Kemp elimination catalysts by computational enzyme design (original) (raw)

References

  1. Radzicka, A. & Wolfenden, R. A proficient enzyme. Science 267, 90–93 (1995)
    Article ADS CAS PubMed Google Scholar
  2. Bolon, D. N. & Mayo, S. L. Enzyme-like proteins by computational design. Proc. Natl Acad. Sci. USA 98, 14274–14279 (2001)
    Article ADS CAS PubMed PubMed Central Google Scholar
  3. Kaplan, J. & DeGrado, W. F. De novo design of catalytic proteins. Proc. Natl Acad. Sci. USA 101, 11566–11570 (2004)
    Article ADS CAS PubMed PubMed Central Google Scholar
  4. Zanghellini, A. et al. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 15, 2785–2794 (2006)
    Article CAS PubMed PubMed Central Google Scholar
  5. Casey, M. L., Kemp, D. S., Paul, K. G. & Cox, D. D. The physical organic chemistry of benzisoxazoles I. The mechanism of the base-catalyzed decomposition of benzisoxazoles. J. Org. Chem. 38, 2294–2301 (1973)
    Article CAS Google Scholar
  6. Kemp, D. S. & Casey, M. L. Physical organic chemistry of benzisoxazoles II. Linearity of the brønsted free energy relationship for the base-catalyzed decomposition of benzisoxazoles. J. Am. Chem. Soc. 95, 6670–6680 (1973)
    Article CAS Google Scholar
  7. Hu, Y., Houk, K. N., Kikuchi, K., Hotta, K. & Hilvert, D. Nonspecific medium effects versus specific group positioning in the antibody and albumin catalysis of the base-promoted ring-opening reactions of benzisoxazoles. J. Am. Chem. Soc. 126, 8197–8205 (2004)
    Article CAS PubMed Google Scholar
  8. Hollfelder, F., Kirby, A. J., Tawfik, D. S., Kikuchi, K. & Hilvert, D. Characterization of proton-transfer catalysis by serum albumins. J. Am. Chem. Soc. 122, 1022–1029 (2000)
    Article CAS Google Scholar
  9. Na, J., Houk, K. N. & Hilvert, D. Transition state of the base-promoted ring-opening of isoxazoles. Theoretical prediction of catalytic functionalities and design of haptens for antibody production. J. Am. Chem. Soc. 118, 6462–6471 (1996)
    Article CAS Google Scholar
  10. Debler, E. W. et al. Structural origins of efficient proton abstraction from carbon by a catalytic antibody. Proc. Natl Acad. Sci. USA 102, 4984–4989 (2005)
    Article ADS CAS PubMed PubMed Central Google Scholar
  11. Lee, C., Yang, W. & Parr, R. G. Development of the Colle–Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B Condens. Matter 37, 785–789 (1988)
    Article ADS CAS PubMed Google Scholar
  12. Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 38, 3098–3100 (1988)
    Article ADS CAS Google Scholar
  13. Frisch, M. J. et al. Gaussian 03, revision C. 02 (Gaussian, Inc., Wallingford, Connecticut, 2004)
    Google Scholar
  14. Hollfelder, F., Kirby, A. J. & Tawfik, D. S. Efficient catalysis of proton transfer by synzymes. J. Am. Chem. Soc. 119, 9578–9579 (1997)
    Article CAS Google Scholar
  15. Misura, K. M., Morozov, A. V. & Baker, D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. J. Mol. Biol. 342, 651–664 (2004)
    Article CAS PubMed Google Scholar
  16. Press, W. H., Teukolsky, S. A., Vetterling, W. T. & Flannery, B. P. Numerical Recipes in C++ 2nd edn (Cambridge Univ. Press, Cambridge, UK, 2002)
    MATH Google Scholar
  17. Kuhlman, B. et al. Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364–1368 (2003)
    Article ADS CAS PubMed Google Scholar
  18. Meiler, J. & Baker, D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65, 538–548 (2006)
    Article CAS PubMed Google Scholar
  19. Chica, R. A., Doucet, N. & Pelletier, J. N. Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr. Opin. Biotechnol. 16, 378–384 (2005)
    Article CAS PubMed Google Scholar
  20. Seelig, B. & Szostak, J. W. Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 448, 828–831 (2007)
    Article ADS CAS PubMed PubMed Central Google Scholar
  21. Cesaro-Tadic, S. et al. Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library. Nature Biotechnol. 21, 679–685 (2003)
    Article CAS Google Scholar
  22. Varadarajan, N., Gam, J., Olsen, M. J., Georgiou, G. & Iverson, B. L. Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity. Proc. Natl Acad. Sci. USA 102, 6855–6860 (2005)
    Article ADS CAS PubMed PubMed Central Google Scholar
  23. Thorn, S. N., Daniels, R. G., Auditor, M. T. & Hilvert, D. Large rate accelerations in antibody catalysis by strategic use of haptenic charge. Nature 373, 228–230 (1995)
    Article ADS CAS PubMed Google Scholar
  24. Hollfelder, F., Kirby, A. J. & Tawfik, D. S. Off-the-shelf proteins that rival tailor-made antibodies as catalysts. Nature 383, 60–62 (1996)
    Article ADS CAS PubMed Google Scholar
  25. Jiang, L. et al. De novo computational design of retro-aldol enzymes. Science 319, 1387–1391 (2008)
    Article ADS CAS PubMed PubMed Central Google Scholar
  26. Vartanian, J. P., Henry, M. & Wain-Hobson, S. Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res. 24, 2627–2631 (1996)
    Article CAS PubMed PubMed Central Google Scholar
  27. Abecassis, V., Pompon, D. & Truan, G. High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2. Nucleic Acids Res. 28, E88 (2000)
    Article CAS PubMed PubMed Central Google Scholar
  28. Herman, A. & Tawfik, D. S. Incorporating synthetic oligonucleotides via gene reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Eng. Des. Sel. 20, 219–226 (2007)
    Article CAS PubMed Google Scholar
  29. The. CCP4 suite: programs for protein crystallography. Acta Crystallogr. 50, 760–763 (1994)
  30. Dantas, G., Kuhlman, B., Callender, D., Wong, M. & Baker, D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J. Mol. Biol. 332, 449–460 (2003)
    Article CAS PubMed Google Scholar
  31. Kunkel, T. A., Roberts, J. D. & Zakour, R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154, 367–382 (1987)
    Article CAS PubMed Google Scholar
  32. Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005)
    Article CAS PubMed Google Scholar
  33. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411–2423 (1995)
    Article CAS PubMed PubMed Central Google Scholar
  34. Barlow, M. & Hall, B. G. Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem β-lactamase. Genetics 160, 823–832 (2002)
    CAS PubMed PubMed Central Google Scholar

Download references