar, BMC Bioinformatics 14 (2013)
  37. A. Bax, G. Kontaxis, and N. Tjandra, N, Nucl. Magn. Reson. Biol. Macromol. Pt B 339, 127 (2001)
  38. M. O'Connell, R. Gamsjaeger, and J. Mackay, Proteomics 9, 5224 (2009) https://doi.org/10.1002/pmic.200900303
  39. P. Bolon, H. Al-Hashimi, and J. Prestegard, J. Mol. Biol. 293, 107 (1999) https://doi.org/10.1006/jmbi.1999.3133