Evaluation of alkyne-modified isoprenoids as chemical reporters of protein prenylation

Chemical Biology and Drug Design

Volumn 76, Issue 6, 2010, Pages 460-471

  DeGraw, Amanda J ^a   Palsuledesai, Charuta ^a   Ochocki, Joshua D ^a   Dozier, Jonathan K ^a   Lenevich, Stepan ^a   Rashidian, Mohammad ^a   Distefano, Mark D ^a  

^a University of Minnesota   (United States)

Author keywords

Chemical proteomics; Click reaction; Farnesyl diphosphate; Prenylome; Prenyltransferase; Protein prenylation; Protein profiling

Indexed keywords

ALKYNE; AZIDE; GERANYLGERANYLTRANSFERASE INHIBITOR; ISOPRENOID; MEVINOLIN; PROTEIN FARNESYLTRANSFERASE; PROTEIN FARNESYLTRANSFERASE INHIBITOR; TRANSFERASE INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CELL CULTURE; CHEMICAL LABELING; CHEMICAL REACTION; CLICK REACTION; CONTROLLED STUDY; DENSITY FUNCTIONAL THEORY; DERIVATIZATION; ENZYME SPECIFICITY; FEMALE; HUMAN; HUMAN CELL; MAMMAL CELL; MASS SPECTROMETRY; MOLECULAR DOCKING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PRENYLATION; PROTEOMICS; TWO DIMENSIONAL ELECTROPHORESIS;

ALKYNES; ANIMALS; AZIDES; BIOLOGICAL MARKERS; CATALYTIC DOMAIN; CELL LINE; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HELA CELLS; HUMANS; PROTEIN PRENYLATION; PROTEOMICS; QUANTUM THEORY; SUBSTRATE SPECIFICITY; TERPENES;

MAMMALIA;

EID: 78349284828     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2010.01037.x     Document Type: Article

References (49)

1. Zhang F.L., Casey P.J. (1996) Protein prenylation: molecular mechanisms and functional consequences. Annu Rev Biochem;65:241-269.
2. Sebti S.M., Hamilton A.D. (2000) Inhibition of Rho GTPases using protein geranylgeranyltransferase I inhibitors. Methods Enzymol;325:381-388.
3. Sebti S.M., Hamilton A.D. (2000) Farnesyltransferase and geranylgeranyltransferase I inhibitors and cancer therapy: lessons from mechanism and bench-to-bedside translational studies. Oncogene;19:6584-6593.
4. Crul M., De Klerk G.J., Beijnen J.H., Schellens J.H. (2001) Ras biochemistry and farnesyl transferase inhibitors: a literature survey. Anticancer Drugs;12:163-184.
5. End D.W.M., Mevellec L., Angibaud P. (2007) Farnesyl protein transferase inhibitors: medicinal chemistry, molecular mechanisms, and progress in the clinic. Top Med Chem;1:133-168.
6. Prendergast G.C. (2001) Actin' up: RhoB in cancer and apoptosis. Nat Rev Cancer;1:162-168.
7. Sebti S.M., Der C.J. (2003) Opinion: searching for the elusive targets of farnesyltransferase inhibitors. Nat Rev Cancer;3:945-951.
8. Sebti S.M. (2005) Protein farnesylation: implications for normal physiology, malignant transformation, and cancer therapy. Cancer Cell;7:297-300.
9. Maurer-Stroh S., Koranda M., Benetka W., Schneider G., Sirota F.L., Eisenhaber F. (2007) Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput Biol;3:e66.
10. Rix U., Superti-Furga G. (2009) Target profiling of small molecules by chemical proteomics. Nat Chem Biol;5:616-624.
11. Heal W.P., Wickramasinghe S.R., Tate E.W. (2008) Activity based chemical proteomics: profiling proteases as drug targets. Curr Drug Discovery Technol;5:200-212.
12. Sletten E.M., Bertozzi C.R. (2009) Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Edit;48:6974-6998.
13. Bertozzi C.R., Kiessling L.L. (2001) Chemical glycobiology. Science;291:2357-2364.
14. Gama C.I., Hsieh-Wilson L.C. (2005) Chemical approaches to deciphering the glycosaminoglycan code. Curr Opin Chem Biol;9:609-619.
15. Laughlin S.T., Bertozzi C.R. (2007) Metabolic labeling of glycans with azido sugars and subsequent glycan-profiling and visualization via Staudinger ligation. Nat Protoc;2:2930-2944.
16. Luchansky S.J., Argade S., Hayes B.K., Bertozzi C.R. (2004) Metabolic functionalization of recombinant glycoproteins. Biochemistry;43:12358-12366.
17. Sprung R., Nandi A., Chen Y., Kim S.C., Barma D., Falck J.R., Zhao Y. (2005) Tagging-via-substrate strategy for probing O-GlcNAc modified proteins. J Proteome Res;4:950-957.
18. Warthaka M., Karwowska-Desaulniers P., Pflum M.K. (2006) Phosphopeptide modification and enrichment by oxidation-reduction condensation. ACS Chem Biol;1:697-701.
19. Zhou H., Watts J.D., Aebersold R. (2001) A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol;19:375-378.
20. Charron G., Zhang M.M., Yount J.S., Wilson J., Raghavan A.S., Shamir E., Hang H.C. (2009) Robust fluorescent detection of protein fatty-acylation with chemical reporters. J Am Chem Soc;131:4967-4975.
21. Hang H.C., Geutjes E.J., Grotenbreg G., Pollington A.M., Bijlmakers M.J., Ploegh H.L. (2007) Chemical probes for the rapid detection of fatty-acylated proteins in Mammalian cells. J Am Chem Soc;129:2744-2745.
22. Heal W.P., Wickramasinghe S.R., Bowyer P.W., Holder A.A., Smith D.F., Leatherbarrow R.J., Tate E.W. (2008) Site-specific N-terminal labelling of proteins in vitro and in vivo using N-myristoyl transferase and bioorthogonal ligation chemistry. Chem Commun;4:480-482.
23. Kostiuk M.A., Corvi M.M., Keller B.O., Plummer G., Prescher J.A., Hangauer M.J., Bertozzi C.R., Rajaiah G., Falck J.R., Berthiaume L.G. (2008) Identification of palmitoylated mitochondrial proteins using a bio-orthogonal azido-palmitate analogue. FASEB J;22:721-732.
24. Martin B.R., Cravatt B.F. (2009) Large-scale profiling of protein palmitoylation in mammalian cells. Nat Methods;6:135-138.
25. Roth A.F., Wan J., Green W.N., Yates J.R., Davis N.G. (2006) Proteomic identification of palmitoylated proteins. Methods;40:135-142.
26. Chan L.N., Hart C., Guo L., Nyberg T., Davies B.S., Fong L.G., Young S.G., Agnew B.J., Tamanoi F. (2009) A novel approach to tag and identify geranylgeranylated proteins. Electrophoresis;30:3598-3606.
27. Kho Y., Kim S.C., Jiang C., Barma D., Kwon S.W., Cheng J., Jaunbergs J., Weinbaum C., Tamanoi F., Falck J., Zhao Y. (2004) A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. Proc Natl Acad Sci U S A;101:12479-12484.
28. Nguyen U.T., Guo Z., Delon C., Wu Y., Deraeve C., Franzel B., Bon R.S., Blankenfeldt W., Goody R.S., Waldmann H., Wolters D., Alexandrov K. (2009) Analysis of the eukaryotic prenylome by isoprenoid affinity tagging. Nat Chem Biol;5:227-235.
29. Berry A.F.H., Heal W.P., Tarafder A.K., Tolmachova T., Baron R.A., Seabra M.C., Tate E.W. (2010) Rapid multilabel detection of geranylgeranylated proteins by using bioorthogonal ligation chemistry. ChemBioChem;11:771-773.
30. Onono F.O., Morgan M.A., Spielmann H.P., Andres D.A., Subramanian T., Ganser A., Reuter C.W.M. (2010) A tagging-via-substrate approach to detect the farnesylated proteome using two-dimensional electrophoresis coupled with Western blotting. Mol Cell Proteomics;9:742-751.
31. Speers A.E., Cravatt B.F. (2004) Profiling enzyme activities in vivo using click chemistry methods. Chem Biol;11:535-546.
32. Duckworth B.P., Zhang Z., Hosokawa A., Distefano M.D. (2007) Selective labeling of proteins using protein farnesyltransferase. ChemBioChem;8:98-105.
33. Hosokawa A., Wollack J.W., Zhang Z., Chen L., Barany G., Distefano M.D. (2007) Evaluation of an alkyne-containing analogue of farnesyl diphosphate as a dual substrate for protein-prenyltransferases. Int J Peptide Res;13:345-354.
34. Gauchet C., Labadie G.R., Poulter C.D. (2006) Regio- and chemoselective covalent immobilization of proteins through unnatural amino acids. J Am Chem Soc;128:9274-9275.
35. Labadie G.R., Viswanathan R., Poulter C.D. (2007) Farnesyl diphosphate analogues with w-bioorthogonal azide and alkyne functional groups for protein farnesyl transferase-catalyzed ligation reactions. J Org Chem;72:9291-9297.
36. Duckworth B.P., Xu J., Taton T.A., Guo A., Distefano M.D. (2006) Site-specific, covalent attachment of proteins to a solid surface. Bioconj Chem;17:967-974.
37. Andersen J.D., Boylan K.L.M., Xue F.S., Anderson L.B., Witthuhn B.A., Markowski T.W., Higgins L., Skubitz A.P.N. (2010) Identification of candidate biomarkers in ovarian cancer serum by depletion of highly abundant proteins and differential in-gel electrophoresis. Electrophoresis;31:599-610.
38. Shevchenko A., Wilm M., Vorm O., Mann M. (1996) Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal Chem;68:850-858.
39. Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem;74:5383-5392.
40. Nesvizhskii A.I., Keller A., Kolker E., Aebersold R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem;75:4646-4658.
41. Cole S.L., Vassar R. (2006) Isoprenoids and Alzheimer's disease: a complex relationship. Neurobiol Dis;22:209-222.
42. Eckert G.P., Hooff G.P., Strandjord D.M., Igbavboa U., Volmer D.A., Muller W.E., Wood W.G. (2009) Regulation of the brain isoprenoids farnesyl- and geranylgeranylpyrophosphate is altered in male Alzheimer patients. Neurobiol Dis;35:251-257.
43. Fiacco T.A., Agulhon C., McCarthy K.D. (2009) Sorting out astrocyte physiology from pharmacology. Annu Rev Pharmacol Toxicol;49:151-174.
44. Hougland J.L., Hicks K.A., Hartman H.L., Kelly R.A., Watt T.J., Fierke C.A. (2009) Identification of novel peptide substrates for protein farnesyltransferase reveals two substrate classes with distinct sequence selectivities. J Mol Biol;395:176-190.
45. Reigard S.A., Zahn T.J., Haworth K.B., Hicks K.A., Fierke C.A., Gibbs R.A. (2005) Interplay of isoprenoid and peptide substrate specificity in protein farnesyltransferase. Biochemistry;44:11214-11223.
46. Strickland C.L., Windsor W.T., Syto R., Wang L., Bond R., Wu Z., Schwartz J., Le H.V., Beese L.S., Weber P.C. (1998) Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue. Biochemistry;37:16601-16611.
47. Hovlid M.L., Edelstein R.L., Henry O., Ochocki J., Talbot T., Lopez-Gallego F., Schmidt-Dannert C., Distefano M.D. (2010) Synthesis and applications of DATFP-containing photoactive analogues of farnesyl diphosphate containing modified linkages for enhanced stability. Chem Biol Drug Des;75:51-67.
48. Hannoush R.N., Arenas-Ramirez N., (2009) Imaging the Lipidome: w-Alkynyl Fatty Acids for Detection and Cellular Visualization of Lipid-Modified Proteins. ACS Chem Biol;4:581-7.
49. Hannoush R.N., Sun J.L., (2010) The chemical toolbox for monitoring protein fatty acylation and prenylation. Nat Chem Biol;6:498-506.