Abstract
Anisotropic magnetic susceptibility tensors χ of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the χ-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D 15N-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable χ-tensor anisotropy parameters from 2D spectra of uniformly 15N-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit ε from E. coli DNA polymerase III in complex with the subunit θ and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.
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Abbreviations
- θ:
-
subunit θ of E. coli polymerase III
- ε186:
-
N-terminal 185 residues of the E. coli polymerase III subunit ε
- PCS:
-
pseudocontact shift
- PRE:
-
paramagnetic relaxation enhancement
- RACS:
-
residual anisotropic chemical shifts.
References
Allegrozzi M., Bertini I., Janik M.B.L., Lee Y.M., Lin G.H. and Luchinat C. (2000). J. Am. Chem. Soc. 122: 4154–4161
Babini E., Bertini I., Capozzi F., Felli I.C., Lelli M. and Luchinat C. (2004). J. Am. Chem. Soc. 126: 10496–10497
Baig I., Bertini I., Del Bianco C., Gupta Y.K., Lee Y.M., Luchinat C. and Quattrone A. (2004). Biochemistry 43: 5562–5573
Banci L., Bertini I., Gori Savellini G.., Romagnoli A., Turano P., Cremonini M.A., Luchinat C. and Gray H.B. (1997). Proteins 29: 68–76
Banci L., Bertini I., Cremonini M.A., Gori-Savellini G., Luchinat C., Wüthrich K. and Güntert P. (1998) J. Biomol. NMR 12: 553–557
Barbieri R., Bertini I., Cavallaro G., Lee Y.M., Luchinat C., Rosato A. (2002). J. Am. Chem. Soc. 124: 5581–5587
Bertini I., Janik M.B., Lee Y.M., Luchinat C. and Rosato A. (2001a). J. Am. Chem. Soc. 123: 4181–4188
Bertini I., Luchinat C. and Parigi G. (2001b). Solution NMR of Paramagnetic Molecules: Applications to Metallobiomolecules and Models. Elsevier, Amsterdam, London
Bertini I., Luchinat C. and Parigi G. (2002) Prog. NMR Spectrosc. 40: 249–273
Brautigam C.A., Aschheim K. and Steitz T.A. (1999) Chem. Biol. 6: 901–908
Carpaneto G. and Toth P. (1980). ACM TOMS 6: 104–111
Cornilescu G. and Bax A. (2000). J. Am. Chem. Soc. 122: 10143–10154
DeRose E.F., Li D., Darden T., Harvey S., Perrino F.W., Schaaper R.M. and London R.E. (2002) Biochemistry 41: 94–110
DeRose E.F., Darden T., Harvey S., Gabel S., Perrino F.W., Schaaper R.M. and London R.E. (2003) Biochemistry 42: 3635–3644
Diaz-Moreno I., Diaz-Quintana A., De la Rosa M.A. and Ubbink M. (2005). J. Biol. Chem., 280, 18908–18915
Frey M.W., Frey S.T., DeW Horrocks W., Jr., Kaboord B. and Benkovic S.J. (1996). Chem. Biol. 3: 393–403
Gaponenko V., Altieri A.S., Li J. and Byrd R.A. (2002). J. Biomol. NMR, 24: 143–148
Gaponenko V., Sarma S.P., Altieri A.S., Horita D.A., Li J. and Byrd R.A. (2004). J. Biomol. NMR 28: 205–212
Gochin M. (1998). J. Biomol. NMR 12: 243–257
Gochin M. (2000). Structure 8: 441–452
Goddard T.D. and Kneller D.G. (2004). SPARKY 3. University of California, San Francisco
Goodfellow B.J., Nunes S.G., Rusnak F., Moura I., Ascenso C., Moura J.J.G., Volkman B.F. and Markley J.L. (2002). Prot. Sci. 11: 2464–2470
Hamdan S., Carr P.D., Brown S.E., Ollis D.L. and Dixon N.E. (2002). Structure 10: 535–546
Hus J.-C., Prompers J.J. and Brüschweiler R. (2002). J. Magn. Reson. 157: 119–123
Ikegami T., Verdier L., Sakhaii P., Grimme S., Pescatore B., Saxena K., Fiebig K.M. and Griesinger C. (2004). J. Biomol. NMR 29: 339–349
John, M., Park, A.Y., Pintacuda, G., Dixon, N.E. and Otting, G. (2005) J. Am. Chem. Soc., 127, 17190–17191
Kuhn H.W. (1955). Naval Res. Logistic Quarterly 2: 83–97
La Mar G.N., Kolczak U., Tran A.T. and Chien E.Y. (2001) J. Am. Chem. Soc. 123: 4266–4274
Leonov A., Voigt B., Rodriguez-Castaneda F., Sakhaii P. and Griesinger C. (2005). Chemistry 11: 3342–3348
Ma C. and Opella S.J. (2000). J. Magn. Reson. 146: 381–384
Markwick P.R.L. and Sattler M. (2005). J. Am. Chem. Soc. 126: 11424–11425
Peters J.A., Huskens J. and Raber D.J. (1996). Prog. NMR Spectrosc. 28: 283–350
Pintacuda G., Keniry M.A., Huber T., Park A.Y., Dixon N.E. and Otting G. (2004). J. Am. Chem. Soc. 126: 2963–2970
Tjandra N. and Bax A. (1997). Science 278: 1111–1114
Tolman J.R., Flanagan J.M., Kennedy M.A. and Prestegard J.H. (1995). Proc. Natl. Acad. Sci. USA 92: 9279–9283
Ubbink M., Ejdebäck M., Karlsson B.G. and Bendall D.S. (1998). Structure 6: 323–335
van Dijk A.D., Fushman D. and Bonvin A.M. (2005). Proteins 60: 367–381
Wöhnert J., Franz K.J., Nitz M., Imperiali B. and Schwalbe H. (2003). J. Am. Chem. Soc. 125: 13338–13339
Acknowledgements
M.J. thanks the Alexander von Humboldt Foundation for a fellowship. Financial support from the Australian Research Council for a Federation Fellowship for G.O. and the 800 MHz NMR spectrometer at ANU is gratefully acknowledged.
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The first two authors contributed equally to the project.
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Schmitz, C., John, M., Park, A. et al. Efficient χ-tensor determination and NH assignment of paramagnetic proteins. J Biomol NMR 35, 79–87 (2006). https://doi.org/10.1007/s10858-006-9002-4
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DOI: https://doi.org/10.1007/s10858-006-9002-4