Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

The chemical toolbox for monitoring protein fatty acylation and prenylation

Nature Chemical Biology volume 6, pages 498–506 (2010)Cite this article

Subjects

Abstract

Lipid modification of cellular proteins plays diverse roles in the regulation of such proteins' trafficking, signaling and behavior. Owing to a lack of robust detection technologies, the mechanisms by which lipids regulate proteins are poorly understood. Recently, various groups have developed innovative chemical probes in conjunction with bio-orthogonal chemistry for the detection of lipid-modified proteins in vitro and in vivo. These new methods enable further understanding of the mechanisms of protein lipidation and its function in physiology and disease. Here we present a comprehensive summary of these detection probes for monitoring fatty acylation and prenylation, and we provide a perspective on their current and future applications.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Protein prenyl and fatty acid modifications.
Figure 2: Reactions of protein prenylation and fatty acylation.
Figure 3: The acyl-biotin exchange method.
Figure 4: Methods for detecting fatty acylation and prenylation of cellular proteins.
Figure 5: Applications of fatty acid and prenyl probes.

Similar content being viewed by others

References

  1. Smotrys, J.E. & Linder, M.E. Palmitoylation of intracellular signaling proteins: regulation and function. Annu. Rev. Biochem. 73, 559–587 (2004).

    Article  CAS  PubMed  Google Scholar 

  2. de Jonge, H.R., Hogema, B. & Tilly, B.C. Protein N-myristoylation: critical role in apoptosis and salt tolerance. Sci. STKE 2000, pe1 (2000).

    Article  CAS  PubMed  Google Scholar 

  3. Resh, M.D. Membrane targeting of lipid modified signal transduction proteins. Subcell. Biochem. 37, 217–232 (2004).

    Article  CAS  PubMed  Google Scholar 

  4. Steinhauer, J. & Treisman, J.E. Lipid-modified morphogens: functions of fats. Curr. Opin. Genet. Dev. 19, 1–7 (2009).

    Article  CAS  Google Scholar 

  5. Rocks, O. et al. An acylation cycle regulates localization and activity of palmitoylated Ras isoforms. Science 307, 1746–1752 (2005).

    Article  CAS  PubMed  Google Scholar 

  6. Hantschel, O. et al. A myristoyl/phosphotyrosine switch regulates c-Abl. Cell 112, 845–857 (2003).

    Article  CAS  PubMed  Google Scholar 

  7. Resh, M.D. Myristylation and palmitylation of Src family members: the fats of the matter. Cell 76, 411–413 (1994).

    Article  CAS  PubMed  Google Scholar 

  8. Benjannet, S. et al. Post-translational processing of beta-secretase (beta-amyloid-converting enzyme) and its ectodomain shedding. The pro- and transmembrane/cytosolic domains affect its cellular activity and amyloid-beta production. J. Biol. Chem. 276, 10879–10887 (2001).

    Article  CAS  PubMed  Google Scholar 

  9. Pepinsky, R.B. et al. Identification of a palmitic acid-modified form of human Sonic hedgehog. J. Biol. Chem. 273, 14037–14045 (1998).

    Article  CAS  PubMed  Google Scholar 

  10. Willert, K. et al. Wnt proteins are lipid-modified and can act as stem cell growth factors. Nature 423, 448–452 (2003).

    Article  CAS  PubMed  Google Scholar 

  11. Resh, M.D. Trafficking and signaling by fatty-acylated and prenylated proteins. Nat. Chem. Biol. 2, 584–590 (2006).

    Article  CAS  PubMed  Google Scholar 

  12. Nadolski, M.J. & Linder, M.E. Protein lipidation. FEBS J. 274, 5202–5210 (2007).

    Article  CAS  PubMed  Google Scholar 

  13. Magee, T. & Seabra, M.C. Fatty acylation and prenylation of proteins: what's hot in fat. Curr. Opin. Cell Biol. 17, 190–196 (2005).

    Article  CAS  PubMed  Google Scholar 

  14. Maurer-Stroh, S. & Eisenhaber, F. Refinement and prediction of protein prenylation motifs. Genome Biol. 6, R55 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Pereira-Leal, J.B., Hume, A.N. & Seabra, M.C. Prenylation of Rab GTPases: molecular mechanisms and involvement in genetic disease. FEBS Lett. 498, 197–200 (2001).

    Article  CAS  PubMed  Google Scholar 

  16. Fivaz, M. & Meyer, T. Reversible intracellular translocation of KRas but not HRas in hippocampal neurons regulated by Ca2+/calmodulin. J. Cell Biol. 170, 429–441 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Bivona, T.G. et al. PKC regulates a farnesyl-electrostatic switch on K-Ras that promotes its association with Bcl-XL on mitochondria and induces apoptosis. Mol. Cell 21, 481–493 (2006).

    Article  CAS  PubMed  Google Scholar 

  18. Seabra, M.C., Mules, E.H. & Hume, A.N. Rab GTPases, intracellular traffic and disease. Trends Mol. Med. 8, 23–30 (2002).

    Article  CAS  PubMed  Google Scholar 

  19. Hoffman, G.R., Nassar, N. & Cerione, R.A. Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI. Cell 100, 345–356 (2000).

    Article  CAS  PubMed  Google Scholar 

  20. An, Y. et al. Geranylgeranyl switching regulates GDI-Rab GTPase recycling. Structure 11, 347–357 (2003).

    Article  CAS  PubMed  Google Scholar 

  21. Towler, D.A., Gordon, J.I., Adams, S.P. & Glaser, L. The biology and enzymology of eukaryotic protein acylation. Annu. Rev. Biochem. 57, 69–99 (1988).

    Article  CAS  PubMed  Google Scholar 

  22. Maurer-Stroh, S., Eisenhaber, B. & Eisenhaber, F. N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J. Mol. Biol. 317, 541–557 (2002).

    Article  CAS  PubMed  Google Scholar 

  23. Maurer-Stroh, S. & Eisenhaber, F. Myristoylation of viral and bacterial proteins. Trends Microbiol. 12, 178–185 (2004).

    Article  CAS  PubMed  Google Scholar 

  24. Lu, J.Y. & Hofmann, S.L. Thematic review series: lipid posttranslational modifications. Lysosomal metabolism of lipid-modified proteins. J. Lipid Res. 47, 1352–1357 (2006).

    Article  CAS  PubMed  Google Scholar 

  25. Sakurai, N. & Utsumi, T. Posttranslational N-myristoylation is required for the anti-apoptotic activity of human tGelsolin, the C-terminal caspase cleavage product of human gelsolin. J. Biol. Chem. 281, 14288–14295 (2006).

    Article  CAS  PubMed  Google Scholar 

  26. Utsumi, T., Sakurai, N., Nakano, K. & Ishisaka, R. C-terminal 15 kDa fragment of cytoskeletal actin is posttranslationally N-myristoylated upon caspase-mediated cleavage and targeted to mitochondria. FEBS Lett. 539, 37–44 (2003).

    Article  CAS  PubMed  Google Scholar 

  27. Vilas, G.L. et al. Posttranslational myristoylation of caspase-activated p21-activated protein kinase 2 (PAK2) potentiates late apoptotic events. Proc. Natl. Acad. Sci. USA 103, 6542–6547 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Martin, D.D. et al. Rapid detection, discovery, and identification of post-translationally myristoylated proteins during apoptosis using a bio-orthogonal azidomyristate analog. FASEB J. 22, 797–806 (2008).

    Article  CAS  PubMed  Google Scholar 

  29. Palmer, D.J., Helms, J.B., Beckers, C.J., Orci, L. & Rothman, J.E. Binding of coatomer to Golgi membranes requires ADP-ribosylation factor. J. Biol. Chem. 268, 12083–12089 (1993).

    CAS  PubMed  Google Scholar 

  30. Wu, Z. et al. Total chemical synthesis of N-myristoylated HIV-1 matrix protein p17: structural and mechanistic implications of p17 myristoylation. Proc. Natl. Acad. Sci. USA 101, 11587–11592 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Provitera, P., El-Maghrabi, R. & Scarlata, S. The effect of HIV-1 Gag myristoylation on membrane binding. Biophys. Chem. 119, 23–32 (2006).

    Article  CAS  PubMed  Google Scholar 

  32. Selvakumar, P. et al. Potential role of N-myristoyltransferase in cancer. Prog. Lipid Res. 46, 1–36 (2007).

    Article  CAS  PubMed  Google Scholar 

  33. Bowyer, P.W. et al. N-myristoyltransferase: a prospective drug target for protozoan parasites. ChemMedChem 3, 402–408 (2008).

    Article  CAS  PubMed  Google Scholar 

  34. Wright, M.H., Heal, W.P., Mann, D.J. & Tate, E.W. Protein myristoylation in health and disease. J. Chem. Biol. (2009).

  35. Zha, J., Weiler, S., Oh, K.J., Wei, M.C. & Korsmeyer, S.J. Posttranslational N-myristoylation of BID as a molecular switch for targeting mitochondria and apoptosis. Science 290, 1761–1765 (2000).

    Article  CAS  PubMed  Google Scholar 

  36. Liang, X., Lu, Y., Neubert, T.A. & Resh, M.D. Mass spectrometric analysis of GAP-43/neuromodulin reveals the presence of a variety of fatty acylated species. J. Biol. Chem. 277, 33032–33040 (2002).

    Article  CAS  PubMed  Google Scholar 

  37. Hallak, H. et al. Covalent binding of arachidonate to G protein alpha subunits of human platelets. J. Biol. Chem. 269, 4713–4716 (1994).

    CAS  PubMed  Google Scholar 

  38. Kordyukova, L.V., Serebryakova, M.V., Baratova, L.A. & Veit, M. Site-specific attachment of palmitate or stearate to cytoplasmic versus transmembrane cysteines is a common feature of viral spike proteins. Virology 398, 49–56 (2010).

    Article  CAS  PubMed  Google Scholar 

  39. Linder, M.E. & Deschenes, R.J. Palmitoylation: policing protein stability and traffic. Nat. Rev. Mol. Cell Biol. 8, 74–84 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Takada, R. et al. Monounsaturated fatty acid modification of Wnt protein: its role in Wnt secretion. Dev. Cell 11, 791–801 (2006).

    Article  CAS  PubMed  Google Scholar 

  41. Greaves, J. & Chamberlain, L.H. Palmitoylation-dependent protein sorting. J. Cell Biol. 176, 249–254 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Simpson, F., Kerr, M.C. & Wicking, C. Trafficking, development and hedgehog. Mech. Dev. 126, 279–288 (2009).

    Article  CAS  PubMed  Google Scholar 

  43. Komekado, H., Yamamoto, H., Chiba, T. & Kikuchi, A. Glycosylation and palmitoylation of Wnt-3a are coupled to produce an active form of Wnt-3a. Genes Cells 12, 521–534 (2007).

    Article  CAS  PubMed  Google Scholar 

  44. Yanai, A. et al. Palmitoylation of huntingtin by HIP14 is essential for its trafficking and function. Nat. Neurosci. 9, 824–831 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Schlesinger, M.J., Magee, A.I. & Schmidt, M.F.G. Fatty acid acylation of proteins in cultured cells. J. Biol. Chem. 255, 10021–10024 (1980).

    CAS  PubMed  Google Scholar 

  46. Peseckis, S.M., Deichaite, I. & Resh, M.D. Iodinated fatty acids as probes for myristate processing and function. Incorporation into pp60v-src. J. Biol. Chem. 268, 5107–5114 (1993).

    CAS  PubMed  Google Scholar 

  47. Giannakouros, T., Armstrong, J. & Magee, A.I. Protein prenylation in Schizosaccharomyces pombe. FEBS Lett. 297, 103–106 (1992).

    Article  CAS  PubMed  Google Scholar 

  48. Goldstein, J.L. & Brown, M.S. Regulation of the mevalonate pathway. Nature 343, 425–430 (1990).

    Article  CAS  PubMed  Google Scholar 

  49. Drisdel, R.C. & Green, W.N. Labeling and quantifying sites of protein palmitoylation. Biotechniques 36, 276–285 (2004).

    Article  CAS  PubMed  Google Scholar 

  50. Wan, J., Roth, A.F., Bailey, A.O. & Davis, N.G. Palmitoylated proteins: purification and identification. Nat. Protoc. 2, 1573–1584 (2007).

    Article  CAS  PubMed  Google Scholar 

  51. Roth, A.F. et al. Global analysis of protein palmitoylation in yeast. Cell 125, 1003–1013 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Kang, R. et al. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature 456, 904–909 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Drisdel, R.C., Alexander, J.K., Sayeed, A. & Green, W.N. Assays of protein palmitoylation. Methods 40, 127–134 (2006).

    Article  CAS  PubMed  Google Scholar 

  54. Roth, A.F., Wan, J., Green, W.N., Yates, J.R. & Davis, N.G. Proteomic identification of palmitoylated proteins. Methods 40, 135–142 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Saxon, E. & Bertozzi, C.R. Cell surface engineering by a modified Staudinger reaction. Science 287, 2007–2010 (2000).

    Article  CAS  PubMed  Google Scholar 

  56. Rostovtsev, V.V., Green, L.G., Fokin, V.V. & Sharpless, K.B. A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew. Chem. Int. Edn Engl. 41, 2596–2599 (2002).

    Article  CAS  Google Scholar 

  57. Tornøe, C.W., Christensen, C. & Meldal, M. Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(i)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67, 3057–3064 (2002).

    Article  CAS  PubMed  Google Scholar 

  58. Wang, Q. et al. Bioconjugation by copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition. J. Am. Chem. Soc. 125, 3192–3193 (2003).

    Article  CAS  PubMed  Google Scholar 

  59. Hannoush, R.N. & Arenas-Ramirez, N. Imaging the lipidome: omega-alkynyl fatty acids for detection and cellular visualization of lipid-modified proteins. ACS Chem. Biol. 4, 581–587 (2009).

    Article  CAS  PubMed  Google Scholar 

  60. Hang, H.C. et al. Chemical probes for the rapid detection of fatty-acylated proteins in mammalian cells. J. Am. Chem. Soc. 129, 2744–2745 (2007).

    Article  CAS  PubMed  Google Scholar 

  61. Kostiuk, M.A. et al. Identification of palmitoylated mitochondrial proteins using a bio-orthogonal azido-palmitate analogue. FASEB J. 22, 721–732 (2008).

    Article  CAS  PubMed  Google Scholar 

  62. Heal, W.P. et al. Site-specific N-terminal labelling of proteins in vitro and in vivo using N-myristoyl transferase and bioorthogonal ligation chemistry. Chem. Commun. (Camb.) 480–482 (2008).

  63. Heal, W.P., Wickramasinghe, S.R., Leatherbarrow, R.J. & Tate, E.W. N-Myristoyl transferase-mediated protein labelling in vivo. Org. Biomol. Chem. 6, 2308–2315 (2008).

    Article  CAS  PubMed  Google Scholar 

  64. Charron, G. et al. Robust fluorescent detection of protein fatty-acylation with chemical reporters. J. Am. Chem. Soc. 131, 4967–4975 (2009).

    Article  CAS  PubMed  Google Scholar 

  65. Martin, B.R. & Cravatt, B.F. Large-scale profiling of protein palmitoylation in mammalian cells. Nat. Methods 6, 135–138 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Agard, N.J., Baskin, J.M., Prescher, J.A., Lo, A. & Bertozzi, C.R. A comparative study of bioorthogonal reactions with azides. ACS Chem. Biol. 1, 644–648 (2006).

    Article  CAS  PubMed  Google Scholar 

  67. Speers, A.E. & Cravatt, B.F. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11, 535–546 (2004).

    Article  CAS  PubMed  Google Scholar 

  68. Kho, Y. et al. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. Proc. Natl. Acad. Sci. USA 101, 12479–12484 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Rose, M.W. et al. Evaluation of geranylazide and farnesylazide diphosphate for incorporation of prenylazides into a CAAX box-containing peptide using protein farnesyltransferase. J. Pept. Res. 65, 529–537 (2005).

    Article  CAS  PubMed  Google Scholar 

  70. Rose, M.W. et al. Enzymatic incorporation of orthogonally reactive prenylazide groups into peptides using geranylazide diphosphate via protein farnesyltransferase: implications for selective protein labeling. Biopolymers 80, 164–171 (2005).

    Article  CAS  PubMed  Google Scholar 

  71. Nguyen, U.T. et al. Exploiting the substrate tolerance of farnesyltransferase for site-selective protein derivatization. ChemBioChem 8, 408–423 (2007).

    Article  CAS  PubMed  Google Scholar 

  72. Chan, L.N. et al. A novel approach to tag and identify geranylgeranylated proteins. Electrophoresis 30, 3598–3606 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Davies, B.S. et al. Increasing the length of progerin's isoprenyl anchor does not worsen bone disease or survival in mice with Hutchinson-Gilford progeria syndrome. J. Lipid Res. 50, 126–134 (2009).

    Article  CAS  PubMed  Google Scholar 

  74. Berry, A.F. et al. Rapid multilabel detection of geranylgeranylated proteins by using bioorthogonal ligation chemistry. ChemBioChem 11, 771–3 (2010).

    Article  CAS  PubMed  Google Scholar 

  75. Duckworth, B.P., Zhang, Z., Hosokawa, A. & Distefano, M.D. Selective labeling of proteins by using protein farnesyltransferase. ChemBioChem 8, 98–105 (2007).

    Article  CAS  PubMed  Google Scholar 

  76. Gauchet, C., Labadie, G.R. & Poulter, C.D. Regio- and chemoselective covalent immobilization of proteins through unnatural amino acids. J. Am. Chem. Soc. 128, 9274–9275 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Dursina, B. et al. Identification and specificity profiling of protein prenyltransferase inhibitors using new fluorescent phosphoisoprenoids. J. Am. Chem. Soc. 128, 2822–2835 (2006).

    Article  CAS  PubMed  Google Scholar 

  78. Troutman, J.M., Roberts, M.J., Andres, D.A. & Spielmann, H.P. Tools to analyze protein farnesylation in cells. Bioconjug. Chem. 16, 1209–1217 (2005).

    Article  CAS  PubMed  Google Scholar 

  79. Nguyen, U.T. et al. Analysis of the eukaryotic prenylome by isoprenoid affinity tagging. Nat. Chem. Biol. 5, 227–235 (2009).

    Article  CAS  PubMed  Google Scholar 

  80. Jao, C.Y., Roth, M., Welti, R. & Salic, A. Metabolic labeling and direct imaging of choline phospholipids in vivo. Proc. Natl. Acad. Sci. USA 106, 15332–15337 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Neef, A.B. & Schultz, C. Selective fluorescence labeling of lipids in living cells. Angew. Chem. Int. Edn Engl. 48, 1498–1500 (2009).

    Article  CAS  Google Scholar 

  82. Gubbens, J. et al. Photocrosslinking and click chemistry enable the specific detection of proteins interacting with phospholipids at the membrane interface. Chem. Biol. 16, 3–14 (2009).

    Article  CAS  PubMed  Google Scholar 

  83. Haberkant, P. & van Meer, G. Protein-lipid interactions: paparazzi hunting for snap-shots. Biol. Chem. 390, 795–803 (2009).

    Article  CAS  PubMed  Google Scholar 

  84. Yap, M.C. et al. Rapid and selective detection of fatty acylated proteins using ω-alkynyl-fatty acids and click chemistry. J. Lipid Res. published online 19 January 2010, doi:10.1194/jlr.D002790.

    Article  CAS  PubMed  Google Scholar 

  85. Ching, W., Hang, H.C. & Nusse, R. Lipid-independent secretion of a Drosophila Wnt protein. J. Biol. Chem. 283, 17092–17098 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Rangan, K.J., Yang, Y.Y., Charron, G. & Hang, H.C. Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters. J. Am. Chem. Soc. published online 15 March 2010, doi: 10.1021/ja101387b.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Frearson, J.A. et al. N-myristoyltransferase inhibitors as new leads to treat sleeping sickness. Nature 464, 728–732 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Chen, Y. & Shoichet, B.K. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat. Chem. Biol. 5, 358–364 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Rual, J.-F. et al. Towards a proteome-scale map of the human protein–protein interaction network. Nature 437, 1173–1178 (2005).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank F. Bazan and M. Bentley for critically reviewing the manuscript.

Author information

Authors and Affiliations

  1. Department of Protein Engineering, Genentech, Inc., South San Francisco, California, USA

    Rami N Hannoush & JingLucy Sun

Authors
  1. Rami N Hannoush
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. JingLucy Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rami N Hannoush.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hannoush, R., Sun, J. The chemical toolbox for monitoring protein fatty acylation and prenylation. Nat Chem Biol 6, 498–506 (2010). https://doi.org/10.1038/nchembio.388

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.388

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing