Photocleavage-based affinity purification and printing of cell-free expressed proteins: Application to proteome microarrays

Analytical Biochemistry

Volumn 383, Issue 1, 2008, Pages 103-115

  Lim, Mark ^a   Rothschild, Kenneth J ^a,b  

^a AMBERGEN INC   (United States)

^b Photonics Center   (United States)

Author keywords

Cell free protein expression; Microarray printing; Misaminoacylated tRNA; Photocleavable biotin; Photocleavage; Protein interaction; Protein isolation; Protein microarrays; Proteome microarrays; Proteomics; tRNA mediated protein engineering

Indexed keywords

BIOCHIPS; COENZYMES; MEDICAL APPLICATIONS; PROTEOMICS; PURIFICATION; SEMICONDUCTOR QUANTUM DOTS;

CELL-FREE PROTEIN EXPRESSION; MICRO-ARRAY PRINTING; MISAMINOACYLATED TRNA; PHOTOCLEAVABLE BIOTIN; PHOTOCLEAVAGES; PROTEIN ENGINEERING; PROTEIN INTERACTION; PROTEIN ISOLATION; PROTEIN MICROARRAY;

CELL ENGINEERING;

BIOTIN; GLUTATHIONE TRANSFERASE; QUANTUM DOT;

ANALYTIC METHOD; ARTICLE; ENZYME ACTIVITY; MICROARRAY ANALYSIS; PHOTOCLEAVAGE; PRIORITY JOURNAL; PROTEIN ISOLATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEOMICS;

ORYCTOLAGUS CUNICULUS;

ANIMALS; CELL-FREE SYSTEM; CHROMATOGRAPHY, AFFINITY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MODELS, BIOLOGICAL; PROTEIN ARRAY ANALYSIS; PROTEINS; PROTEOMICS; RABBITS;

EID: 53049105500     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.07.038     Document Type: Article

References (53)

1. Zhu H., and Snyder M. Protein arrays and microarrays. Curr. Opin. Chem. Biol. 5 (2001) 40-45
2. Lopez M.F., and Pluskal M.G. Protein micro- and macroarrays: Digitizing the proteome. J. Chromatogr. B 787 (2003) 19-27
3. Melton L. Protein arrays: proteomics in multiplex. Nature 429 (2004) 101-107
4. Ramachandran N., Hainsworth E., Bhullar B., Eisenstein S., Rosen B., Lau A.Y., Walter J.C., and LaBaer J. Self-assembling protein microarrays. Science 305 (2004) 86-90
5. Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Bidlingmaier S., Houfek T., Mitchell T., Miller P., Dean R.A., Gerstein M., and Snyder M. Global analysis of protein activities using proteome chips. Science 293 (2001) 2101-2105
6. MacBeath G., and Schreiber S.L. Printing proteins as microarrays for high-throughput function determination. Science 289 (2000) 1760-1763
7. Zhu H., Klemic J.F., Chang S., Bertone P., Casamayor A., Klemic K.G., Smith D., Gerstein M., Reed M.A., and Snyder M. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26 (2000) 283-289
8. Michaud G.A., Salcius M., Zhou F., Bangham R., Bonin J., Guo H., Snyder M., Predki P.F., and Schweitzer B.I. Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21 (2003) 1509-1512
9. Sheridan C. Protein chip companies turn to biomarkers. Nat. Biotechnol. 23 (2005) 3-4
10. Robinson W.H., Fontoura P., Lee B.J., de Vegvar H.E., Tom J., Pedotti R., DiGennaro C.D., Mitchell D.J., Fong D., Ho P.P., Ruiz P.J., Maverakis E., Stevens D.B., Bernard C.C., Martin R., Kuchroo V.K., van Noort J.M., Genain C.P., Amor S., Olsson T., Utz P.J., Garren H., and Steinman L. Protein microarrays guide tolerizing DNA vaccine treatment of autoimmune encephalomyelitis. Nat. Biotechnol. 21 (2003) 1033-1039
11. Robinson W.H., DiGennaro C., Hueber W., Haab B.B., Kamachi M., Dean E.J., Fournel S., Fong D., Genovese M.C., de Vegvar H.E., Skriner K., Hirschberg D.L., Morris R.I., Muller S., Pruijn G.J., van Venrooij W.J., Smolen J.S., Brown P.O., Steinman L., and Utz P.J. Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat. Med. 8 (2002) 295-301
12. Kawahashi Y., Doi N., Takashima H., Tsuda C., Oishi Y., Oyama R., Yonezawa M., Miyamoto-Sato E., and Yanagawa H. In vitro protein microarrays for detecting protein-protein interactions: application of a new method for fluorescence labeling of proteins. Proteomics 3 (2003) 1236-1243
13. He M., and Taussig M.J. Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). Nucleic Acids Res. 29 (2001) E73
14. Middleton R.B., and Bulleid N.J. Reconstitution of the folding pathway of collagen in a cell-free system: formation of correctly aligned and hydroxylated triple helices. Biochem. J. 296 (1993) 511-517
15. Pensiero M.N., Dveksler G.S., Cardellichio C.B., Jiang G.S., Elia P.E., Dieffenbach C.W., and Holmes K.V. Binding of the coronavirus mouse hepatitis virus A59 to its receptor expressed from a recombinant vaccinia virus depends on posttranslational processing of the receptor glycoprotein. J. Virol. 66 (1992) 4028-4039
16. Vorburger K., Kitten G.T., and Nigg E.A. Modification of nuclear lamin proteins by a mevalonic acid derivative occurs in reticulocyte lysates and requires the cysteine residue of the C-terminal CXXM motif. EMBO J. 8 (1989) 4007-4013
17. Hirose S., Kim S., Miyazaki H., Park Y.S., and Murakami K. In vitro biosynthesis of human renin and identification of plasma inactive renin as an activation intermediate. J. Biol. Chem. 260 (1985) 16400-16405
18. Gibbs P.E., Zouzias D.C., and Freedberg I.M. Differential post-translational modification of human type I keratins synthesized in a rabbit reticulocyte cell-free system. Biochim. Biophys. Acta 824 (1985) 247-255
19. Popov M., Tam L.Y., Li J., and Reithmeier R.A. Mapping the ends of transmembrane segments in a polytopic membrane protein: scanning N-glycosylation mutagenesis of extracytosolic loops in the anion exchanger, band 3. J. Biol. Chem. 272 (1997) 18325-18332
20. Lyford L.K., and Rosenberg R.L. Cell-free expression and functional reconstitution of homo-oligomeric α7 nicotinic acetylcholine receptors into planar lipid bilayers. J. Biol. Chem. 274 (1999) 25675-25681
21. Beckler G.S., Thompson D., and Van Oosbree T. In vitro translation using rabbit reticulocyte lysate. Methods Mol. Biol. 37 (1995) 215-232
22. Noren C.J., Anthony-Cahill S.J., Griffith M.C., and Schultz P.G. A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244 (1989) 182-188
23. Rothschild K.J., and Gite S. TRNA-mediated protein engineering. Curr. Opin. Biotechnol. 10 (1999) 64-70
24. Rothschild K.J., Gite S., Mamaev S., and Olejnik J. Building photonic proteins. In: Horspool W.M., and Lenci F. (Eds). CRC Handbook of Organic Photochemistry and Photobiology, 2nd ed. (2003), CRC Press, Boca Raton, FL 121-131
25. Forster A.C. Engineering translation: a nano-review. Methods 36 (2005) 225-320
26. Anthony-Cahill S.J., Griffith M.C., Noren C.J., Suich D.J., and Schultz P.G. Site-specific mutagenesis with unnatural amino acids. Trends Biochem. Sci. 14 (1990) 400-403
27. Sonar S., Lee C.P., Coleman M., Patel N., Liu X., Marti T., Khorana H.G., Rajbhandary U.L., and Rothschild K. Site-directed isotope labelling and FTIR spectroscopy of bacteriorhodopsin. Nat. Struct. Biol. 1 (1994) 512-517
28. Gite S., Mamaev S., Olejnik J., and Rothschild K. Ultrasensitive fluorescence-based detection of nascent proteins in gels. Anal. Biochem. 279 (2000) 218-225
29. Mamaev S., Olejnik J., Olejnik E.K., and Rothschild K.J. Cell-free N-terminal protein labeling using initiator suppressor tRNA. Anal. Biochem. 326 (2004) 25-32
30. Olejnik J., Gite S., Mamaev S., and Rothschild K.J. N-terminal labeling of proteins using initiator tRNA. Methods 36 (2005) 252-260
31. Krieg U.C., Johnson A.E., and Walter P. Protein translocation across the endoplasmic reticulum membrane: Identification by photocross-linking of a 39-kD integral membrane glycoprotein as part of a putative translocation tunnel. J. Cell Biol. 109 (1989) 2033-2043
32. Gite S., Lim M., Carlson R., Olejnik J., Zehnbauer B., and Rothschild K. A high-throughput nonisotopic protein truncation test. Nat. Biotechnol. 21 (2003) 194-197
33. Hecht S.M., Alford B.L., Kuroda Y., and Kitano S. Chemical aminoacylation of tRNAs. J. Biol. Chem. 253 (1978) 4517-4520
34. Lodder M., Wang B., and Hecht S.M. The N-pentenoyl protecting group for aminoacyl-tRNAs. Methods 36 (2005) 245-251
35. Olejnik J., Sonar S., Krzymanska-Olejnik E., and Rothschild K.J. Photocleavable biotin derivatives: A versatile approach for the isolation of biomolecules. Proc. Natl. Acad. Sci. USA 92 (1995) 7590-7594
36. Pandori M.W., Hobson D.A., Olejnik J., Krzymanska-Olejnik E., Rothschild K.J., Palmer A.A., Phillips T.J., and Sano T. Photochemical control of the infectivity of adenoviral vectors using a novel photocleavable biotinylation reagent. Chem. Biol. 9 (2002) 567-573
37. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 (1970) 680-685
38. Beckler G., Bhatia A., Brisco P., Brondyk W., Butler B., DeMars S., Doers M., and Doyle K. Protein translation in vitro. In: Doyle K. (Ed). Protocols and Applications Guide (Promega) (1996), Promega Corporation, Madison, WI 261-262
39. Sinha P., Poland J., Schnolzer M., and Rabilloud T. A new silver staining apparatus and procedure for matrix-assisted laser desorption/ionization-time of flight analysis of proteins after two-dimensional electrophoresis. Proteomics 1 (2001) 835-840
40. Wilchek M., and Bayer E.A. Introduction to avidin-biotin technology. Methods Enzymol. 184 (1990) 5-13
41. Hale J.E. Irreversible, oriented immobilization of antibodies to cobalt-iminodiacetate resin for use as immunoaffinity media. Anal. Biochem. 231 (1995) 46-49
42. Muszynska G., Andersson L., and Porath J. Selective adsorption of phosphoproteins on gel-immobilized ferric chelate. Biochemistry 25 (1986) 6850-6853
43. Thiele C., and Fahrenholz F. Photocleavable biotinylated ligands for affinity chromatography. Anal. Biochem. 218 (1994) 330-337
44. Ranadive G.N., and Bloomer W.D. Solid phase labeling of monoclonal antibodies with 99mTc using two bifunctional photocleavable reagents. Nuclear Med. Biol. 22 (1995) 607-612
45. Klee C.B., Crouch T.H., and Krinks M.H. Calcineurin: A calcium- and calmodulin-binding protein of the nervous system. Proc. Natl. Acad. Sci. USA 76 (1979) 6270-6273
46. Michael K.L., Taylor L.C., Schultz S.L., and Walt D.R. Randomly ordered addressable high-density optical sensor arrays. Anal. Chem. 70 (1998) 1242-1248
47. Bottger A., Bottger V., Garcia-Echeverria C., Chene P., Hochkeppel H.K., Sampson W., Ang K., Howard S.F., Picksley S.M., and Lane D.P. Molecular characterization of the hdm2-p53 interaction. J. Mol. Biol. 269 (1997) 744-756
48. Han M., Gao X., Su J.Z., and Nie S. Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. Nat. Biotechnol. 19 (2001) 631-635
49. Gunderson K.L., Kruglyak S., Graige M.S., Garcia F., Kermani B.G., Zhao C., Che D., Dickinson T., Wickham E., Bierle J., Doucet D., Milewski M., Yang R., Siegmund C., Haas J., Zhou L., Oliphant A., Fan J.B., Barnard S., and Chee M.S. Decoding randomly ordered DNA arrays. Genome Res. 14 (2004) 870-877
50. Olejnik J., Krzymanska-Olejnik E., and Rothschild K.J. Photocleavable biotin phosphoramidite for 5′-end-labeling, affinity purification, and phosphorylation of synthetic oligonucleotides. Nucleic Acids Res. 24 (1996) 361-366
51. Olejnik J., Krzymanska-Olejnik E., and Rothschild K.J. Photocleavable aminotag phosphoramidites for 5′-termini DNA/RNA labeling. Nucleic Acids Res. 26 (1998) 3572-3576
52. Olejnik J., Ludemann H.C., Krzymanska-Olejnik E., Berkenkamp S., Hillenkamp F., and Rothschild K.J. Photocleavable peptide-DNA conjugates: Synthesis and applications to DNA analysis using MALDI-MS. Nucleic Acids Res. 27 (1999) 4626-4631
53. Nord O., Uhlen M., and Nygren P.A. Microbead display of proteins by cell-free expression of anchored DNA. J. Biotechnol. 106 (2003) 1-13