Skip to main content
SpringerLink
Log in

First principle calculations of 113Cd chemical shifts for proteins and model systems

  • Original Article
  • Published:
JBIC Journal of Biological Inorganic Chemistry Aims and scope Submit manuscript

Abstract

113Cd isotropic NMR shieldings are calculated for a number of metal ion binding sites in proteins, using the GIAO-B3LYP and GIAO-HF methods with the uncontracted (19s15p9d4f) polarized basis set of Kellö and Sadlej on cadmium and 6-31G(d) on the ligands. The results compare favorably with experimental data, indicating that first principle calculations are a useful tool for structural interpretation of 113Cd chemical shift data from metal ion containing proteins. The effect of different ligand types (thiolate, imidazole, water, and monodentate carboxylate), coordination number, and deviations of the coordination geometry from ideal structures is evaluated. In particular, the ligand type and coordination number are important factors, but also changes in cadmium–ligand bond lengths may cause significant changes of the chemical shift.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4a–c
Fig. 5

Similar content being viewed by others

References

  1. Bertini I, Luchinat C (1994) In: Bertini I, Gray HB, Lippard SJ, Valentine JS (eds) Bioinorganic chemistry. University Science Books, Sausalito, Calif., USA

  2. Summers MF (1988) Coord Chem Rev 86:43–134

    Article  CAS  Google Scholar 

  3. Bauer R (1985) Q Rev Biophys 18:1–64

    CAS  PubMed  Google Scholar 

  4. Hemmingsen L, Damblon C, Antony J, Jensen M, Adolph HW, Wommer S, Roberts GCK, Bauer R (2001) J Am Chem Soc 123:10329–10335

    Article  CAS  PubMed  Google Scholar 

  5. Öz G, Pountney DL, Armitage IM (1998) Biochem Cell Biol 76:223–234

    Article  PubMed  Google Scholar 

  6. Ellis PD (1983) Science 221:1141–1146

    CAS  Google Scholar 

  7. Forsén S, Drakenberg T, Wennerström H (1987) Q Rev Biophys 19:83–114

    PubMed  Google Scholar 

  8. Armitage IM, Pajer RT, Uiterkamp A, Schoot JM, Chlebowski JF, Coleman JE (1976) J Am Chem Soc 98:5710–5712

    CAS  PubMed  Google Scholar 

  9. Nakatsuji H, Kanda K, Endo K, Yonezawa T (1984) J Am Chem Soc 106:4653–4660

    CAS  Google Scholar 

  10. Nakatsuji H, Nakao T, Kanda K (1987) Chem Phys 118:25–32

    Article  CAS  Google Scholar 

  11. Ellis PD, Odom JD, Lipton AS, Gulik JM (1993) J Am Chem Soc 115:755–759

    Google Scholar 

  12. Kidambi SS, Ramamoorthy A (2003) Inorg Chem 42:2200–2202

    Article  CAS  PubMed  Google Scholar 

  13. Kidambi SS, Ramamoorthy A (2003) Inorg Chem 42:3142–3151

    Article  CAS  PubMed  Google Scholar 

  14. Kidambi SS, Ramamoorthy A (2002) J Phys Chem A 106:10363–10369

    Article  CAS  Google Scholar 

  15. Krauss M, Olsen L, Antony J, Hemmingsen L (2002) J Phys Chem B 106:9446–9453

    Article  CAS  Google Scholar 

  16. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789

    Article  CAS  Google Scholar 

  17. Becke AD (1993) J Chem Phys 98:1372–1377

    CAS  Google Scholar 

  18. Becke AD (1993) J Chem Phys 98:5648–5652

    CAS  Google Scholar 

  19. Kellö V, Sadlej AJ (1995) Theor Chim Acta 91:353–371

    Article  Google Scholar 

  20. Ditchfield R, Hehre WJ, Pople JA (1971) J Chem Phys 54:724–728

    CAS  Google Scholar 

  21. Hehre WJ, Ditchfield R, Pople JA (1972) J Chem Phys 56:2257–2261

    CAS  Google Scholar 

  22. Hariharan PC, Pople JA (1974) Mol Phys 27:209–214

    CAS  Google Scholar 

  23. Gordon MS (1980) Chem Phys Lett 76:163–168

    Article  CAS  Google Scholar 

  24. Hariharan PC, Pople JA (1973) Theor Chim Acta 28:213–222

    CAS  Google Scholar 

  25. Wolinski K, Hilton JF, Pulay P (1990) J Am Chem Soc 112:8251–8260

    CAS  Google Scholar 

  26. Dodds JL, McWeeny R, Sadlej AJ (1977) Mol Phys 34:1779–1791

    CAS  Google Scholar 

  27. Ditchfield R (1974) Mol Phys 27:789–807

    CAS  Google Scholar 

  28. McWeeny R (1962) Phys Rev 126:1028

    Article  Google Scholar 

  29. London F (1937) J Phys Radium (Paris) 8:397–409

    Google Scholar 

  30. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98, revision A.7. Gaussian, Pittsburgh, Pa., USA

  31. Biosym Technologies (1993) InsightII, version 2.3.0. Biosym Technologies, San Diego, Calif., USA

  32. Bauer R, Jensen SJ, Schmidt-Nielsen B (1988) Hyperfine Interact 39:203–234

    CAS  Google Scholar 

  33. Wadt WR, Hay PJ (1985) J Chem Phys 82:270–283

    Article  Google Scholar 

  34. Hay PJ, Wadt WR (1985) J Chem Phys 82:284–298

    Article  Google Scholar 

  35. Hay PJ, Wadt WR (1985) J Chem Phys 82:299–310

    Google Scholar 

  36. Meijers R, Morris RJ, Adolph HW, Merli A, Lamzin VS, Cedergren-Zeppezauer ES (2001) J Biol Chem 276:9316–9321

    Article  CAS  PubMed  Google Scholar 

  37. Arseniev A, Schultze P, Worgotter E, Braun W, Wagner G, Vasak M, Kagi JHR, Wuthrich K (1988) J Mol Biol 201:637–657

    CAS  PubMed  Google Scholar 

  38. Shepard WEB, Kingston RL, Anderson BF, Baker EN (1993) Acta Crystallogr D 49:331–343

    Article  Google Scholar 

  39. Jensen AF, Bukrinsky JT, Bjerrum MJ, Larsen S (2002) J Biol Inorg Chem 7:490–499

    Article  CAS  PubMed  Google Scholar 

  40. Coleman JE, Gettins P (1986) In: Bertini I, Gray HB (eds) Zinc enzymes. Birkhäuser, Basel, pp 77–99

  41. Visscher L, Enevoldsen T, Saue T, Jensen HJH, Oddershede J (1999) J Comput Chem 20:1262–1273

    Article  CAS  Google Scholar 

  42. Bühl M, Kaupp M, Malkina O, Malkin VG (1999) J Comput Chem 20:91–105

    Article  Google Scholar 

  43. Honkonen RS, Doty FD, Ellis PD (1983) J Am Chem Soc 105:4163–4168

    CAS  Google Scholar 

  44. Honkonen RS, Ellis PD (1984) J Am Chem Soc 106:5488–5497

    CAS  Google Scholar 

  45. Hemmingsen L, Bauer R, Bjerrum MJ, Schwarz K, Blaha P, Andersen P (1999) Inorg Chem 38:2860–2867

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the TMR network of the European Union (CT98-0232), the Danish Research Council for Natural Sciences Supercomputer Center, grant no. 9800533, and the Carlsberg Foundation.

Author information

Authors and Affiliations

  1. Quantum Protein Centre (QUP), Department of Physics, The Technical University of Denmark, Building 309, 2800 , Lyngby, Denmark

    Lars Hemmingsen

  2. Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, 2100, Copenhagen, Denmark

    Lars Olsen

  3. Scientific Computing, Free University of Berlin, Arnimallee 2–6, 14195 , Berlin, Germany

    Jens Antony

  4. Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 , Copenhagen, Denmark

    Stephan P. A. Sauer

Authors
  1. Lars Hemmingsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lars Olsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jens Antony
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Stephan P. A. Sauer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lars Hemmingsen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hemmingsen, L., Olsen, L., Antony, J. et al. First principle calculations of 113Cd chemical shifts for proteins and model systems. J Biol Inorg Chem 9, 591–599 (2004). https://doi.org/10.1007/s00775-004-0553-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00775-004-0553-0

Keywords

Search

Navigation