Controlling and fine tuning the physical properties of two identical metal coordination sites in de novo designed three stranded coiled coil peptides

Journal of the American Chemical Society

Volumn 133, Issue 2, 2011, Pages 239-251

  Iranzo, Olga ^a,b   Chakraborty, Saumen ^a   Hemmingsen, Lars ^c   Pecoraro, Vincent L ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CDS; COILED COIL PEPTIDE; COORDINATE STRUCTURES; COORDINATION ENVIRONMENT; COORDINATION SITES; DYNAMIC BEHAVIORS; FINE TUNING; HELICAL COILED-COIL; LINEAR SEQUENCE; METAL CENTERS; METAL SITES; METAL-COORDINATION SITES; METALATIONS; NMR CHEMICAL SHIFTS; PSEUDOTETRAHEDRAL; RIGID STRUCTURE; WATER MOLECULE;

AMINO ACIDS; BINDING SITES; BIOCHEMISTRY; CADMIUM; CADMIUM SULFIDE; CHEMICAL SHIFT; METALS; PEPTIDES; PHYSICAL PROPERTIES; RIGID STRUCTURES; STRUCTURAL PROPERTIES; TOPOLOGY;

CADMIUM COMPOUNDS;

CADMIUM DERIVATIVE; CADMIUM SULFIDE; CYSTEINE DERIVATIVE; GRAND PEPTIDE; LEUCINE; PEPTIDE; THIOL DERIVATIVE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CIRCULAR DICHROISM; METAL BINDING; METAL COORDINATION SITE; METALLATION; MOLECULE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH; PKA; PROTEIN BINDING; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; PROTON TRANSPORT; STOICHIOMETRY;

CADMIUM; HYDROGEN-ION CONCENTRATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; ORGANOMETALLIC COMPOUNDS; PEPTIDES;

EID: 78651398662     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja104433n     Document Type: Article

References (59)

1. DeGrado, W. F., Summa, C. M., Pavone, V., Nastri, F., and Lombardi, A. Annu. Rev. Biochem. 1999, 68, 779-819
2. Gibney, B., Rabanal, F., and Dutton, P. Curr. Opin. Chem. Biol. 1997, 1, 537-542
3. Peacock, A. F. A., Iranzo, O., and Pecoraro, V. L. Dalton Trans. 2009, 2271-2280
4. Lu, Y., Yeung, N., Sieracki, N., and Marshall, N. M. Nature 2009, 460, 855-862
5. Iranzo, O., Ghosh, D., and Pecoraro, V. L. Inorg. Chem. 2006, 45, 9959-9973
6. Gibney, B. R., Rabanal, F., Skalicky, J. J., Wand, A. J., and Dutton, P. L. J. Am. Chem. Soc. 1999, 121, 4952-4960
7. Gibney, B. R. and Dutton, P. L. Adv. Inorg. Chem. 2001, 51, 409-455
8. Reedy, C. J. and Gibney, B. R. Chem. Rev. 2004, 104, 617-649
9. Zhuang, J., Amoroso, J. H., Kinloch, R., Dawson, J. H., Baldwin, M. J., and Gibney, B. R. Inorg. Chem. 2004, 43, 8218-8220
10. Kennedy, M. L., Petros, A. K., and Gibney, B. R. J. Inorg. Biochem. 2004, 98, 727-732
11. Cochran, F. V., Wu, S. P., Wang, W., Nanda, V., Saven, J. G., Therien, M. J., and DeGrado, W. F. J. Am. Chem. Soc. 2005, 128, 663
12. McAllister, K. A., Zou, H., Cochran, F. V., Bender, G. M., Senes, A., Fry, H. C., Nanda, V., Keenan, P. A., Lear, J. D., Saven, J. G., Therien, M. J., Blasie, J. K., and DeGrado, W. F. J. Am. Chem. Soc. 2008, 130, 11921-11927
13. Ghirlanda, G., Osyczka, A., Liu, W., Antolovich, M., Smith, K. M., Dutton, P. L., Wand, A. J., and DeGrado, W. F. J. Am. Chem. Soc. 2004, 126, 8141-8147
14. Nastri, F., Lombardi, A., D'Andrea, L. D., Sanseverino, M., Maglio, O., and Pavone, V. Peptide Sci. 1998, 47, 5-22
15. Sakamoto, S. O., I., Ueno, A., and Mihara, H. J. Chem. Soc., Perkin Trans. 2, 1999, 2059-2069
16. Obataya, I., Kotaki, T., Sakamoto, S., Ueno, A., and Mihara, H. Bioorg. Med. Chem. Lett. 2000, 10, 2719-2722
17. Calhoun, J. R., Nastri, F., Maglio, O., Pavone, V.; A.;, L., and DeGrado, W. F. Peptide Sci. 2005, 80, 264-278
18. Geremia, S., DiCostanzo, L., Randaccio, L., Engel, D. E., Lombardi, A., Nastri, F., and DeGrado, W. F. J. Am. Chem. Soc. 2005, 127, 17266-17276
19. Kharenko, O. A. and Ogawa, M. Y. J. Inorg. Biochem. 2004, 98, 1971-1974
20. Kharenko, O. A., Kennedy, D. C., Demeler, B., Maroney, M. J., and Ogawa, M. Y. J. Am. Chem. Soc. 2005, 127, 7678-7679
21. Li, X. Q., Suzuki, K., Kanaori, K., Tajima, K., Kashiwada, A., Hiroaki, H., Kohda, D., and Tanaka, T. Protein Sci. 2000, 9, 1327-1333
22. Suzuki, K., Hiroaki, H., Kohda, D., Nakamura, H., and Tanaka, T. J. Am. Chem. Soc. 1998, 120, 13008-13015
23. Kiyokawa, T., Kanaori, K., Tajima, K., Koike, M., Mizuno, T., Oku, J., and Tanaka, T. J. Peptide Res. 2004, 63, 347-353
24. Shiga, D., Nakane, D., Inomata, T., Masuda, H., Oda, M., Noda, M., Uchiyama, S., Fukui, K., Takano, Y., Nakamura, H., Mizuno, T., and Tanaka, T. Biopolymers 2009, 91, 907-916
25. Ghosh, D. and Pecoraro, V. L. Inorg. Chem. 2004, 43, 7902-7915
26. Farrer, B. and Pecoraro, V. L. Proc. Natl. Acad. Sci., U.S.A. 2003, 100, 3760-3765
27. Dieckmann, G. R., McRorie, D. K., Lear, J. D., Sharp, K. A., DeGrado, W. F., and Pecoraro, V. L. J. Mol. Biol. 1998, 280, 897-912
28. Dieckmann, G. R., McRorie, D. K., Tierney, D. L., Utschig, L. M., Singer, C. P., O'Halloran, T. V., Penner-Hahn, J. E., DeGrado, W. F., and Pecoraro, V. L. J. Am. Chem. Soc. 1997, 119, 6195-6196
29. Farrer, B. T., Harris, N. P., Balchus, K. E., and Pecoraro, V. L. Biochemistry 2001, 40, 14696-14705
30. Touw, D. S., Nordman, C. E., Stuckey, J. A., and Pecoraro, V. L. Proc. Natl. Acad. Sci., U.S.A. 2007, 104, 11969-11974
31. Luczkowski, M., Stachura, M., Schirf, V., Demeler, B., Hemmingsen, L., and Pecoraro, V. L. Inorg. Chem. 2008, 47, 10875-10888
32. Matzapetakis, M., Farrer, B. T., Weng, T.-C., Hemmingsen, L., Penner-Hahn, J. E., and Pecoraro, V. L. J. Am. Chem. Soc. 2002, 124, 8042-8054
33. Lee, K. H., Matzapetakis, M., Mitra, S., Marsh, E. N. G., and Pecoraro, V. L. J. Am. Chem. Soc. 2004, 126, 9178-9179
34. Lee, K.-H., Cabello, C., Hemmingsen, L., Marsh, E. N. G., and Pecoraro, V. L. Angew. Chem., Int. Ed. 2006, 45, 2864-2868
35. Peacock, A. F. A., Hemmingsen, L., and Pecoraro, V. L. Proc. Natl. Acad. Sci., U.S.A. 2008, 105, 16566-16571
36. Iranzo, O., Cabello, C., and Pecoraro, V. L. Angew. Chem., Int. Ed. 2007, 46, 6688-6691
37. DeLano, W. L. The PyMOL Molecular Graphics System, DeLano Scientific, Palo Alto, California, USA, 2005, http://www.pymol.org.
38. -).
39. Chan, W. C. and White, P. D. Fmoc Solid Phase Peptide Synthesis: A Practical Approach; Oxford University Press: New York, 2000.
40. Mantle, M., Stewart, G., Zayas, G., and King, M. Biochem. J. 1990, 266, 597-604
41. Matzapetakis, M., Ghosh, D., Weng, T.-C., Penner-Hahn, J. E., and Pecoraro, V. L. J. Biol. Inorg. Chem. 2006, 11, 876-890
42. Iranzo, O., Jakusch, T., Lee, K.-H., Hemmingsen, L., and Pecoraro, V. L. Chem. - Eur. J. 2009, 15, 3761-3772
43. Pace, C. N. and Scholtz, J. M. Protein Structure: A Practical Approach; Oxford University Press: Oxford, 1997.
44. Boice, J. A., Dieckmann, G. R., Degrado, W. F., and Fairman, R. Biochemistry 1996, 35, 14480-14485
45. Cobas, C., Cruces, J., and Sardina, F. J. MestRe-C, 2.3 ed.; Universidad de Santiago de Compostela, Spain, 2000.
46. Jeener, J., Meier, B. H., Bachmann, P., and Ernst, R. R. J. Chem. Phys. 1979, 71
47. Hoult, D. I. J. Magn. Reson. 1976, 21, 337-347
48. Rance, M. J. Magn. Reson. 1987, 74, 557-564
49. MestReNova, version 6.XX, Mestrelab Research S.L., Santiago de Compostela, Spain, www.mestrelab.com, 2009.
50. Hemmingsen, L., Bauer, R., Bjerrum, M. J., Zeppezauer, M., Adolph, H. W., Formicka, G., and Cedergren-Zeppezauer, E. Biochemistry 1995, 34, 7145-7153
51. Hemmingsen, L., B., R., Bjerrum, M., Adolph, H., Zeppezauer, M., and Cedergren-Zeppezauer, E. Eur. J. Biochem. 1996, 241, 546-551
52. Matzapetakis, M. and Pecoraro, V. L. J. Am. Chem. Soc. 2005, 127, 18229-18233
53. Tanaka, T., Mizuno, T., Fukui, S., Hiroaki, H., Oku, J.-i., Kanaori, K., Tajima, K., and Shirakawa, M. J. Am. Chem. Soc. 2004, 126, 14023-14028
54. Lombardi, A., Summa, C. M., Geremia, S., Randaccio, L., Pavone, V., and DeGrado, W. F. Proc. Natl. Acad. Sci., U.S.A. 2000, 97, 6298-6305
55. Summa, C. M., Rosenblatt, M. M., Hong, J.-K., Lear, J. D., and DeGrado, W. F. J. Mol. Biol. 2002, 321, 923-938
56. Spiegel, K., De Grado, W. F., and Klein, M. L. Proteins: Struct., Funct., Bioinf. 2006, 65, 317-330
57. Peacock, A. F. A., Stuckey, J. A., and Pecoraro, V. L. Angew. Chem., Int. Ed. 2009, 48, 7371-7374
58. Chakraborty, S., Touw, D. S., Peacock, A. F. A., Stuckey, J. A., and Pecoraro, V. L. J. Am. Chem. Soc. 2010, 132, 13240-13250
59. Lovejoy, B., Choe, S., Cascio, D., McRorie, D., DeGrado, W., and Eisenberg, D. Science 1993, 259, 1288-1293