Transition metal catalyzed methods for site-selective protein modification

Current Opinion in Chemical Biology

Volumn 10, Issue 3, 2006, Pages 253-262

  Antos, John M ^a   Francis, Matthew B ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINE; AMINO ACID; CYSTEINE; FUNCTIONAL GROUP; IRON SUPEROXIDE DISMUTASE; LYSINE; PALLADIUM; SODIUM PEROXIDE; TRANSITION ELEMENT; TRYPTOPHAN; TYROSINE;

AMINATION; CATALYSIS; CHEMICAL REACTION; ESCHERICHIA COLI; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR BIOLOGY; NONHUMAN; OXIDATION; PH; PROTEIN CROSS LINKING; PROTEIN MODIFICATION; REVIEW; SACCHAROMYCES CEREVISIAE; STOP CODON; SYNTHESIS;

AMINO ACIDS; CATALYSIS; METALS; PROTEINS;

EID: 33744544685     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.04.009     Document Type: Review

References (50)

1. Hermanson G.T. Bioconjugate Techniques. 1st Edn (1996), Academic Press
2. Muir T.W. Semisynthesis of proteins by expressed protein ligation. Annu Rev Biochem 72 (2003) 249-289
3. Joshi N.S., Whitaker L.R., and Francis M.B. A three-component mannich-type reaction for selective tyrosine bioconjugation. J Am Chem Soc 126 (2004) 15942-15943
4. Gilmore JM, Scheck RA, Esser-Kahn AP, Joshi NS, Francis MB: N-terminal protein modification through a biomimetic transamination reaction. Angew Chem Int Ed Engl 2006, in press.
5. Chen I., Howarth M., Lin W., and Ting A.Y. Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nat Methods 2 (2005) 99-104
6. Fancy D.A. Elucidation of protein-protein interactions using chemical cross-linking or label transfer techniques. Curr Opin Chem Biol 4 (2000) 28-33
7. Kodadek T., Duroux-Richard I., and Bonnafous J.C. Techniques: oxidative cross-linking as an emergent tool for the analysis of receptor-mediated signalling events. Trends Pharmacol Sci 26 (2005) 210-217. Kodadek et al. review the methods and mechanism of oxidative cross-linking. The authors provide a comprehensive list of protein-protein interactions that have been studied using oxidative cross-linking, and include a detailed discussion of efforts to apply this chemistry to the study of complex multiprotein systems.
8. Brown K.C., Yu Z.H., Burlingame A.L., and Craik C.S. Determining protein-protein interactions by oxidative cross-linking of a glycine-glycine-histidine fusion protein. Biochemistry 37 (1998) 4397-4406
9. Fancy D.A., and Kodadek T. A critical role for tyrosine residues in His(6)Ni-mediated protein cross-linking. Biochem Biophys Res Commun 247 (1998) 420-426
10. Gill G., RichterRusli A.A., Ghosh M., Burrows C.J., and Rokita S.E. Nickel-dependent oxidative cross-linking of a protein. Chem Res Toxicol 10 (1997) 302-309
11. Kim K., Fancy D.A., Carney D., and Kodadek T. Photoinduced protein cross-linking mediated by palladium porphyrins. J Am Chem Soc 121 (1999) 11896-11897
12. Campbell L.A., Kodadek T., and Brown K.C. Protein cross-linking mediated by metalloporphyrins. Bioorg Med Chem 6 (1998) 1301-1307
13. Brown K.C., Yang S.H., and Kodadek T. Highly specific oxidative cross-linking of proteins mediated by a nickel-peptide complex. Biochemistry 34 (1995) 4733-4739
14. Meunier S., Strable E., and Finn M.G. Crosslinking of and coupling to viral capsid proteins by tyrosine oxidation. Chem Biol 11 (2004) 319-326
15. Person M.D., Brown K.C., Mahrus S., Craik C.S., and Burlingame A.L. Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer. Protein Sci 10 (2001) 1549-1562
16. Fancy D.A., Melcher K., Johnston S.A., and Kodadek T. New chemistry for the study of multiprotein complexes: the six-histidine tag as a receptor for a protein crosslinking reagent. Chem Biol 3 (1996) 551-559
17. Fancy D.A., and Kodadek T. Site-directed oxidative protein crosslinking. Tetrahedron 53 (1997) 11953-11960
18. Amini F., Kodadek T., and Brown K.C. Protein affinity labeling mediated by genetically encoded peptide tags. Angew Chem Int Ed Engl 41 (2002) 356-359
19. Stemmler A.J., and Burrows C.J. The Sal-XH motif for metal-mediated oxidative DNA-peptide cross-linking. J Am Chem Soc 121 (1999) 6956-6957
20. Fancy D.A., and Kodadek T. Chemistry for the analysis of protein-protein interactions: rapid and efficient cross-linking triggered by long wavelength light. Proc Natl Acad Sci USA 97 (2000) 1317
21. Denison C., and Kodadek T. Toward a general chemical method for rapidly mapping multi-protein complexes. J Proteome Res 3 (2004) 417-425
22. Duroux-Richard I., Vassault P., Subra G., Guichou J.F., Richard E., Mouillac B., Barberis C., Marie J., and Bonnafous J.C. Crosslinking photosensitized by a ruthenium chelate as a tool for labeling and topographical studies of G-protein-coupled receptors. Chem Biol 12 (2005) 15-24
23. van Dijk J., Lafont C., Knetsch M.L.W., Derancourt J., Manstein D.J., Long E.C., and Chaussepied P. Conformational changes in actin-myosin isoforms probed by Ni(II)-Gly-Gly-His reactivity. J Muscle Res Cell Motil 25 (2004) 527-537
24. Stayner R.S., Min D.J., Kiser P.F., and Stewart R.J. Site-specific cross-linking of proteins through tyrosine hexahistidine tags. Bioconjug Chem 16 (2005) 1617-1623
25. Antos J.M., and Francis M.B. Selective tryptophan modification with rhodium carbenoids in aqueous solution. J Am Chem Soc 126 (2004) 10256-10257. The authors describe the use of in situ generated rhodium carbenoids to selectively modify tryptophan side chains in aqueous solution. This is one of the first examples of using transition metal catalysis to modify a natural amino acid side chain in a full protein.
26. Tilley S.D., and Francis M.B. Tyrosine-selective protein alkylation using pi-allylpalladium complexes. J Am Chem Soc 128 (2006) 1080-1081. Tilley and Francis describe the use of pi-allyl palladium complexes for the selective modification of tyrosine side chains in aqueous solution. The authors exploit this reaction to synthesize an artificial lipoprotein that was subsequently incorporated into lipid vesicles.
27. Trost B.M., and Toste F.D. Asymmetric O- and C-alkylation of phenols. J Am Chem Soc 120 (1998) 815-816
28. McFarland J.M., and Francis M.B. Reductive alkylation of proteins using iridium catalyzed transfer hydrogenation. J Am Chem Soc 127 (2005) 13490-13491
29. Ogo S., Uehara K., Abura T., and Fukuzumi S. pH-dependent chemoselective synthesis of alpha-amino acids. Reductive amination of alpha-keto acids with ammonia catalyzed by acid-stable iridium hydride complexes in water. J Am Chem Soc 126 (2004) 3020-3021
30. Wang L., and Schultz P.G. Expanding the genetic code. Angew Chem Int Ed Engl 44 (2004) 34-66. Wang and Schultz review methods for expanding the functional group repertoire of proteins. The authors discuss chemical strategies as well as in vitro and in vivo methods for unnatural amino acid incorporation.
31. Link A.J., Mock M.L., and Tirrell D.A. Non-canonical amino acids in protein engineering. Curr Opin Biotechnol 14 (2003) 603-609. The authors review strategies for the incorporation of unnatural amino acids. Residue-specific and site-specific methods are discussed.
32. Prescher J.A., Dube D.H., and Bertozzi C.R. Chemical remodelling of cell surfaces in living animals. Nature 430 (2004) 873-877
33. Dibowski H., and Schmidtchen F.P. Bioconjugation of peptides by palladium-catalyzed C-C cross-coupling in water. Angew Chem Int Ed 37 (1998) 476-478
34. Bong D.T., and Ghadiri M.R. Chemoselective Pd(0)-catalyzed peptide coupling in water. Org Lett 3 (2001) 2509-2511
35. Ojida A., Tsutsumi H., Kasagi N., and Hamachi I. Suzuki coupling for protein modification. Tetrahedron Lett 46 (2005) 3301-3305
36. Kodama K., Fukuzawa S., Nakayama H., Kigawa T., Sakamoto K., Yabuki T., Matsuda N., Shirouzu M., Takio K., Tachibana K., et al. Regioselective carbon-carbon bond formation in proteins with palladium catalysis; new protein chemistry by organometallic chemistry. ChemBioChem 7 (2006) 134-139
37. Kolb H.C., Finn M.G., and Sharpless K.B. Click chemistry: diverse chemical function from a few good reactions. Angew Chem Int Ed Engl 40 (2001) 2004-2021
38. Lewis W.G., Magallon F.G., Fokin V.V., and Finn M.G. Discovery and characterization of catalysts for azide-alkyne cycloaddition by fluorescence quenching. J Am Chem Soc 126 (2004) 9152-9153
39. Wang Q., Chan T.R., Hilgraf R., Fokin V.V., Sharpless K.B., and Finn M.G. Bioconjugation by copper(I)-catalyzed azide-alkyne 3 + 2 cycloaddition. J Am Chem Soc 125 (2003) 3192-3193. Wang et al. describe the use of the copper(I)-catalyzed (3 + 2) cycloaddition between azides and alkynes to label the CPMV viral capsid. This is the first use of the (3 + 2) cycloaddition for protein modification.
40. Sen Gupta S., Kuzelka J., Singh P., Lewis W.G., Manchester M., and Finn M.G. Accelerated bioorthogonal conjugation: a practical method for the ligation of diverse functional molecules to a polyvalent virus scaffold. Bioconjug Chem 16 (2005) 1572-1579
41. Sen Gupta S., Raja K.S., Kaltgrad E., Strable E., and Finn M.G. Virus-glycopolymer conjugates by copper(I) catalysis of atom transfer radical polymerization and azide-alkyne cycloaddition. Chem Commun (Camb) (2005) 4315-4317
42. Dirks A.J., van Berkel S.S., Hatzakis N.S., Opsteen J.A., van Delft F.L., Cornelissen J.J., Rowan A.E., van Hest J.C., Rutjes F.P., and Nolte R.J. Preparation of biohybrid amphiphiles via the copper catalysed huisgen 3 + 2 dipolar cycloaddition reaction. Chem Commun (Camb) (2005) 4172-4174
43. Speers A.E., Adam G.C., and Cravatt B.F. Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition. J Am Chem Soc 125 (2003) 4686-4687
44. Ballell L., Alink K.J., Slijper M., Versluis C., Liskamp R.M.J., and Pieters R.J. A new chemical probe for proteomics of carbohydrate-binding proteins. ChemBioChem 6 (2005) 291-295
45. Link A.J., and Tirrell D.A. Cell surface labeling of escherichia coli via copper(I)-catalyzed 3 + 2 cycloaddition. J Am Chem Soc 125 (2003) 11164-11165. The authors generate azide-bearing cell surface proteins using E. coli methionine auxotrophs. The copper(I)-catalyzed (3 + 2) cycloaddition was then used to label the azide containing proteins expressed on the surface of the E. coli cells.
46. Beatty K.E., Xie F., Wang Q., and Tirrell D.A. Selective dye-labeling of newly synthesized proteins in bacterial cells. J Am Chem Soc 127 (2005) 14150-14151
47. Sun X.L., Stabler C.L., Cazalis C.S., and Chaikof E.L. Carbohydrate and protein immobilization onto solid surfaces by sequential Diels-Alder and azide-alkyne cycloadditions. Bioconjug Chem 17 (2006) 52-57
48. Deiters A., Cropp T.A., Summerer D., Mukherji M., and Schultz P.G. Site-specific PEGylation of proteins containing unnatural amino acids. Bioorg Med Chem Lett 14 (2004) 5743-5745
49. Deiters A., Cropp T.A., Mukherji M., Chin J.W., Anderson J.C., and Schultz P.G. Adding amino acids with novel reactivity to the genetic code of saccharomyces cerevisiae. J Am Chem Soc 125 (2003) 11782-11783. Deiters et al. employ an orthogonal tRNA/tRNA-synthetase pair from E. coli for the site-specific incorporation of both azide- and alkyne-containing amino acids into superoxide dismutase-1 (SOD) expressed in Saccharomyces cerevisiae. The unnatural amino acids were then selectively modified using the copper(I)-catalyzed (3 + 2) cycloaddition.
50. Deiters A., and Schultz P.G. In vivo incorporation of an alkyne into proteins in Escherichia coli. Bioorg Med Chem Lett 15 (2005) 1521-1524