Copper(II) ion binding to cellular prion protein

Journal of Chemical Information and Modeling

Volumn 48, Issue 2, 2008, Pages 283-287

  Zidar, Jernej ^a   Pire, Elizabeta T ^b   Hodošček, Milan ^a   Bukovec, Peter ^b  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b UNIVERSITY OF LJUBLJANA   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; MEDICAL PROBLEMS; NEUROLOGY;

CELLULAR PRION PROTEINS; NEURODEGENERATIVE DISEASES;

PROTEINS;

COPPER; HISTIDINE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METABOLISM; PRION;

BINDING SITES; COPPER; HISTIDINE; HUMANS; MODELS, MOLECULAR; PRIONS;

EID: 41549126784     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700226c     Document Type: Article

References (36)

1. Dormont, D. Prion diseases: pathogenesis and public health concerns. FEBS Lett. 2002, 529, 325-342.
2. Prusiner, S. B. Prions. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 13363-13383.
3. Riek, R.; Hornemann, S.; Wider, G.; Billeter, M.; Glockshuber, R.; Wtithrich, K. NMR structure of the mouse prion protein domain PrP(121-231). Nature 1996, 382, 180-182.
4. Donne, D. G.; Villes, J. H.; Groth, D.; Mehlhorn, I.; James, T. J.; Cohen, T. E.; Prusiner, S. B.; Wright, P. E.; Dyson, H. J. Structure of the recombinant full-length hamster prion protein PrP(29-231): The N-terminus is highly flexible. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 13452-13457.
5. Garcia, F. L.; Zahn, R.; Riek, R.; Wüthrich, K. NMR structure of the bovine prion protein. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8334-8339.
6. Zahn, R. A.; Liu, A.; Lührs, T.; Riek, R.; von Schroetter, C.; Garcia, F. L.; Billeter, M.; Calzolai, L.; Wider, G.; Wüthrich, K. NMR solution structure of the human prion protein, Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 145-150.
7. Brown, D. R.; Qin, K.; Herms, J. W.; Madlung, A.; Manson, J.; Strome, R.; Fraser, P. E.; Kruck, T.; von Bohlen, A.; Schulz-Schaeffer, W.; Giese, A.; Westaway, D.; Kretzschmar, H. The celullar prion protein binds copper in vivo. Nature 1997, 390, 684-687.
8. Hornshaw, M. P.; McDermott, J. R.; Candy, J. M. Copper binding to the N-terminal tandem repeat region of mammalian and avian prion protein. Biochem. Biophys. Res. Commun. 1995, 207, 621-629.
9. Hornshaw, M. P.; McDermott, J. R.; Candy, J. M.; Lakey, J. H. Copper binding to the N-terminal tandem repeat region of mammalian and avian prion protein: structural studies using synthetic peptides. Biochem. Biophys. Res. Commun. 1995, 214, 993-999.
10. Stöckel, J.; Safar, J.; Wallace, A. C.; Cohen, F. E.; Prusiner, S. B. Prion protein selectively binds copper(II) ions. Biochemistry 1998, 37, 7185-7193.
11. Villes, J. H.; Cohen, F. E.; Prusiner, S. B.; Goodin, D. B.; Wright, P. E.; Dyson, H. J. Copper binding to the prion protein: structural implications of four identical cooperative binding sites, Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 2042-2047.
12. Miura, T.; Hori-I, A.; Mototani, H.; Takeuchi, H. Raman spectroscopic study on the copper(II) binding mode of prion octapeptide and its pH dependence. Biochemistry 1999, 38, 11560-11569.
13. 2+ binding sites in the N-terminal domain of the prion protein by EPR and CD spectroscopy. Biochemistry 2000, 39, 13760-13771.
14. Jackson, G. S.; Murray, I.; Hosszu, L. L. P.; Gibbs, N.; Waltho, J. P.; Clarke, A. R.; Collinge, J. Location and properties of metal-binding sites on the human prion protein. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 8531-8535.
15. Hasanin, S. S.; Murphy, L. M.; Strange, R. W.; Grossman, J. G.; Clarke, A. R.; Jackson, G. S.; Collinge, J. XAFS study of the highaffinity copper-binding site of human PrP(91-231) and its low-resolution structure in solution. J. Mol. Biol. 2001, 311, 467-473.
16. Whittal, R. M.; Ball, H. L.; Cohen, F. E.; Burlingame, A. L.; Prusiner, S. B.; Baldwin, M. A. Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry. Protein Sci. 2000, 9, 332-343.
17. Kramer, M. L.; Kratzin, H. D.; Schmidt, B.; Romer, A.; Windl, O.; Liemann, S.; Hornemann, S.; Kretzschmar, H. Prion protein binds copper within the physiological concentration range. J. Biol. Chem. 2001, 276, 16711-16719.
18. 2+ to the C-terminal domain of the murine prion protein. Biophys. J. 2001, 81, 516-525.
19. 2+ binding sites in the C-terminal domain of the murine prion protein: a pulse EPR and ENDOR study. J. Phys. Chem. B 2001, 105, 1631-1639.
20. Cereghetti, G. M.; Schweiger, A.; Glockshuber, R.; Van Doorslaer, S. Stability and Cu (II) Binding of Prion Protein Variants Related to Inherited Human Prion Diseases. Biophys. J. 2003, 84, 1985-1997.
21. Brown, D. R.; Guantieri, V.; Grasso, G.; Impelizzeri, G.; Pappalardo, G.; Rizzarelli, R. Copper(II) complexes of peptide fragments of the prion protein. Conformation changes induced by copper(II) and the binding motif in C-terminal protein region. J. Inorg. Biochem. 2004, 98, 133-143.
22. Praprotnik, M.; Janežič, D. Molecular dynamics integration and molecular vibrational theory, II, Simulation of non-linear molecules. J. Chem. Phys. 2005, 122, 174102.
23. Praprotnik, M.; Janežič, D. Molecular dynamics integration and molecular vibrational theory. III, The IR spectrum of water. J. Chem. Phys. 2005, 122, 174103.
24. Warshel, A.; Levitt, M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 1976, 103, 227-248.
25. Eurenius, K.; Chatfield, D. C.; Brooks, B. R.; Hodoscek, M. Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I., Theoretical considerations, Int. J. Quantum Chem. 1996, 60, 1189-1200.
26. Borštnik, U.; Hodošček, M.; Janežič, D. Improving the performance of molecular dynamics simulations on parallel clusters. J. Chem. Inf. Comput. Sci. 2004, 44, 359-364.
27. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, Jr., R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., Ill; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. Allatom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
28. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187-217.
29. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
30. Essman, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, A. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103, 8577-8593.
31. Humphrey, W.; Dalke, A.; Schulten, K. VMD: visual molecular dynamics. J. Mol. Graphics Modell. 1996, 14, 33-38.
32. http://www.gnuplot.info (accessed June 20th 2007).
33. Imanishi, M.; Hori, Y.; Nagaoka, M.; Sugiura, Y. Design of novel zinc finger proteins: towards artificial control of specific gene expression. Eur. J. Pharm. Sci. 2001, 13, 91-97.
34. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley and Sons: New York, 1991.
35. Bren, M.; Florian, J.; Mavri, J.; Bren, U. Do all pieces make a whole? Thiele cumulants and the free energy decomposition. Theor. Chem. Acc. 2007, 117, 535-540.
36. Bren, U.; Martinek, V.; Florian, J. Decomposition of the solvation free energies of deoxyribonucleoside triphosphates using the free energy perturbation method. J. Phys. Chem. B 2006, 110, 12782-12788.