Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

Nature Chemical Biology

Volumn 8, Issue 3, 2012, Pages 294-300

  Khare, Sagar D ^a   Kipnis, Yakov ^a   Greisen, Per J ^b   Takeuchi, Ryo ^c   Ashani, Yacov ^d   Goldsmith, Moshe ^d   Song, Yifan ^a   Gallaher, Jasmine L ^a   Silman, Israel ^d   Leader, Haim ^d   Sussman, Joel L ^d   Stoddard, Barry L ^c   Tawfik, Dan S ^d   Baker, David ^a,e  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c Fred Hutchinson Cancer Research Center   (United States)

^d WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^e UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DEAMINASE; COUMARIN; CYCLOSARIN; METALLOPROTEINASE; ORGANOPHOSPHATE; ZINC;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; MONONUCLEAR CELL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN HYDROLYSIS; PROTEIN PURIFICATION; PROTEIN STRUCTURE;

EID: 84862776507     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.777     Document Type: Article

References (37)

1. Toscano, M.D., Woycechowsky, K.J. & Hilvert, D. Minimalist active-site redesign: teaching old enzymes new tricks. Angew. Chem. Int. Ed. Engl. 46, 3212-3236 (2007 (Pubitemid 46973466)
2. Gerlt, J.A. & Babbitt, P.C. Enzyme (re)design: lessons from natural evolution and computation. Curr. Opin. Chem. Biol. 13, 10-18 (2009
3. Khersonsky, O. & Tawfik, D.S. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu. Rev. Biochem. 79, 471-505 (2010
4. Yin, de L.T. et al. Switching catalysis from hydrolysis to perhydrolysis in Pseudomonas fluorescens esterase. Biochemistry 49, 1931-1942 (2010
5. Terao, Y., Miyamoto, K. & Ohta, H. Introduction of single mutation changes arylmalonate decarboxylase to racemase. Chem. Commun. (Camb.) 2006, 3600-3602 (2006 (Pubitemid 44267641)
6. Schmidt, D.M.Z. et al. Evolutionary potential of (-/-)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry 42, 8387-8393 (2003 (Pubitemid 36875403)
7. Leopoldseder, S., Claren, J., Jurgens, C. & Sterner, R. Interconverting the catalytic activities of 8-barrel enzymes from different metabolic pathways: Sequence requirements and molecular analysis. J. Mol. Biol. 337, 871-879 (2004 (Pubitemid 38368931)
8. Williams, S.D. & David, S.S. A single engineered point mutation in the adenine glycosylase MutY confers bifunctional glycosylase/AP lyase activity. Biochemistry 39, 10098-10109 (2000 (Pubitemid 30663031)
9. Xiang, H., Luo, L.S., Taylor, K.L. & Dunaway-Mariano, D. Interchange of catalytic activity within the 2-enoyl-coenzyme A hydratase isomerase superfamily based on a common active site template. Biochemistry 38, 7638-7652 (1999
10. Park, H.S. et al. Design and evolution of new catalytic activity with an existing protein scaffold. Science 311, 535-538 (2006
11. Jochens, H. et al. Converting an esterase into an epoxide hydrolase. Angew. Chem. Int. Edn. Engl. 48, 3532-3535 (2009
12. Chen, B. et al. Morphing activity between structurally similar enzymes: from heme-free bromoperoxidase to lipase. Biochemistry 48, 11496-11504 (2009
13. Raushel, F.M. Chemical biology: catalytic detoxification. Nature 469, 310-311 (2011
14. Gupta, R.D. et al. Directed evolution of hydrolases for prevention of G-type nerve agent intoxication. Nat. Chem. Biol. 7, 120-125 (2011
15. Tsai, P.C. et al. Stereoselective hydrolysis of organophosphate nerve agents by the bacterial phosphotriesterase. Biochemistry 49, 7978-7987 (2010
16. Murphy, P.M., Bolduc, J.M., Gallaher, J.L., Stoddard, B.L. & Baker, D. Alteration of enzyme specificity by computational loop remodeling and design. Proc. Natl. Acad. Sci. USA 106, 9215-9220 (2009
17. Röthlisberger, D. et al. Kemp elimination catalysts by computational enzyme design. Nature 453, 190-195 (2008). (Pubitemid 351667979)
18. Jiang, L. et al. De novo computational design of retro-aldol enzymes. Science 319, 1387-1391 (2008) (Pubitemid 351354873)
19. Siegel, J.B. et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329, 309-313 (2010
20. Zanghellini, A. et al. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci. 15, 2785-2794 (2006 (Pubitemid 44833759)
21. McCall, K.A., Huang, C. & Fierke, C.A. Function and mechanism of zinc metalloenzymes. J. Nutr. 130, 1437S-1446S (2000 (Pubitemid 30244143)
22. Aubert, S.D., Li, Y. & Raushel, F.M. Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase. Biochemistry 43, 5707-5715 (2004 (Pubitemid 38623605)
23. Dyguda-Kazimierowicz, E., Sokalski, W.A. & Leszczynski, J. Gas-phase mechanisms of degradation of hazardous organophosphorus compounds: do they follow a common pattern of alkaline hydrolysis reaction as in phosphotriesterase? J. Phys. Chem. B 112, 9982-9991 (2008
24. Kuhlman, B. & Baker, D. Native protein sequences are close to optimal for their structures. Proc. Natl. Acad. Sci. USA 97, 10383-10388 (2000
25. Lawrence, M.C. & Colman, P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946-950 (1993 (Pubitemid 24027225)
26. Davis, I.W. & Baker, D. RosettaLigand docking with full ligand and receptor flexibility. J. Mol. Biol. 385, 381-392 (2009
27. Wang, Z. & Quiocho, F.A. Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity. Biochemistry 37, 8314-8324 (1998 (Pubitemid 28275450)
28. Pegg, S.C. et al. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry 45, 2545-2555 (2006
29. Afriat, L., Roodveldt, C., Manco, G. & Tawfik, D.S. The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. Biochemistry 45, 13677-13686 (2006 (Pubitemid 44788738)
30. Blum, M.M., Lohr, F., Richardt, A., Ruterjans, H. & Chen, J.C. Binding of a designed substrate analogue to diisopropyl fluorophosphatase: implications for the phosphotriesterase mechanism. J. Am. Chem. Soc. 128, 12750-12757 (2006 (Pubitemid 44527751)
31. Baker D. An exciting but challenging road ahead for computational enzyme design. Protein Sci. 19, 1817-1819 (2010).
32. Kunkel, T.A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82, 488-492 (1985 (Pubitemid 15128292)
33. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997 (Pubitemid 27085611)
34. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007 (Pubitemid 47080256)
35. Winn, M.D., Murshudov, G.N. & Papiz, M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300-321 (2003 (Pubitemid 37531815)
36. Khersonsky, O. & Tawfik, D.S. Structure-reactivity studies of serum paraoxonase PON1 suggest that its native activity is lactonase. Biochemistry 44, 6371-6382 (2005 (Pubitemid 40570731)
37. Ashani, Y. et al. Stereo-specific synthesis of analogs of nerve agents and their utilization for selection and characterization of paraoxonase (PON1) catalytic scavengers. Chem. Biol. Interact. 187, 362-369 (2010