De novo computational enzyme design

Current Opinion in Biotechnology

Volumn 29, Issue 1, 2014, Pages 132-138

  Zanghellini, Alexandre ^a  

^a Arzeda Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSTS; DESIGN; INDUSTRIAL CHEMICALS; SYNTHETIC FUELS;

ACTIVE PROTEINS; COMPUTATIONAL DESIGN; DIFFERENT CLASS; INDUSTRIAL BIOTECHNOLOGY; PROTEIN ENGINEERING; STRUCTURAL CHARACTERIZATION; SUSTAINABLE PRODUCTION; SYNTHETIC BIOLOGY;

ENZYMES;

DIELS ALDERASE; ESTERASE; FRUCTOSE BISPHOSPHATE ALDOLASE; KEMP ELIMINASE; OXIDOREDUCTASE; RECOMBINANT ENZYME; SUPEROXIDE DISMUTASE; UNCLASSIFIED DRUG;

CHEMICAL COMPOSITION; CHEMICAL REACTION; CHEMICAL STRUCTURE; CLASSIFICATION ALGORITHM; COMPUTER AIDED DESIGN; COMPUTER ANALYSIS; CRYSTAL STRUCTURE; CRYSTALLIZATION; DIELS ALDER REACTION; ENZYME ACTIVITY; ENZYME ENGINEERING; MOLECULAR DYNAMICS; MORITA BAYLIS HILLMA REACTION; PRIORITY JOURNAL; PROCESS CONTROL; PROCESS DESIGN; PROCESS DEVELOPMENT; PROCESS TECHNOLOGY; REVIEW; STRUCTURE ANALYSIS; BIOCATALYSIS; METABOLIC ENGINEERING; PROCEDURES; PROTEIN ENGINEERING; SYNTHETIC BIOLOGY;

BIOCATALYSIS; METABOLIC ENGINEERING; PROTEIN ENGINEERING; SYNTHETIC BIOLOGY;

EID: 84899824651     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.03.002     Document Type: Review

References (42)

1. Ro D.-K., Paradise E.M., Ouellet M., Fisher K.J., Newman K.L., Ndungu J.M., Ho K.A., Eachus R.A., Ham T.S., Kirby J., et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006.
2. Yim H., Haselbeck R., Niu W., Pujol-Baxley C., Burgard A., Boldt J., Khandurina J., Trawick J.D., Osterhout R.E., Stephen R., et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 2011, 7:445-452.
3. Hatzimanikatis V., Li C., Ionita J.A., Henry C.S., Jankowski M.D., Broadbelt L.J. Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21:1603-1609.
4. Pharkya P., Burgard A.P., Maranas C.D. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 2004, 14:2367-2376.
5. Carbonell P., Planson A.-G., Fichera D., Faulon J.-L. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst Biol 2011, 5:122.
6. Prather K.L.J., Martin C.H. De novo biosynthetic pathways: rational design of microbial chemical factories. Curr Opin Biotechnol 2008, 19:468-474.
7. Dahiyat B.I., Mayo S.L. De novo protein design: fully automated sequence selection. Science 1997, 278:82-87.
8. Hellinga H.W., Richards F.M. Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. J Mol Biol 1991, 222:763-785.
9. Hellinga H.W., Caradonna J.P., Richards F.M. Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. J Mol Biol 1991, 222:787-803.
10. Bolon D.N., Mayo S.L. Enzyme-like proteins by computational design. Proc Natl Acad Sci U S A 2001, 98:14274-14279.
11. Lassila J.K., Privett H.K., Allen B.D., Mayo S.L. Combinatorial methods for small-molecule placement in computational enzyme design. Proc Natl Acad Sci U S A 2006, 103:16710-16715.
12. Zanghellini A., Jiang L., Wollacott A.M., Cheng G., Meiler J., Althoff E.A., Röthlisberger D., Baker D. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci Publ Protein Soc 2006, 15:2785-2794.
13. Richter F., Leaver-Fay A., Khare S.D., Bjelic S., Baker D. De novo enzyme design using Rosetta3. PLoS ONE 2011, 6:e19230.
14. Malisi C., Kohlbacher O., Höcker B. Automated scaffold selection for enzyme design. Proteins 2009, 77:74-83.
15. Lei Y., Luo W., Zhu Y. A matching algorithm for catalytic residue site selection in computational enzyme design. Protein Sci 2011, 20:1566-1575.
16. Liu S., Liu S., Zhu X., Liang H., Cao A., Chang Z., Lai L. Nonnatural protein-protein interaction-pair design by key residues grafting. Proc Natl Acad Sci U S A 2007, 104:5330-5335.
17. Fazelinia H., Cirino P.C., Maranas C.D. OptGraft: a computational procedure for transferring a binding site onto an existing protein scaffold. Protein Sci Publ Protein Soc 2009, 18:180-195.
18. Jiang L., Althoff E.A., Clemente F.R., Doyle L., Röthlisberger D., Zanghellini A., Gallaher J.L., Betker J.L., Tanaka F., Barbas C.F., et al. De novo computational design of retro-aldol enzymes. Science 2008, 319:1387-1391.
19. Rothlisberger D., Khersonsky O., Wollacott A.M., Jiang L., DeChancie J., Betker J., Gallaher J.L., Althoff E.A., Zanghellini A., Dym O., et al. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453:190-195.
20. Althoff E.A., Wang L., Jiang L., Giger L., Lassila J.K., Wang Z., Smith M., Hari S., Kast P., Herschlag D., et al. Robust design and optimization of retroaldol enzymes. Protein Sci Publ Protein Soc 2012, 21:717-726.
21. Leaver-Fay A., Tyka M., Lewis S.M., Lange O.F., Thompson J., Jacak R., Kaufman K., Renfrew P.D., Smith C.A., Sheffler W., et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 2011, 487:545-574.
22. Wang L., Althoff E.A., Bolduc J., Jiang L., Moody J., Lassila J.K., Giger L., Hilvert D., Stoddard B., Baker D. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. J Mol Biol 2012, 415:615-625.
23. Korendovych I.V., Kulp D.W., Wu Y., Cheng H., Roder H., DeGrado W.F. Design of a switchable eliminase. Proc Natl Acad Sci U S A 2011, 108:6823-6827.
24. Allen B.D., Mayo S.L. Dramatic performance enhancements for the FASTER optimization algorithm. J Comput Chem 2006, 27:1071-1075.
25. Privett H.K., Kiss G., Lee T.M., Blomberg R., Chica R.A., Thomas L.M., Hilvert D., Houk K.N., Mayo S.L. Iterative approach to computational enzyme design. Proc Natl Acad Sci U S A 2012, 109:3790-3795.
26. Siegel J.B., Zanghellini A., Lovick H.M., Kiss G., Lambert A.R., St Clair J.L., Gallaher J.L., Hilvert D., Gelb M.H., Stoddard B.L., et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010, 329:309-313.
27. Eiben C.B., Siegel J.B., Bale J.B., Cooper S., Khatib F., Shen B.W., Players F., Stoddard B.L., Popovic Z., Baker D. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat Biotechnol 2012, 30:190-192.
28. Richter F., Blomberg R., Khare S.D., Kiss G., Kuzin A.P., Smith A.J.T., Gallaher J., Pianowski Z., Helgeson R.C., Grjasnow A., et al. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc 2012, 134:16197-16206.
29. Bjelic S., Nivon L.G., Celebi-Olcum N., Kiss G., Rosewall C.F., Lovick H.M., Ingalls E.L., Gallaher J.L., Seetharaman J., Lew S., et al. Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction. ACS Chem Biol 2013, 8:749-757.
30. Kiss G., Röthlisberger D., Baker D., Houk K.N. Evaluation and ranking of enzyme designs. Protein Sci Publ Protein Soc 2010, 19:1760-1773.
31. Ruscio J.Z., Kohn J.E., Ball K.A., Head-Gordon T. The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc 2009, 131:14111-14115.
32. Allen B.D., Mayo S.L. An efficient algorithm for multistate protein design based on FASTER. J Comput Chem 2010, 31:904-916.
33. Leaver-Fay A., Jacak R., Stranges P.B., Kuhlman B. A generic program for multistate protein design. PLoS ONE 2011, 6:e20937.
34. Bar-Even A., Noor E., Savir Y., Liebermeister W., Davidi D., Tawfik D.S., Milo R. The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry (Mosc) 2011, 50:4402-4410.
35. Khersonsky O., Röthlisberger D., Dym O., Albeck S., Jackson C.J., Baker D., Tawfik D.S. Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. J Mol Biol 2010, 396:1025-1042.
36. Khersonsky O., Röthlisberger D., Wollacott A.M., Murphy P., Dym O., Albeck S., Kiss G., Houk K.N., Baker D., Tawfik D.S. Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution. J Mol Biol 2011, 407:391-412.
37. Khersonsky O., Kiss G., Röthlisberger D., Dym O., Albeck S., Houk K.N., Baker D., Tawfik D.S. Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Proc Natl Acad Sci U S A 2012, 109:10358-10363.
38. Blomberg R., Kries H., Pinkas D.M., Mittl P.R.E., Grütter M.G., Privett H.K., Mayo S.L., Hilvert D. Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature 2013, 503:418-421.
39. Kipnis Y., Baker D. Comparison of designed and randomly generated catalysts for simple chemical reactions. Protein Sci 2012, 21:1388-1395.
40. Benson D.E., Haddy A.E., Hellinga H.W. Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry (Mosc) 2002, 41:3262-3269.
41. Suarez M., Tortosa P., Garcia-Mira M.M., Rodríguez-Larrea D., Godoy-Ruiz R., Ibarra-Molero B., Sanchez-Ruiz J.M., Jaramillo A. Using multi-objective computational design to extend protein promiscuity. Biophys Chem 2010, 147:13-19.
42. Kaplan J., DeGrado W.F. De novo design of catalytic proteins. Proc Natl Acad Sci U S A 2004, 101:11566-11570.