Regulation of protein function: Crystal packing interfaces and conformational dimerization

Biochemistry

Volumn 47, Issue 25, 2008, Pages 6583-6589

  Crowley, Peter B ^a   Matias, Pedro M ^b   Mi, Hualing ^c   Firbank, Susan J ^d   Banfield, Mark J ^d   Dennison, Christopher ^d  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^d NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE HYPOTHESIS; CRYSTAL FORMS; CRYSTAL PACKINGS; DONOR AND ACCEPTOR; ELECTRON TRANSPORT (ET); IN-VIVO; INTEGRAL COMPONENTS; PHOTOSYNTHETIC ELECTRON TRANSPORT; PLASTOCYANIN; PROTEIN CHAINS; PROTEIN FUNCTIONS; REDOX SITES; SUPRAMOLECULAR ASSEMBLIES;

PLASTOCYANIN;

ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIMERIZATION; ELECTRON TRANSPORT; PHOTOSYNTHESIS; PRIORITY JOURNAL; PROTEIN FUNCTION; RESPIRATORY CHAIN;

BACTERIAL PROTEINS; COPPER; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; CYANOBACTERIA; ELECTRON TRANSPORT; MODELS, MOLECULAR; PLASTOCYANIN; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS;

EID: 45749083319     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800125h     Document Type: Article

References (50)

1. Whitesides, G. M., and Grzybowski, B. (2002) Self-assembly at all scales. Science 295, 2418-2421.
2. Srere, P. A. (2000) Macromolecular interactions: Tracing the roots. Trends Biochem. Sci. 25, 150-153.
3. Bendall D. S., Ed. (1996) Protein Electron Transfer, Bios Scientific, Oxford, U.K.
4. Williams, P. A., Fulop, V., Leung, Y. C., Chan, C., Moir, J. W. B., Howlett, G., Ferguson, S. J., Radford, S. E., and Hajdu, J. (1995) Pseudospecific docking surfaces on electron transfer proteins as illustrated by pseudoazurin, cytochrome c550 and cytochrome cdl nitrite reductase. Nat. Struct. Biol. 2, 975-982.
5. Ellis, R. J. (2001) Macromolecular crowding: An important but neglected aspect of the intracellular environment. Curr. Opin. Struct. Biol. 11, 114-119.
6. Minton, A. P. (2006) How can biochemical reactions within cells differ from those in test tubes? J. Cell Sci. 119, 2863-2869.
7. De Rienzo, F., Gabdoulline, R. R., Menzani, M. C., and Wade, R. C. (2000) Blue copper proteins: A comparative analysis of their molecular interaction properties. Protein Sci. 9, 1439-1454.
8. Sato, K., Kohzuma, T., and Dennison, C. (2003) Active-site structure and electron-transfer reactivity of plastocyanins. J. Am. Chem. Soc. 125, 2101-2112.
9. Dennison, C. (2005) Investigating the structure and function of cupredoxins. Coord. Chem. Rev. 249, 3025-3054.
10. Li, C., Yanagisawa, S., Martins, B. M., Messerschmidt, A., Banfield, M. J., and Dennison, C. (2006) Basic requirements for a metal-binding site in a protein: The influence of loop shortening on the cupredoxin azurin. Proc. Natl. Acad. Sci. U.S.A. 103, 7258-7263.
11. Kannt, A., Young, S., and Bendall, D. S. (1996) The role of acidic residues of plastocyanin in its interaction with cytochrome f. Biochim. Biophys. Acta 1277, 115-126.
12. Schlarb-Ridley, B. G., Bendall, D. S., and Howe, C. J. (2003) Relation between interface properties and kinetics of electron transfer in the interaction of cytochrome f and plastocyanin from plants and the cyanobacterium Phormidium laminosum. Biochemistry 42, 4057-4063.
13. Sato, K., Kohzuma, T., and Dennison, C. (2004) Pseudospecificity of the acidic patch of plastocyanin for the interaction with cytochrome f. J. Am. Chem. Soc. 126, 3028-3029.
14. Crowley, P. B., and Carrondo, M. A. (2004) The architecture of the binding site in redox protein complexes: Implications for fast dissociation. Proteins 55, 603-612.
15. Sato, K., Crowley, P. B., and Dennison, C. (2005) Transient homodimer interactions studied using the electron self-exchange reaction. J. Biol. Chem. 280, 19281-19288.
16. Crowley, P. B., Otting, G., Schlarb-Ridley, B. G., Canters, G. W., and Ubbink, M. (2001) Hydrophobic interactions in a cyanobacterial plastocyanin-cytochrome f complex. J. Am. Chem. Soc. 123, 10444-10453.
17. Crowley, P. B., and Ubbink, M. (2003) Close encounters of the transient kind: Protein interactions in the photosynthetic redox chain investigated by NMR spectroscopy. Acc. Chem. Res. 36, 723-730.
18. Soriano, G. M., Ponamarev, M. V., Tae, G. S., and Cramer, W. A. (1996) Effect of the interdomain basic region of cytochrome f on its redox reactions in vivo. Biochemistry 35, 14590-14598.
19. Tezcan, F. A., Crane, B. A., Winkler, J. R., and Gray, H. B. (2001) Electron tunneling in protein crystals. Proc. Natl. Acad. Sci. U.S.A. 98, 5002-5006.
20. Crane, B. R., Di Bilio, A. J., Winkler, J. R., and Gray, H. B. (2001) Electron tunneling in single crystals of Pseudomonas aeruginosa azurins. J. Am. Chem. Soc. 123, 11623-11631.
21. Guo, M., Bhaskar, B., Li, H., Barrows, T. P., and Poulos, T. L. (2004) Crystal structure and characterization of a cytochrome c peroxidase-cytochrome c site-specific cross-link. Proc. Natl. Acad. Sci. U.S.A. 101, 5940-5945.
22. Pearson, A. R., Mozzarelli, A., and Rossi, G. L. (2004) Microspectrophotometry for structural enzymology. Curr. Opin. Struct. Biol. 14, 656-662.
23. Kang, S. A., and Crane, B. R. (2005) Effects of interface mutations on association modes and electron-transfer rates between proteins. Proc. Natl. Acad. Sci. U.S.A. 102, 15465-15470.
24. Crosio, M. P., Janin, J., and Jullien, M. (1992) Crystal packing in six crystal forms of pancreatic ribonuclease. J. Mol. Biol. 228, 243-251.
25. Huang, D. B., Ainsworth, C. F., Stevens, F. J., and Schiffer, M. (1996) Three quaternary structures for a single protein. Proc. Natl. Acad. Sci. U.S.A. 93, 7017-7021.
26. Carrell, C. J., Sun, D., Jiang, S., Davidson, V. L., and Mathews, F. S. (2004) Structural studies of two mutants of amicyanin from Paracoccus denitrificans that stabilize the reduced state of the copper. Biochemistry 43, 9372-9380.
27. Mapelli, M., Filipp, F. V., Rancati, G., Massimiliano, L., Nezi, L., Stier, G., Hagan, R. S., Confalonieri, S., Piatti, S., Sattler, M., and Musacchio, A. (2006) Determinants of conformational dimerization of Mad2 and its inhibition by p31 comet. EMBO J. 25, 1273-1284.
28. Schlarb, B. G., Wagner, M. J., Vijgenboom, E., Ubbink, M., Bendall, D. S., and Howe, C. J. (1999) Expression of plastocyanin and cytochrome f of the cyanobacterium Phormidium laminosum in Escherichia coli and Paracoccus denitrificans and the role of leader peptides. Gene 234, 275-283.
29. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol. 276, 307-326.
30. Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., and Richardson, D. C. (2003) Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50, 437-450.
31. Navaza, J. (1994) AMoRe: an Automated Package for Molecular Replacement. Acta Crystallogr. A50, 157-163.
32. Bond, C. S., Bendall, D. S., Freeman, H. C., Guss, J. M., Howe, C. J., Wagner, M. J., and Wilce, M. C. J. (1999) The structure of plastocyanin from the cyanobacterium Phormidium laminosum. Acta Crystallogr. D55, 414-421.
33. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50, 760-763.
34. Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132.
35. Krissinel, E., and Henrick, K. (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774-797.
36. Bachar, O., Fischer, D., Nussinov, R., and Wolfson, H. (1993) A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng. 6, 279-287.
37. Bertini, I., Bryant, D. A., Ciurli, S., Dikiy, A., Fernandez, C. O., Luchinat, C., Safarov, N., Vila, A. J., and Zhao, J. (2001) Backbone dynamics of plastocyanin in both oxidation states. Solution structure of the reduced form and comparison with the oxidized state. J. Biol. Chem. 276, 47217-47226.
38. Bahadur, R. P., Chakrabarti, P., Rodier, F., and Janin, J. (2004) A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol. 336, 943-955.
39. Collins, K. D., and Washabaugh, M. W. (1985) The Hofmeister effect and the behaviour of water at interfaces. Q. Rev. Biophys. 18, 323-422.
40. Gallivan, J. P., and Dougherty, D. A. (1999) Cation-π interactions in structural biology. Proc. Natl. Acad. Sci. U.S.A. 96, 9459-9464.
41. Crowley, P. B., and Golovin, A. (2005) Cation-π interactions in protein-protein interfaces. Proteins 59, 231-239.
42. Whitmarsh, J. (1986) Mobile electron carriers in thylakoids. In Encyclopedia of Plant Physiology (Staehlin, L. A., and Arntzen, C. J., Eds.) pp 508, Springer, Berlin.
43. Haehnel, W., Ratajczak, R., and Robenek, H. (1989) Lateral distribution and diffusion of plastocyanin in chloroplast thylakoids. J. Cell Biol. 108, 1397-1405.
44. Cruz, J. A., Salbilla, B. A., Kanazawa, A., and Kramer, D. M. (2001) Inhibition of plastocyanin to P700 electron transfer in Chlamydomonas reinhardtii by hyperosmotic stress. Plant Physiol. 127, 1167-1179.
45. Schottler, M. A., Kirchhoff, H., and Weis, E. (2004) The role of plastocyanin in the adjustment of the photosynthetic electron transport to the carbon metabolism in tobacco. Plant Physiol. 136, 4265-4274.
46. Guss, J. M., Harrowell, P. R., Murata, M., Norris, V. A., and Freeman, H. C. (1986) Crystal structure analyses of reduced (Cu I) poplar plastocyanin at six pH values. J. Mol. Biol. 192, 361-387.
47. Kieselbach, T., Hagman, Å., Andersson, B., and Schroder, W. P. (1998) The thylakoid lumen of chloroplasts, isolation and characterization. J. Biol. Chem. 273, 6710-6716.
48. van Amsterdam, I. M. C., Ubbink, M., Einsle, O., Messerschmidt, A., Merli, A., Cavazzini, D., Rossi, G. L., and Canters, G. W. (2002) Dramatic modulation of electron transfer in protein complexes by crosslinking. Nat. Struct. Biol. 9, 48-52.
49. Doye, J. P. K., and Poon, W. C. K. (2006) Protein crystallization in vivo. Curr. Opin. Colloid Interface Sci. 11, 40-46.
50. Kirchhoff, H., Haase, W., Wegner, S., Danielsson, R., Ackermann, R., and Albertsson, P. A. (2007) Low-light-induced formation of semi-crystalline photosystem II arrays in higher plant chloroplasts. Biochemistry 46, 11169-11176.