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Protein engineering 20 years on

Abstract

It is 20 years since site-directed mutagenesis was first used to modify the active site of an enzyme of known structure and mechanism. Since then, this method has contributed far-reaching insights into catalysis, specificity, stability and folding of proteins. Engineered proteins are now being used in industry and for the improved treatment of human disease.

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Figure 1: The active site of tyrosyl–transfer RNA synthetase.
Figure 2: Oxygen saturation curves for haemoglobin.
Figure 3: Ribbon diagrams of insulin.

References

  1. Knowles, J. R. & Albery, W. J. Perfection in enzyme catalysis: the energetics of triose phosphate isomerase. Acc. Chem. Res. 10, 105–111 (1977).

    CAS  Google Scholar 

  2. Fersht, A. R. Enzyme Structure and Mechanism (W. H. Freeman & Co., San Francisco, 1977).

    Google Scholar 

  3. Campbell, I. D. The march of structural biology. Nature Rev. Mol. Cell Biol. 3, 377–381 (2002).

    CAS  Google Scholar 

  4. Winter, G., Fersht, A. R., Wilkinson, A. J., Zoller, M. & Smith, M. Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding. Nature 299, 756–758 (1982).

    CAS  PubMed  Google Scholar 

  5. Dalbadie-MacFarland, G. et al. Oligonucleotide-directed mutagenesis as a powerful method for studies of protein function. Proc. Natl Acad. Sci. USA 79, 6409–6413 (1982).

    Google Scholar 

  6. Sigal, I. S., Harwood, B. G. & Arentzen, R. Thiol β-lactamase: replacement of the active site serine of RTEM β-lactamase by a cysteine residue. Proc. Natl Acad. Sci. USA 79, 7157–7160 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Jones, P. T., Dear, P. H., Foote, J., Neuberger, M. S. & Winter, G. Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature 321, 522–525 (1986).

    CAS  PubMed  Google Scholar 

  8. Neuberger, M. S., Williams, G. T. & Fox, R. O. Recombinant antibodies possessing novel effector functions. Nature 312, 604–608 (1984).

    CAS  PubMed  Google Scholar 

  9. Wilkinson, A. J., Fersht, A. R., Blow, D. M. & Winter, G. Site-directed mutagenesis as a probe of enzyme structure and catalysis: tyrosyl-tRNA synthetase cysteine-35 to glycine-35 mutation. Biochemistry 22, 3581–3586 (1983).

    CAS  PubMed  Google Scholar 

  10. Leatherbarrow, R. J., Fersht, A. R. & Winter, G. Transition-state stabilisation in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering. Proc. Natl Acad. Sci. USA 82, 7840–7844 (1985).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Wilkinson, A. J., Fersht, A. R., Blow, D. M., Carter, P. & Winter, G. A large increase in enzyme-substrate affinity by protein engineering. Nature 307, 187–188 (1984).

    CAS  PubMed  Google Scholar 

  12. Fersht, A. R. et al. Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314, 235–238 (1985).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  14. Carter, P. & Wells, J. A. Dissecting the catalytic triad of a serine protease. Nature 332, 564–568 (1988).

    CAS  PubMed  Google Scholar 

  15. Wells, J. A., Cunningham, B. C., Graycar, T. P. & Estell, D. A. Importance of hydrogen-bond formation in stabilizing the transition state of subtilisin. Phil. Trans. R. Soc. Lond. A 317, 415–423 (1986).

    CAS  Google Scholar 

  16. Bryan, P., Pantoliano, M. W., Quill, S. G., Hsiao, H. -Y. & Poulos, T. Site-directed mutagenesis and the role of the oxyanion hole in subtilisin. Proc. Natl Acad. Sci. USA 83, 3743–3745 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Springer, B. A. et al. Discrimination between oxygen and carbon monoxide and inhibition of autooxidation by myoglobin. J. Biol. Chem. 264, 3057–3060 (1989).

    CAS  PubMed  Google Scholar 

  18. Gardell, S. J., Craik, C. S., Hilvert, D., Urdea, M. S. & Rutter, W. J. Site-directed mutagenesis shows that tyrosine 248 of carboxypeptidase A does not play a crucial role in catalysis. Nature 317, 551–555 (1985).

    CAS  PubMed  Google Scholar 

  19. Blake, C. C. F. et al. Structure of hen egg white lysozyme. A three-dimensional fourier synthesis at 2Å resolution. Nature 206, 757–763 (1965).

    CAS  PubMed  Google Scholar 

  20. Vocadlo, D. J., Davies, G. J., Laine, R. & Withers, S. G. Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate. Nature 412, 835–838 (2001).

    CAS  PubMed  Google Scholar 

  21. Kantrowitz, E. R. & Lipscomb, W. N. Escherichia coli. aspartate transcarbamylase: the relation between structure and function. Science 241, 669–674 (1988).

    CAS  PubMed  Google Scholar 

  22. Matouschek, A., Kellis J. T. Jr, Serrano, L. & Fersht, A. R. Mapping the transition state and pathway of protein folding by protein engineering. Nature 340, 122–126 (1989).

    CAS  PubMed  Google Scholar 

  23. Fersht, A. R. & Daggett, V. Protein folding and unfolding at atomic resolution. Cell 108, 573–582 (2002).

    CAS  PubMed  Google Scholar 

  24. Matthews, B. W. Genetic and structural analysis of the protein stability problem. Biochemistry 26, 6855–6888 (1987).

    Google Scholar 

  25. Shortle, D. Probing the determinants of protein folding and stability with amino acid substitutions. J. Biol. Chem. 264, 5315–5318 (1989).

    CAS  PubMed  Google Scholar 

  26. Arnold, F. H. Engineering enzymes for non-aqueous solvents. Trends Biotechnol. 8, 244–249 (1990).

    CAS  PubMed  Google Scholar 

  27. Perry, L. J. & Wetzel, R. Disulfide bond engineering into T4 lysozyme: stabilization of the protein toward thermal inactivation. Science 226, 555–557 (1984).

    CAS  PubMed  Google Scholar 

  28. Van den Burg, B., Vriend, G., Veltman, O. R., Venema, G. & Eijsink, V. G. H. Engineering an enzyme to resist boiling. Proc. Natl Acad. Sci. USA 95, 2056–2060 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Russell, A. J. & Fersht, A. R. Rational modification of enzyme catalysis by engineering surface charge. Nature 328, 496–500 (1987).

    CAS  PubMed  Google Scholar 

  30. Fersht, A. R., Leatherbarrow, R. J. & Wells, T. N. C. Structure–activity relationships in engineered proteins: analysis of use of binding energy by linear free energy relationships. Biochemistry 26, 6030–6038 (1987).

    CAS  PubMed  Google Scholar 

  31. Wells, J. A. Additivity of mutational effects in proteins. Biochemistry 29, 8509–8517 (1990).

    CAS  PubMed  Google Scholar 

  32. Wilks, H. M. et al. A specific, highly active malate dehydrogenase by redesign of a lactate dehydrogenase framework. Science 242, 1541–1544 (1988).

    CAS  PubMed  Google Scholar 

  33. Wilks, H. M. et al. Designs for a broad substrate specificity keto acid dehydrogenase. Biochemistry 29, 8587–8591 (1990)

    CAS  PubMed  Google Scholar 

  34. Wilks, H. M. et al. Design of a specific phenyllactate dehydrogenase by peptide loop exchange on the Bacillus stearothermophilus lactate dehydrogenase framework. Biochemistry 31, 7802–7806 (1992).

    CAS  PubMed  Google Scholar 

  35. Graf, L. et al. Selective alteration of substrate specificity by replacement of aspartic acid-189 with lysine in the binding pocket of trypsin. Biochemistry 26, 2616–2623 (1987).

    CAS  PubMed  Google Scholar 

  36. Perona, J. J. et al. Structural origins of substrate discrimination in trypsin and chymotrypsin. Biochemistry 34, 1489–1499 (1995).

    CAS  PubMed  Google Scholar 

  37. Venekei, I., Szilagyi, L., Graf, L. & Rutter, W. J. Attempts to convert chymotrypsin to trypsin. FEBS Lett. 379, 143–147 (1996).

    CAS  PubMed  Google Scholar 

  38. Bedouelle, H. & Winter, G. A model of synthetase/transfer RNA interaction as deduced by protein engineering. Nature 320, 371–373 (1986).

    CAS  PubMed  Google Scholar 

  39. Cunningham, B. C. & Wells, J. A. High-resolution epitope mapping of HGH-receptor interactions by alanine-scanning mutagenesis. Science 244, 1081–1085 (1989).

    CAS  PubMed  Google Scholar 

  40. Wells, J. A. & Estell, D. A. Subtilisin — an enzyme designed to be engineered. Trends Biochem. Sci. 13, 291–297 (1988).

    CAS  PubMed  Google Scholar 

  41. Duncan, A. R. & Winter, G. The binding site for C1q on IgG. Nature 332, 738–740 (1988).

    CAS  PubMed  Google Scholar 

  42. Oliphant, A. R. & Struhl, K. An efficient method for generating proteins with altered enzymatic properties: application to β-lactamase. Proc. Natl Aad. Sci. USA 86, 9094–9098 (1989).

    CAS  Google Scholar 

  43. Loeb, D. D. et al. Complete mutagenesis of the HIV-1 protease. Nature 340, 397–400 (1989).

    CAS  PubMed  Google Scholar 

  44. Merino, E., Osuna, J., Bolivar, F. & Soberon, X. A general, PCR-based method for single or combinatorial oligonucleotide-directed mutagenesis on pUC/M13 vectors. Biotechniques 12, 508–510 (1992).

    CAS  PubMed  Google Scholar 

  45. Dawkins, R. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design (Longman, London, 1986).

    Google Scholar 

  46. Chen, K. & Arnold, F. H. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl Acad. Sci. USA 90, 5618–5622 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Winter, G. & Milstein, C. Man-made antibodies. Nature 349, 293–299 (1991).

    CAS  PubMed  Google Scholar 

  48. Stemmer, W. P. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389–391 (1994).

    CAS  PubMed  Google Scholar 

  49. Crameri, A., Raillard, S. A., Bermudez, E. & Stemmer, W. P. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288–291 (1998).

    CAS  PubMed  Google Scholar 

  50. Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998).

    CAS  Google Scholar 

  51. Stemmer, W. P. C. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl Acad. Sci USA 91, 10747–10751 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Miyazaki, K. & Arnold, F. H. Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J. Mol. Evol. 49, 716–720 (1999).

    CAS  PubMed  Google Scholar 

  53. Gaytan, P., Osuna, J. & Soberon, X. Novel ceftazidime-resistance β-lactamases generated by a codon–based mutagenesis method and selection. Nucleic Acids Res. 30, e84 (2002).

    PubMed  PubMed Central  Google Scholar 

  54. Murakami, H., Hohsaka, T. & Sisido, M. Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nature Biotechnol. 20, 76–81 (2002).

    CAS  Google Scholar 

  55. Xia, G., Chen, L., Sera, T., Fa, M., Schultz, P. G. & Romesberg, F. E. Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase. Proc. Natl Acad. Sci. USA 99, 6597–6602 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Griffiths, A. D. & Tawfik, D. S. Man-made enzymes – from design to in vitro compartmentalisation. Curr. Opin. Biotechnol. 11, 338–353 (2000).

    CAS  PubMed  Google Scholar 

  57. Ghadessy, F. J., Ong, J. L. & Holliger, P. Directed evolution of polymerase function by compartmentalised self-replication. Proc. Natl Acad. Sci. USA 98, 4552–4557 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Facciotti, M. T., Bertain, P. B. & Yuan, L. Improved stearate phenotype in transgenic canola expressing a modified acyl–acyl carrier protein thioesterase. Nature Biotechnol. 17, 593–597 (1999).

    CAS  Google Scholar 

  59. Lehmann, M. et al. The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Eng. 15, 403–411 (2002).

    CAS  PubMed  Google Scholar 

  60. Burton, S. G. The search for the ideal biocatalyst. Nature Biotechnol. 20, 37–45 (2002).

    CAS  Google Scholar 

  61. Kumamaru, T., Suenaga, H., Mitsuoka, M., Watanabe, T. & Furukawa, K. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl oxygenase. Nature Biotechnol. 16, 663–666 (1998).

    CAS  Google Scholar 

  62. Bayley, H. & Cremer, P. S. Stochastic sensors inspired by biology. Nature 413, 226–230 (2001).

    CAS  PubMed  Google Scholar 

  63. Holliger P. & Bohlen, H. Engineering antibodies for the clinic. Cancer Metastasis Rev. 18, 411–419 (1999).

    CAS  PubMed  Google Scholar 

  64. McCafferty, J. & Glover, D. R. Engineering therapeutic proteins. Curr. Opin. Struct. Biol. 10, 417–420 (2000).

    CAS  PubMed  Google Scholar 

  65. Winslow, R. M. Blood substitutes: refocusing an elusive goal. Br. J. Haematol. 111, 387–396 (2000).

    CAS  PubMed  Google Scholar 

  66. Perutz, M. F. Stereochemistry of the cooperative effects in haemoglobin. Nature 228, 726–734 (1970).

    CAS  PubMed  Google Scholar 

  67. Dickerson, R. E. & Geis, I. Haemoglobin: Structure, Function, Evolution and Pathology (Benjamin/Cummings Publishing Co., Inc., Menlo Park, California, 1983).

    Google Scholar 

  68. Looker, D. et al. A human recombinant haemoglobin designed for use as a blood substitute. Nature 356, 258–260 (1992).

    CAS  PubMed  Google Scholar 

  69. Olson, J, S., Eich, R., Smith, L. P., Warren, J. J. & Knowles, B. C. Protein engineering strategies for designing more stable hemoglobin-based blood substitutes. Artif. Cells Blood Substit. Immobil. Biotechnol. 25, 227–241 (1997).

    CAS  PubMed  Google Scholar 

  70. Doherty, D. H. et al. Rate of reaction with nitric oxide determines the hypertensive effect of cell-free hemoglobin. Nature Biotechnol. 16, 672–676 (1998).

    CAS  Google Scholar 

  71. Brange, J. & Vølund, A. Insulin analogs with improved pharmacokinetic profiles. Adv. Drug Deliv. Rev. 35, 307–335 (1999).

    CAS  PubMed  Google Scholar 

  72. Vajo, Z. & Duckworth, W. C. Genetically engineered insulin analogues: diabetes in the new millennium. Pharmacol. Rev. 52, 1–10 (2000).

    CAS  PubMed  Google Scholar 

  73. Blundell, T., Dodson, G., Hodgkin, D. & Mercola, D. Insulin: the structure in the crystal and its reflection in chemistry and biology. Adv. Protein Chem. 26, 279–402 (1972).

    CAS  Google Scholar 

  74. Brange, J. et al. Monomeric insulins obtained by protein engineering and their medical implications. Nature 333, 679–682 (1988).

    CAS  PubMed  Google Scholar 

  75. Knowles, J. R. Tinkering with enzymes: What are we learning. Science 236, 1252–1259 (1987).

    CAS  PubMed  Google Scholar 

  76. Yano, T. & Kagamiyama, H. Directed evolution of ampicillin-resistant activity from a functionally unrelated DNA fragment: a laboratory model of molecular evolution. Proc. Natl Acad. Sci. USA 98, 903–907 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Mendel, D., Cornish, V. W. & Schultz, P. G. Site-directed mutagenesis with an expanded code. Annu. Rev. Biophys. Biomol. Struct. 24, 435–462 (1995).

    CAS  PubMed  Google Scholar 

  78. Wang, L., Brock, A., Herberich, B. & Schultz, P. G. Expanding the genetic code of Escherichia coli. Science 292, 498–504 (2001).

    CAS  PubMed  Google Scholar 

  79. Kiga, D. et al. An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system. Proc. Natl Acad. Sci. USA 99, 9715–9720 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Hutchison, C. A. et al. Mutagenesis at a specific position in a DNA sequence. J. Biol. Chem. 253, 6551–6560 (1978).

    CAS  PubMed  Google Scholar 

  81. Chang, C. C. et al. Evolution of a cytokine using DNA family shuffling. Nature Biotechnol. 17, 793–797 (1999).

    CAS  Google Scholar 

  82. Sieber, V., Martinez, C. A. & Arnold, F. H. Libraries of hybrid proteins from distantly related sequences. Nature Biotechnol. 19, 456–460 (2001).

    CAS  Google Scholar 

  83. Lutz, S., Ostermeier, M. & Benkovic, S. J. Rapid generation of incremental truncation libraries for protein engineering using α-phosphothioate nucleotides. Nucleic Acids Res. 29, 16e (2001).

    Google Scholar 

  84. Lutz, S., Ostermeier, M., Moore, G. L., Maranas, C. D. & Benkovic, S. J. Creating multiple-crossover DNA libraries independent of sequence identity. Proc. Natl Acad. Sci. USA 98, 11248–11253 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. O'Maille, P. E., Bakhtina, M. & Tsai, M. -D. Structure-based combinatorial protein engineering (SCOPE). J. Mol. Biol. 321, 677–691 (2002).

    CAS  PubMed  Google Scholar 

  86. Kilmartin, J. V. & Rossi-Bernardi, L. Interaction of haemoglobin with hydrogen ions, carbon dioxide and organic phosphates Physiol. Rev. 53, 836–890 (1973).

    CAS  PubMed  Google Scholar 

  87. Whittingham, J. L., Havelund, S. & Jonassen, I. Crystal structure of a prolonged-acting insulin with albumin-binding properties. Biochemistry 36, 2826–2831 (1997).

    CAS  PubMed  Google Scholar 

  88. McCafferty, J., Griffiths, A. D., Winter, G. & Chiswell, D. J. Phage antibodies: filamentous phage displaying antibody variable domains. Nature 348, 552–554 (1990).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank G. Winter for his critical comments and helpful advice, and the Wellcome Trust and the Biotechnology and Biological Sciences Research Council for supporting our research.

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Correspondence to James A. Brannigan or Anthony J. Wilkinson.

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DATABASES

Swiss-Prot

β-lacatamse

insulin

lysozyme

myoglobin

TyrRS

FURTHER INFORMATION

York Structural Biology Laboratory

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Brannigan, J., Wilkinson, A. Protein engineering 20 years on. Nat Rev Mol Cell Biol 3, 964–970 (2002). https://doi.org/10.1038/nrm975

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