Rigid-rod β-barrel ion channels with internal "cascade blue" cofactors - Catalysis of amide, carbonate, and ester hydrolysis

European Journal of Organic Chemistry

Volumn , Issue 22, 2002, Pages 3874-3883

  Som, Abhigyan ^a   Matile, Stefan ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

Bioorganic chemistry; Catalysis; Ion channels; Molecular recognition; Supramolecular chemistry

Indexed keywords

AMIDE; BENZALDEHYDE DERIVATIVE; CARBONIC ACID; ESTER; SULFONIC ACID DERIVATIVE;

ARTICLE; BINDING AFFINITY; CATALYSIS; ENANTIOMER; HYDROLYSIS; ION CHANNEL; MOLECULAR RECOGNITION; STEREOCHEMISTRY; SUPRAMOLECULAR CHEMISTRY;

EID: 0036856444     PISSN: 1434193X     EISSN: None     Source Type: Journal    
DOI: 10.1002/1099-0690(200211)2002:22<3874::AID-EJOC3874>3.0.CO;2-6     Document Type: Article

References (46)

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6. A cofactor is defined as "inorganic ion or coenzyme (small molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes, often by forming a covalent bond to the substrate) that is required for an enzymes activity" (B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, J. D. Watson, Molecular Biology of the Cell, 3rd Edn., Garland, New York, 1994, G-6). Although consistent with the role of CB in this study, "cofactor" is used mainly for convenience and could be replaced by another term if desired.
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18. Some β-barrels: [10a] W. T. Taylor, Nature 2002, 416, 657-660. [10b] C. R. Calladine, A. Sharff, B. Luisi, J. Mol. Biol. 2001, 305, 603-618. [10c] D. Qi, C.-M. Tann, D. Haring, M. D. Distefano, Chem. Rev. 2001, 101, 3081-3112. [10d] N. Nagano, E. G. Hutchinson, J. M. Thornton, Protein Sci. 1999, 8, 2072-2084. [10e] S. K. Buchanan, Curr. Opin. Struct. Biol. 1999, 9, 445-461. [10f] D. R. Flower, Biochem. J 1996, 318, 1-14. [10g] M. H. Hecht, Proc. Natl. Acad. Sci. USA 1994, 91, 8729-8730.
19. Some β-barrels: [10a] W. T. Taylor, Nature 2002, 416, 657-660. [10b] C. R. Calladine, A. Sharff, B. Luisi, J. Mol. Biol. 2001, 305, 603-618. [10c] D. Qi, C.-M. Tann, D. Haring, M. D. Distefano, Chem. Rev. 2001, 101, 3081-3112. [10d] N. Nagano, E. G. Hutchinson, J. M. Thornton, Protein Sci. 1999, 8, 2072-2084. [10e] S. K. Buchanan, Curr. Opin. Struct. Biol. 1999, 9, 445-461. [10f] D. R. Flower, Biochem. J 1996, 318, 1-14. [10g] M. H. Hecht, Proc. Natl. Acad. Sci. USA 1994, 91, 8729-8730.
20. Some β-barrels: [10a] W. T. Taylor, Nature 2002, 416, 657-660. [10b] C. R. Calladine, A. Sharff, B. Luisi, J. Mol. Biol. 2001, 305, 603-618. [10c] D. Qi, C.-M. Tann, D. Haring, M. D. Distefano, Chem. Rev. 2001, 101, 3081-3112. [10d] N. Nagano, E. G. Hutchinson, J. M. Thornton, Protein Sci. 1999, 8, 2072-2084. [10e] S. K. Buchanan, Curr. Opin. Struct. Biol. 1999, 9, 445-461. [10f] D. R. Flower, Biochem. J 1996, 318, 1-14. [10g] M. H. Hecht, Proc. Natl. Acad. Sci. USA 1994, 91, 8729-8730.
21. Some β-barrels: [10a] W. T. Taylor, Nature 2002, 416, 657-660. [10b] C. R. Calladine, A. Sharff, B. Luisi, J. Mol. Biol. 2001, 305, 603-618. [10c] D. Qi, C.-M. Tann, D. Haring, M. D. Distefano, Chem. Rev. 2001, 101, 3081-3112. [10d] N. Nagano, E. G. Hutchinson, J. M. Thornton, Protein Sci. 1999, 8, 2072-2084. [10e] S. K. Buchanan, Curr. Opin. Struct. Biol. 1999, 9, 445-461. [10f] D. R. Flower, Biochem. J 1996, 318, 1-14. [10g] M. H. Hecht, Proc. Natl. Acad. Sci. USA 1994, 91, 8729-8730.
22. Some β-barrels: [10a] W. T. Taylor, Nature 2002, 416, 657-660. [10b] C. R. Calladine, A. Sharff, B. Luisi, J. Mol. Biol. 2001, 305, 603-618. [10c] D. Qi, C.-M. Tann, D. Haring, M. D. Distefano, Chem. Rev. 2001, 101, 3081-3112. [10d] N. Nagano, E. G. Hutchinson, J. M. Thornton, Protein Sci. 1999, 8, 2072-2084. [10e] S. K. Buchanan, Curr. Opin. Struct. Biol. 1999, 9, 445-461. [10f] D. R. Flower, Biochem. J 1996, 318, 1-14. [10g] M. H. Hecht, Proc. Natl. Acad. Sci. USA 1994, 91, 8729-8730.
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24. Innovative scaffolds other than rigid rods in β-sheet architecture: [12a] H. Zeng, X. Yang, R. A. Flowers II, B. Gong, J. Am. Chem. Soc. 2002, 124, 2903 -2910. [12b] Y. Hamuro, A. D. Hamilton, Bioorg. Med. Chem. 2001, 9, 2355-2363. [12c] R. Kaul, A. R. Angeles, M. Jäger, E. T. Powers, J. W. Kelly, J. Am. Chem. Soc. 2001, 123, 5206-5212. [12d] J. S. Nowick, Acc. Chem. Res. 1999, 32, 287-296, and references therein. [12e] T. Sazaki and M. Lieberman, Protein mimetics, in: Comprehensive Supramolecular Chemistry, Vol. 4, (Ed.: Y. Murakami, Elsevier, Oxford, 1996, 193-243.
25. Innovative scaffolds other than rigid rods in β-sheet architecture: [12a] H. Zeng, X. Yang, R. A. Flowers II, B. Gong, J. Am. Chem. Soc. 2002, 124, 2903 -2910. [12b] Y. Hamuro, A. D. Hamilton, Bioorg. Med. Chem. 2001, 9, 2355-2363. [12c] R. Kaul, A. R. Angeles, M. Jäger, E. T. Powers, J. W. Kelly, J. Am. Chem. Soc. 2001, 123, 5206-5212. [12d] J. S. Nowick, Acc. Chem. Res. 1999, 32, 287-296, and references therein. [12e] T. Sazaki and M. Lieberman, Protein mimetics, in: Comprehensive Supramolecular Chemistry, Vol. 4, (Ed.: Y. Murakami, Elsevier, Oxford, 1996, 193-243.
26. Innovative scaffolds other than rigid rods in β-sheet architecture: [12a] H. Zeng, X. Yang, R. A. Flowers II, B. Gong, J. Am. Chem. Soc. 2002, 124, 2903 -2910. [12b] Y. Hamuro, A. D. Hamilton, Bioorg. Med. Chem. 2001, 9, 2355-2363. [12c] R. Kaul, A. R. Angeles, M. Jäger, E. T. Powers, J. W. Kelly, J. Am. Chem. Soc. 2001, 123, 5206-5212. [12d] J. S. Nowick, Acc. Chem. Res. 1999, 32, 287-296, and references therein. [12e] T. Sazaki and M. Lieberman, Protein mimetics, in: Comprehensive Supramolecular Chemistry, Vol. 4, (Ed.: Y. Murakami, Elsevier, Oxford, 1996, 193-243.
27. Innovative scaffolds other than rigid rods in β-sheet architecture: [12a] H. Zeng, X. Yang, R. A. Flowers II, B. Gong, J. Am. Chem. Soc. 2002, 124, 2903 -2910. [12b] Y. Hamuro, A. D. Hamilton, Bioorg. Med. Chem. 2001, 9, 2355-2363. [12c] R. Kaul, A. R. Angeles, M. Jäger, E. T. Powers, J. W. Kelly, J. Am. Chem. Soc. 2001, 123, 5206-5212. [12d] J. S. Nowick, Acc. Chem. Res. 1999, 32, 287-296, and references therein. [12e] T. Sazaki and M. Lieberman, Protein mimetics, in: Comprehensive Supramolecular Chemistry, Vol. 4, (Ed.: Y. Murakami, Elsevier, Oxford, 1996, 193-243.
28. Innovative scaffolds other than rigid rods in β-sheet architecture: [12a] H. Zeng, X. Yang, R. A. Flowers II, B. Gong, J. Am. Chem. Soc. 2002, 124, 2903 -2910. [12b] Y. Hamuro, A. D. Hamilton, Bioorg. Med. Chem. 2001, 9, 2355-2363. [12c] R. Kaul, A. R. Angeles, M. Jäger, E. T. Powers, J. W. Kelly, J. Am. Chem. Soc. 2001, 123, 5206-5212. [12d] J. S. Nowick, Acc. Chem. Res. 1999, 32, 287-296, and references therein. [12e] T. Sazaki and M. Lieberman, Protein mimetics, in: Comprehensive Supramolecular Chemistry, Vol. 4, (Ed.: Y. Murakami, Elsevier, Oxford, 1996, 193-243.
29. p-Octiphenyl β-barrels with internal aspartates: G. Das, S. Matile, Proc. Natl. Acad. Sci. USA 2002, 99, 5183-5188.
30. p-Octiphenyl β-barrels with internal lysines: [14a] N. Sakai, S. Matile, J. Am. Chem. Soc. 2002, 124, 1184-1185. [14b] B. Baumeister, N. Sakai, S. Matile, Angew. Chem. 2000, 112, 2031-2034; Angew. Chem. Int. Ed. 2000, 39, 1955-1958. [14c] N. Sakai, B. Baumeister, S. Matile, ChemBioChem. 2000, 1, 123-125.
31. p-Octiphenyl β-barrels with internal lysines: [14a] N. Sakai, S. Matile, J. Am. Chem. Soc. 2002, 124, 1184-1185. [14b] B. Baumeister, N. Sakai, S. Matile, Angew. Chem. 2000, 112, 2031-2034; Angew. Chem. Int. Ed. 2000, 39, 1955-1958. [14c] N. Sakai, B. Baumeister, S. Matile, ChemBioChem. 2000, 1, 123-125.
32. p-Octiphenyl β-barrels with internal lysines: [14a] N. Sakai, S. Matile, J. Am. Chem. Soc. 2002, 124, 1184-1185. [14b] B. Baumeister, N. Sakai, S. Matile, Angew. Chem. 2000, 112, 2031-2034; Angew. Chem. Int. Ed. 2000, 39, 1955-1958. [14c] N. Sakai, B. Baumeister, S. Matile, ChemBioChem. 2000, 1, 123-125.
33. p-Octiphenyl β-barrels with internal lysines: [14a] N. Sakai, S. Matile, J. Am. Chem. Soc. 2002, 124, 1184-1185. [14b] B. Baumeister, N. Sakai, S. Matile, Angew. Chem. 2000, 112, 2031-2034; Angew. Chem. Int. Ed. 2000, 39, 1955-1958. [14c] N. Sakai, B. Baumeister, S. Matile, ChemBioChem. 2000, 1, 123-125.
34. p-Oligophenyl β-barrels with internal leucines: [15a] G. Das, S. Matile, Chirality 2001, 13, 170-176. B. Baumeister, S. Matile, Chem. Eur. J. 2000, 6, 1739-1749.
35. p-Oligophenyl β-barrels with internal leucines: [15a] G. Das, S. Matile, Chirality 2001, 13, 170-176. B. Baumeister, S. Matile, Chem. Eur. J. 2000, 6, 1739-1749.
36. G. Das, L. Ouali, M. Adrian, B. Baumeister, K. J. Wilkinson, S. Matile, Angew. Chem. 2001, 113, 4793-4797; Angew. Chem. Int. Ed. 2001, 40, 4657-4661.
37. G. Das, L. Ouali, M. Adrian, B. Baumeister, K. J. Wilkinson, S. Matile, Angew. Chem. 2001, 113, 4793-4797; Angew. Chem. Int. Ed. 2001, 40, 4657-4661.
38. B. Baumeister, A. Som, G. Das, N. Sakai, F. Vilbois, D. Gerard, S. P. Shahi, S. Matile, Helv. Chim. Acta in press.
39. B. Baumeister, S. Matile, Macromolecules 2002, 35, 1549-1555.
40. Elaborating on the "intrinsic hydrophilic character of organic compounds", Hine and Mookerjee pointed out that the solubility of, for example, 2-methylpropane in water is 850 μM: [19a] J. Hine, P. K. Mookerjee, J. Org. Chem. 1975, 40, 292-298. Poly(HL) is insoluble in water: [19b] B. Barbier, A. Brack, J. Am. Chem. Soc. 1992, 114, 3511-3515.
41. Elaborating on the "intrinsic hydrophilic character of organic compounds", Hine and Mookerjee pointed out that the solubility of, for example, 2-methylpropane in water is 850 μM: [19a] J. Hine, P. K. Mookerjee, J. Org. Chem. 1975, 40, 292-298. Poly(HL) is insoluble in water: [19b] B. Barbier, A. Brack, J. Am. Chem. Soc. 1992, 114, 3511-3515.
42. A. Som, N. Sakai, S. Matile, unpublished results.
43. Please note that an acyl-imidazole intermediate is highly reactive at pH 5.5: W. P. Jencks, J. Carriuolo, J. Biol. Chem. 1959, 234, 1272-1285.
44. [4] as well as preliminary results indicating that replacement of every second histidine in barrel 1 by an arginine residue does not significantly influence catalytic activity.
45. N. Sakai, D. Gerard, S. Matile, J. Am. Chem. Soc. 2001, 123, 2517-2524.
46. L. A. Weiss, N. Sakai, B. Ghebremariam, C. Ni, S. Matile, J. Am. Chem. Soc. 1997, 119, 12,142-12,149.