The essential dynamics of Cu, Zn superoxide dismutase: Suggestion of intersubunit communication

Biophysical Journal

Volumn 73, Issue 2, 1997, Pages 1007-1018

  Chillemi, G ^a   Falconi, M ^b   Amadei, A ^c   Zimatore, G ^a,d   Desideri, A ^b   Di Nola, A ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

^c UNIVERSITY OF GRONINGEN   (Netherlands)

^d CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COPPER ZINC SUPEROXIDE DISMUTASE; PROTEIN SUBUNIT;

ARTICLE; CELL COMMUNICATION; COUPLING FACTOR; ENZYME ACTIVE SITE; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN DOMAIN; SAMPLING; WATER TRANSPORT;

EID: 0030836641     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78134-7     Document Type: Article

References (54)

1. Amadei, A., A. B. M. Linssen, and H. J. C. Berendsen. 1993. Essential dynamics of proteins. Proteins Struct. Funct. Genet. 17:412-425.
2. Amadei, A., A. B. M. Linssen, B. L. de Groot, D. M. F. van Aalten, and H. J. C. Berendsen. 1996. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13:615-625.
3. Andreani, C., A. Filabozzi, F. Menzinger, A. Desideri, A. Deriu, and D. Di Cola. 1995. Dynamics of hydrogen atoms in superoxide dismutase by quasi-elastic neutron scattering. Biophys. J. 68:2519-2523.
4. Banci, L., P. Carloni, G. La Penna, and P. L. Orioli. 1992. Molecular dynamics studies on superoxide dismutase and its mutants: the structural and functional role of Arg143. J. Am. Chem. Soc. 114:6994-7001.
5. Banci, L., P. Carloni, and P. L. Orioli. 1994. Molecular dynamics studies on mutants of Cu, Zn superoxide dismutase: the functional role of charged residues in the electrostatic loop VII. Proteins Struct. Funct. Genet. 18:216-230.
6. Bannister, J. V., W. M. Bannister, and G. Rotilio. 1987. Aspects of the structure, function and applications of superoxide dismutase. CRC Crit. Rev. Biochem. 22:111-180.
7. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. Di Nola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
8. Bernstein, F., T. Koetzle, G. Williams, E. Meyer, Jr., M. Brice, J. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
9. Cockle, S. A., and R. C. Bray. 1977. Do all the copper atoms in bovine superoxide dismutase function in catalysis? In Superoxide and Superoxide Dismutase. A. M. Michelson, J. M. McCord, and I. Fridovich, editors. Academic Press, London. 215.
10. Cupane, A., M. Leone, V. Militello, M. E. Stroppolo, F. Polticelli, and A. Desideri. 1994. Low-temperature optical spectroscopy of native and azide reacted bovine Cu, Zn superoxide dismutase. A structural dynamics study. Biochemistry. 33:15103-15109.
11. Cupane, A., M. Leone, V. Militello, M. E. Stroppolo, F. Polticelli, and A. Desideri. 1995. Low-temperature optical spectroscopy of cobalt in Cu, Co superoxide dismutase. A structural dynamics study of the solvent-unaccessible metal site. Biochemistry. 34:16313-16319.
12. de Groot, B. L., A. Amadei, and H. J. C. Berendsen. 1996a. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone Guanylin. J. Biomol. Struct. Dyn. 13:741-751.
13. de Groot, B. L., A. Amadei, R. M. Scheek, N. A. J. van Nuland, and H. J. C. Berendsen. 1996b. An extended sampling of the configurational space of HPr of E. coli. Proteins Struct. Funct. Genet. 26:314-322.
14. de Groot, B. L., D. M. F. van Aalten, A. Amadei, and H. J. C. Berendsen. 1996c. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys. J. 71:1707-1713.
15. Desideri, A., M. Falconi, F. Polticelli, M. Bolognesi, K. Djinovic, and G. Rotilio. 1992. Evolutionary conservativeness of electric field in the Cu, Zn superoxide dismutase active site. J. Mol. Biol. 223:337-342.
16. Djinovic, K., G. Gatti, A. Coda, L. Antolini, G. Pelosi, A. Desideri, M. Falconi, F. Marmocchi, G. Rotilio, and M. Bolognesi. 1992. Crystal structure of yeast Cu,Zn enzyme superoxide dismutase. Crystallographic refinement at 2.5 Å resolution. J. Mol. Biol. 225:791-890.
17. Djinovic-Carugo, K., A. Battistoni, M. T. Carrí, F. Polticelli, A. Desideri, G. Rotilio, A. Coda, and M. Bolognesi. 1994. Crystal structure of the cyanide-inhibited Xenopus laevis Cu, Zn superoxide dismutase at 98K. FEBS Lett. 349:93-98.
18. Djinovic-Carugo, K., A. Coda, A. Battistoni, M. T. Carrí, F. Polticelli, A. Desideri, G. Rotilio, K. S. Wilson, and M. Bolognesi. 1996. Three-dimensional structure of Xenopus laevis Cu, Zn superoxide dismutase B determined by x-ray crystallography at 1.5 Å resolution. Acta Crystallogr. D52:176-188.
19. Doster, W., S. Cusack, and W. Petri. 1989. Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature. 337: 754-756.
20. Falconi, M., R. Gallimbeni, and E. Paci. 1996. Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation. J. Comput. Aided Mol. Des. 10:490-498.
21. Fielden, E. M., P. B. Roberts, R. C. Bray, D. J. Lowe, G. N. Mautner, G. Rotilio, and L. Calabrese. 1974. The mechanism of action of superoxide dismutase from pulse radiolysis and electron paramagnetic resonance. Evidence that only half the active sites function in catalysis. Biochem. J. 139:49-60.
22. Fisher, C. L., D. E. Cabelli, J. A. Tainer, R. A. Hallewell, and E. D. Getzoff. 1994. The role of arginine 143 in the electrostatic and mechanism of Cu, Zn superoxide dismutase: computational and experimental evaluation by mutational analysis. Proteins Struct. Funct. Genet. 19: 24-34.
23. Gaber, B. P., R. D. Brown, S. H. Koening, and J. A. Fee. 1972. Nuclear magnetic relaxation dispersion in protein solutions. Bovine erythrocyte superoxide dismutase. Biochim. Biophys. Acta. 271:1-5.
24. Garcia, A. E. 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696-2699.
25. Getzoff, E. D., D. E. Cabelli, C. L. Fisher, H. E. Parge, M. S. Viezzoli, L. Banci, and R. A. Hallewell. 1992. Faster superoxide dismutase mutants designed by enhancing electrostatic guidance. Nature. 358:347-351.
26. Getzoff, E. D., J. A. Tainer, P. K. Weiner, P. A. Kollman, J. S. Richardson, and D. C. Richardson. 1983. Electrostatic recognition between superoxide and copper zinc superoxide dismutase. Nature. 306:287-290.
27. Hayward, S., A. Kitao, F. Hirata, and N. Go. 1993. Effect of solvent on collective motions in globular proteins. J. Mol. Biol. 234:1207-1217.
28. Ichiye, T., and M. Karplus. 1991. Collective motions in proteins; a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins. 11:205-217.
29. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
30. Klapper, I., R. Hagstrom, R. Fine, K. Sharp, and B. Honig. 1986. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins Struct. Funct. Genet. 1:47-59.
31. Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
32. Lawrence, G. D., and D. T. Sawyer. 1979. Potentiometric titrations and oxidation-reduction potentials of manganese and copper-zinc superoxide dismutases. Biochemistry. 18:3045-3050.
33. Luty, B. A., S. El Amrani, and J. A. McCammon. 1993. Simulation of the bimolecular reaction between superoxide and superoxide dismutase: synthesis of the encounter and reaction steps. J. Am. Chem. Soc. 115: 11874-11877.
34. Polticelli, F., A. Battistoni, P. O'Neill, G. Rotilio, and A. Desideri. 1996. Identification of the residues responsible for the alkaline inhibition of Cu,Zn superoxide dismutase: a site-directed mutagenesis approach. Protein Sci. 5:248-253.
35. Polticelli, F., G. Bottaro, A. Battistoni, M. T. Carrí, K. Djinovic-Carugo, M. Bolognesi, P. O'Neill, G. Rotilio, and A. Desideri. 1995. Modulation of the catalytic rate of Cu, Zn superoxide dismutase in single and double mutants of conserved positively and negatively charged residues. Biochemistry. 34:6043-6049.
36. Rigo, A., P. Viglino, M. Bonori, D. Cocco, L. Calabrese, and G. Rotilio. 1978. The binding of copper ions to copper-free bovine superoxide dismutase. Kinetic aspects. Biochem. J. 169:277-280.
37. Rigo, A., P. Viglino, L. Calabrese, D. Cocco, and G. Rotilio. 1977. The binding of copper ions to copper-free bovine superoxide dismutase. Copper distribution in protein samples recombined with less than stoichiometric copper ion/protein ratios. Biochem. J. 161:27-30.
38. Romo, T. D., J. B. Clarage, D. C. Sorensen, and G. N. Phillips, Jr. 1995. Singular value decomposition analysis of time-averaged cristallographic refinement. Proteins. 22:311-321.
39. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the cartesian equations of motions of a system with constraints: molecular dynamics of N-alkanes. J. Comp. Phys. 23: 327-341.
40. Scheck, R. M., N. A. J. Van Nuland, B. L. De Groot, A. B. M. Lissen, A. Amadei. 1995. Structure from NMR and molecular dynamics: distance restraining inhibits motion in the essential subspace. J. Biomol. NMR. 6:106-111.
41. Sergi, A., M. Ferrario, F. Polticelli, P. O'Neill, and A. Desideri. 1994. Simulation of superoxide-superoxide dismutase association rate for six natural variants. Comparison with the experimental catalytic rate. J. Phys. Chem. 98:10554-10557.
42. Shen, J., and J. A. McCammon. 1991. Molecular dynamics simulation of superoxide interacting with superoxide dismutase. Chem. Phys. 158: 191-198.
43. Shen, J., S. Subramaniam, C. F. Wong, and J. A. McCammon. 1989. Superoxide dismutase: fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation. Biopolymers. 28:2085-2096.
44. Shen, J., C. F. Wong, S. Subramaniam, T. A. Albright, and J. A. McCammon. 1990. Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase. J. Comp. Chem. 11:346-350.
45. Sines, J. J., S. A. Allison, and J. A. McCammon. 1990. Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases. Biochemistry. 29:9403-9412.
46. Sneddon, S. F., and C. L. Brooks, III. 1993. Protein motions: structural and functional aspects. In Molecular Structures in Biology. R. Diamod, T. F. Koetzle, K. Prout, and J. S. Richardson, editors. Oxford University Press, Oxford. 115-163.
47. Tainer, J. A., E. D. Getzoff, K. M. Beem, J. S. Richardson, and D. C. Richardson. 1982. Determination and analysis of 2 Å structure of copper zinc superoxide dismutase. J. Mol. Biol. 160:181-217.
48. van Aalten, D. M. F., A. Amadei, A. B. M. Linssen, V. G. H. Eijsink, G. Vriend, and H. J. C. Berendsen. 1995. The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water. Proteins Struct. Funct. Genet. 22:45-54.
49. van Aalten, D. M. F., B. L. de Groot, J. B. C. Findlay, H. J. C. Berendsen, and A. Amadei. 1996. A comparison of techniques for calculating protein essential dynamics. J. Comput. Chem. 18:169-181.
50. van Gunsteren, W. F., and H. J. C. Berendsen. 1987. GROMOS: Groningen Molecular Simulation (GROMOS) Library Manual. Biomos, Groningen.
51. 19F relaxation as a probe of the oxidation state of Cu, Zn superoxide dismutase. Studies of the enzyme in steady-state turnover. Biochem. Biophys. Res. Commun. 100:125-130.
52. Vriend, G. 1990. WHAT IF. A molecular modeling drug design program. J. Mol. Graph. 8:52-56.
53. Wong, C. F., C. Zheng, J. Shen, A. McCammon, and P. G. Wolynes. 1993. Cytochrome c: a molecular proving ground for computer simulations. J. Phys. Chem. 97:3100-3110.
54. Wong, Y., T. W. Clark, J. Shen, and J. A. McCammon. 1993. Molecular dynamics simulation of substrate-enzyme interactions in the active site channel of superoxide dismutase. Mol. Simul. 10:277-289.