Skip to main content

Identification of Posttranslational Modification Sites by Site-Directed Mutagenesis

  • Protocol
Regulatory Protein Modification

Part of the book series: Neuromethods ((NM,volume 30))

  • 2085 Accesses

Abstract

Following translation, many proteins undergo further modifications that can dramatically affect both their physical properties and biological function (Wold and Moldave, 1984; Freedman and Hawkins, 1985; Harding and Crabbe, 1992). These posttranslational modifications are essential to the vitality of all eukaryotic cells, including neurons. Techniques that identify amino acid residues in a given protein that are modified and assess the effect of eliminating a specific modification site on a protein’s function, both in vitro or in the context of cellular expression, are useful in studying posttranslational modifications. The more traditional biochemical and immunological methods of studying posttranslational modification are discussed elsewhere in this book. However, the resources required for these approaches may not always be available or may yield equivocal results. Thus, the powerful tools of molecular biology may provide a viable alternative for identifying sites of posttranslational modification.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ausubel, F. M., Kingston, R. E., Moore, D D., Seidman, J. G., Smith, J A., and Struhl, K., eds. (1995) Current Protocols in Molecular Biology on CD-ROM. Liss, New York.

    Google Scholar 

  • Batt, C. A., Cho, Y., and Jamieson, A. C. (1993) Selection of oligodeoxy-nucleotide-directed mutants, in Methods in Enzymology: Recombinant DNA, part H, vol. 217 (Wu, R., ed.), Academic, New York, pp. 280–286.

    Google Scholar 

  • Bernhardt, G., Bibb, J. A., Bradley, J., and Wimmer, E. (1994) Molecular characterization of the cellular receptor for poliovirus. Virology 199, 105–113.

    Article  PubMed  CAS  Google Scholar 

  • Bibb, J. A., Bernhardt, G., and Wimmer, E. (1994) The human poliovirus receptor PVR alpha is a serine phosphoprotein. J Virol. 68, 6111–6115.

    PubMed  CAS  Google Scholar 

  • Carter, P. (1991) Mutagenesis facilitated by the removal or introduction of unique restriction sites, in Directed Mutagenesis, A Practical Approach (McPherson, M. J., ed.), Academic, New York, pp. 1–24.

    Google Scholar 

  • Conley, E. C. and Saunders, J. R. (1984) Recombination-dependent recircularization of linearized pBR322 plasmid following transformation of Escherichia coli. Mol Gen Genet. 194, 211–218.

    Article  PubMed  CAS  Google Scholar 

  • Crowe, J, Dobeli, H., Gentz, R., Hochuli, E., Stüber, D., and Henco, K. (1994) 6XHis-Ni-NTA chromatography as a superior technique in recombinant protein expression/purification, in Methods in Molecular Biology, vol. 31: Protocols for Gene Analysis (Harwood, A. J., ed.), Humana, Totowa, NJ, pp 371–387.

    Chapter  Google Scholar 

  • da Cruz e Silva, O. A, Iverfeldt, K., Oltersdorf, T., Sinha, S., Lieberburg, I., Ramabhadran, T. V., Suzuki, T., Sisodia, S. S., Gandy, S., and Greengard, P. (1993) Regulated cleavage of Alzheimer beta-amyloid precursor protein in the absence of the cytoplasmic tail. Neuroscience 57, 873–877.

    Article  Google Scholar 

  • Deng, W. P. and Nickoloff, J. A. (1992) Site-directed mutagenesis of virtually any plasmid by eliminating a unique site. Anal. Biochem 200, 81–88.

    Article  PubMed  CAS  Google Scholar 

  • Desdouits, F., Cohen, D, Nairn, A. C, Greengard, P., and Girault, J.-A. (1995a) Phosphorylation of DARPP-32, a dopamine-and cAMP-regulated posphoprotein, by casein kinase I in vitro and in vivo. J Biol. Chem 270, 8772–8778.

    Article  PubMed  CAS  Google Scholar 

  • Desdouits, F., Siciliano, J. L., Greengard, P., and Girault, J.-A. (1995b) Dopamine-and cAMP-regulated phosphoprotein DARPP-32: phosphorylation of Ser-137 by casein kinase-I inhibits dephosphorylation of Thr-34 by calcineurin. Proc. Natl Acad. Sci. USA 42, 2682–2685.

    Article  Google Scholar 

  • Dieffenbach, C. W. (1995) in PCR Primer. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp. 581–622.

    Google Scholar 

  • Dohadwala, M., da Cruz e Silva, E. F., Williams, R. T., Carbonaro-Hall, D. A., Nairn, A. C, Greengard, P., and Berndt, N. (1994) Phosphorylation and inactivation of protein phosphatase 1 by cyclin-dependent kinases. Proc. Natl. Acad. Sci. USA 91, 6408–6412.

    Article  PubMed  CAS  Google Scholar 

  • Dubendorff, J. W. and Studier, F. W. (1991) Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor. J. Mol. Biol. 219, 45–59

    Article  PubMed  CAS  Google Scholar 

  • Freedman, R. B. and Hawkins, H. C. (1985) The Enzymology of Posttranslational Modification of Proteins, vol. 2, Academic, New York.

    Google Scholar 

  • Gandy, S. E., Czernik, A. J., and Greengard, P. (1988) Phosphorylation of Alzheimer disease amyloid precursor protein peptide by protein kinase C and Ca2+/calmodulin-dependent protein kinases II. Proc Natl. Acad Sci. USA 85, 6218–6221.

    Article  PubMed  CAS  Google Scholar 

  • Harding, J. J. and Crabbe, M. J. C. (1992) Posttranslational Modification of Proteins. CRC, Ann Arbor, MI.

    Google Scholar 

  • Hemmings, H. C. J., Nairn, A. C, Bibb, J. A., and Greengard, P. (1995) Signal transduction in the striatum: DARPP-32 a molecular integrator of multiple signalling pathways, in Molecular and Cellular Mechanisms of Neostriatal Function (Ariano, M. A. and Surmeier, D J., eds.), Landes, Austin, TX, pp. 283–297.

    Google Scholar 

  • Hofer, B. and Kühlein, B. (1993) Site-specific mutagenesis in plasmids-a gapped circle method, in Methods in Enzymology: Recombinant DNA, part H, vol. 217 (Wu, R, ed), Academic, New York, pp 173–189.

    Google Scholar 

  • Horton, R. M. and Pease, L. R. (1991) Recombinantion and mutagenesis of DNA sequences using PCR, in Directed Mutagenesis, A Practical Approach (McPherson, M. J., ed.), IRL, New York, pp. 217–247

    Google Scholar 

  • Horton, R. M., Ho, S. N., Pullen, J. K., Hunt., H. D., Cai, Z., and Pease, L R (1993) Gene splicing by overlap extension, in Methods in Enzymology: Recombinant DNA, part H, vol. 217 (Wu, R., ed), Academic, New York, pp. 270–279.

    Google Scholar 

  • Hughes, M. J. G. and Andrews, D. W. (1996) Creation of deletion, insertion and substitution mutations using a single pair of primers and PCR. Biotechniques 20, 188–196.

    PubMed  CAS  Google Scholar 

  • Hunkapiller, M. W. (1991) Advances in DNA sequencing technology. Curr Opinion Gen Dev. 1, 88–92.

    Article  CAS  Google Scholar 

  • Innis, M. A., Gelfand, D. H., and Sninsky, J. J (1994) PCR Strategies. Academic, New York

    Google Scholar 

  • Inouye, S. and Inouye, M. (1991) Site-directed mutagenesis using gapped-heteroduplex plasmid DNA, in Directed Mutagenesis, A Practical Approach (McPherson, M. J., ed.), Oxford University, New York, pp. 71–82.

    Google Scholar 

  • Ju, J., Ruan, C, Fuller, C. W., Glazer, A. N., and Mathies, R. A. (1995) Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. Proc Natl Acad Sci. USA 92, 4347–5351

    Article  PubMed  CAS  Google Scholar 

  • Kaslow, D. C. and Rawlings, D. J. (1993) Introducing restriction sites into double-stranded plasmid DNA, in Methods in Enzymology Recombinant DNA, part H, vol. 217 (Wu, R, ed.), Academic, New York, pp. 295–301.

    Google Scholar 

  • Kennelly, P. J. (1994) Identification of sites of serine and threonine phosphorylation via site-directed mutagenesis—site transformation versus site elimination. Anal Biochem 219, 384–386

    Article  PubMed  CAS  Google Scholar 

  • King, L. A. and Possee, R. D. (1992) The Baculovirus Expression System: A Laboratory Guide. Chapman and Hall, London

    Google Scholar 

  • Kleina, L G. and Miller, J. H (1990) Genetic studies of the lac repressor, XII. Extensive amino acid replacements generated by the use of natural and synthetic nosnsense suppressors. J. Mol. Biol. 212, 295–318.

    Article  PubMed  CAS  Google Scholar 

  • Kleina, L. G., Masson, J.-M, Normanly, J., Abelson, J., and Miller, J. H. (1990) Construction of Eschenchia coli amber suppressor tRNA genes, II. Synthesis of additional tRNA genes and improvement of suppressor efficiency J Mol Biol, 213, 705–717.

    Article  PubMed  CAS  Google Scholar 

  • Kriegler, M. (1990) Gene Transfer and Expression A Laboratory Manual. Freeman, New York.

    Google Scholar 

  • Kunkel, T. A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl Acad Sci. USA 82, 488–492.

    Article  PubMed  CAS  Google Scholar 

  • Kunkel, T. A. (1987) Rapid and efficient site-specific mutagenesis without phenotypic selection, in Methods in Enzymology: Recombinant DNA, part E, vol. 154 (Roberts, J. D. and Zakour, R. A., eds.), Academic, New York.

    Google Scholar 

  • Lamb, C. J. (1990) Plant Gene Transfer. Liss, New York.

    Google Scholar 

  • Marck, C. (1988) “DNA Strider”: a “C” program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers. Nucleic Acid Res 16, 1829–1836.

    Article  PubMed  CAS  Google Scholar 

  • McPherson, M. J. (1991) Directed Mutagenesis, A Practical Approach, IRL, New York.

    Google Scholar 

  • McPherson, M. J. (1995) PCR 2 A Practical Approach, IRL, New York

    Google Scholar 

  • Means, A. R. (1994) Calcium regulation of cellular function. Adv Sec Messeng Phosphopro. Res. 30, 1–416

    Google Scholar 

  • Moffatt, B. A, Dunn, J J., and Studier, F W. (1984) Nucleotide sequence of the gene for bacteriophage T7 RNA polymerase. J. Mol Biol 173, 265–269

    Article  PubMed  CAS  Google Scholar 

  • Murray, E. J. (1991) Gene Transfer and Expression Protocols. Humana, Clifton, NJ.

    Book  Google Scholar 

  • NATO Advanced Study Institute on Plant Molecular Biology (1991) Plant Mol Biol 2. Plenum, New York.

    Google Scholar 

  • Normanly, J., Kleina, L. G., Masson, J.-M., Abelson, J., and Miller, J. H. (1990) Construction of Eschenchia coli amber suppressor tRNA genes, III. Determination of tRNA specificity. J. Mol Biol. 213, 719–726

    Article  PubMed  CAS  Google Scholar 

  • Olsen, D. B., Sayers, J. R., and Eckstein, F. (1993) Site-directed mutagenesis of single-stranded and double-stranded DNA by phosphorothioate approach, in Methods in Enzymology: Recombinant DNA, part H, vol 217 (Wu, R, ed.), Academic, New York, pp. 189–217.

    Google Scholar 

  • Piechocki, M. P. and Hines, R. N. (1994) Oligonucleotide design and optimized protocol for site-directed mutagenesis. Bio Techniques 16, 702–707.

    CAS  Google Scholar 

  • Rychlik, W. and Rhoads, R. E. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA Nucleic Acid Res 17, 8543–8551

    Article  PubMed  CAS  Google Scholar 

  • Saiki, R K, Gelfand, D. H, Stoffel, S., Scharf, S J., Higuchi, R, Horn, G T., Mullis, K. B., and Erlich, H. A. (1985) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.

    Article  Google Scholar 

  • Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning, A Laboratory Manual 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

    Google Scholar 

  • Sarkar, G. (1995) PCR in Neuroscience. Academic, New York.

    Google Scholar 

  • Sayers, J. R., Krekel, C, and Eckstein, F. (1992) Rapid high-efficiency site-directed mutagenesis by the phosphorothioate approach. BioTechniques 13, 542–546.

    Google Scholar 

  • Selbert, M A., Anderson, K. A., Huang, Q.-H., Goldstein, E. G., Means, A. R., and Edelman, A. M. (1995) Phosphorylation and activation of Ca2+-calmodulin-dependent protein kinase IV by Ca2+-calmodulin-dependent protein kinase Ia kinase. J Biol Chem 270, 17,616–17,621.

    Article  PubMed  CAS  Google Scholar 

  • Seto, D., Seto, J, Deshpande, P., and Hood, L (1995) DMSO resolves certain compressions and signal dropouts in fluorscent dye labeled primer-based DNA sequencing reactions. DNA Sequence 5, 131–140.

    PubMed  CAS  Google Scholar 

  • Shortle, D. and Botstein, D. (1985) Strategies and applications of in vitro mutagenesis. Science 229, 1193–1201.

    Article  PubMed  Google Scholar 

  • Smith, D. B and Johnson, K. S (1988) Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene 67, 31–40.

    Article  PubMed  CAS  Google Scholar 

  • Smith, M. (1985) In vitro mutagenesis. Ann. Rev. Genet 19, 423–462.

    Article  PubMed  CAS  Google Scholar 

  • Steen, R., Dahlberg, A. E., Lade, B. N., Studier, F. W., and Dunn, J. J. (1986) T7 RNA polymerase directed expression of the Escherichia coli rrnB operon. EMBO J 5, 1099–1103.

    PubMed  CAS  Google Scholar 

  • Studier, F. W. and Moffatt, B. A. (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol. Biol 189, 113–130

    Article  PubMed  CAS  Google Scholar 

  • Studier, F. W., Rosenberg, A. H., Dunn, J. J., and Dubendorff, J. W. (1990) Use of T7 RNA polymerase to direct expression of cloned genes, in Methods in Enzymology, Gem Expression Technology, vol 185, pp. 60–89.

    CAS  Google Scholar 

  • Suzuki, T., Nairn, A. C, Gandy, S. E., and Greengard, P. (1992) Phosphorylation of Alzheimer amyloid precursor protein by protein kinase C. Neuroscience 48, 755–761.

    Article  PubMed  CAS  Google Scholar 

  • Taylor, J. W., Ott, J., and Eckstein, F. (1985) The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA. Nucleic Acid Res 13, 8765–8785.

    Article  PubMed  CAS  Google Scholar 

  • Vandeyar, M A., Weiner, M. P, Hutton, C. J., and Batt, C. A. (1988) Identification of a simple and rapid method for the selection of oligodeoxynucleotide directed mutants. Gene 65, 129–133.

    Article  PubMed  CAS  Google Scholar 

  • Wang, Y. and Kent, C. (1995) Effects of altered phosphorylation sites on the properties of CTP: phosphocholine cytidylyltransferase. J Biol Chem 270, 17,843–17,849.

    Article  PubMed  CAS  Google Scholar 

  • Weiner, M. P., Costa, G. L., Schoettlin, W., Cline, J., Mathur, E., and Bauer, J. C. (1994) Site-directed mutagenesis of double-stranded DNA by the polymerase chain reaction Gene 151, 119–123.

    Article  PubMed  CAS  Google Scholar 

  • Werner, M. P., Felts, K, Simcox, T., and Braman, J. (1993) Directional method for the site-directed mono-and multi-mutagenesis of double-stranded DNA. Gene 126, 35–41.

    Article  Google Scholar 

  • Wold, F. and Moldave, K (1984) Methods in Enzymology, Posttranslational Modifications, parts A and B, vols. 106,107. Academic, New York

    Google Scholar 

  • Wu, R. (1993) in, Methods in Enzymology, Recombinant DNA, part H, vol. 217. Academic, New York.

    Google Scholar 

  • Yuckenberg, P. D., Witney, F., Geisselsoder, J., and McClary, J. (1991) Site-directed in vitro mutagenesis using uracil-containing DNA and phagemid vectors, in Directed Mutagenesis, A Practical Approach (McPherson, M J, ed.), IRL, New York, pp. 27–48.

    Google Scholar 

  • Zhao, L.-J. and Padmanabhan, R. (1993) Polymerase chain reaction-based point mutagenesis protocol, in Methods in Enzymology. Recombinant DNA, part H, vol 217 (Wu, R., ed.), Academic, New York, pp. 218–227

    Google Scholar 

  • Zhu, L. and Holtz, A E (1993) Improved protocol for the Transformer™ site-directed mutagenesis kit. Clontechniques Oct., 1–3.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1997 Humana Press Inc.

About this protocol

Cite this protocol

Bibb, J.A., da Cruz e Silva F., E. (1997). Identification of Posttranslational Modification Sites by Site-Directed Mutagenesis. In: Hemmings, H.C. (eds) Regulatory Protein Modification. Neuromethods, vol 30. Humana Press. https://doi.org/10.1385/0-89603-415-1:275

Download citation

  • DOI: https://doi.org/10.1385/0-89603-415-1:275

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-415-0

  • Online ISBN: 978-1-59259-635-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics