Evaluation and ranking of enzyme designs

Protein Science

Volumn 19, Issue 9, 2010, Pages 1760-1773

  Kiss, Gert ^a   Röthlisberger, Daniela ^b   Baker, David ^b   Houk, K N ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Acid base catalysis; Cluster model; Design refinement; Enzyme active site; Enzyme design; Kemp elimination; Molecular dynamics; Proton transfer; QM MM

Indexed keywords

ENZYME; PROTEIN; WATER;

ARTICLE; CATALYSIS; COMPUTATIONAL FLUID DYNAMICS; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME INACTIVATION; GEOMETRY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUANTUM MECHANICS; WATER PERMEABILITY;

CATALYSIS; CATALYTIC DOMAIN; ENZYMES; HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; QUANTUM THEORY; WATER;

EID: 77956357583     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.462     Document Type: Article

References (49)

1. Fersht AR (2002) Structure and mechanism in protein science. New York: W.H. Freeman and Co.
2. Gouverneur VE, Houk KN, Pascual-Teresa BD, Beno B, Janda KD, Lerner RA (1993) Control of the exo and endo pathways of the Diels-Alder reaction by antibody catalysis. Science 262:204-208. (Pubitemid 23344463)
3. Thorn SN, Daniels RG, Auditor MM, Hilvert D (1995) Large rate accelerations in antibody catalysis by strategic use of haptenic charge. Nature 373:228-230.
4. Wagner J, Lerner RA, Barbas CF, III (1995) Efficient aldolase catalytic antibodies that use the enamine mechanism of natural enzymes. Science 270:1797-1800. (Pubitemid 26007222)
5. Kikuchi K, Hannak RB, Guo M, Kirby AJ, Hilvert D (2006) Toward bifunctional antibody catalysis. Bioorg Med Chem 14:6189-6196.
6. Müller R, Debler EW, Steinmann M, Seebeck FP, Wilson IA, Hilvert D (2007) Bifunctional catalysis of proton transfer at an antibody active site. J Am Chem Soc 129:460-461. (Pubitemid 46147726)
7. Dahiyat BI, Mayo SL (1996) Protein design automation. Protein Sci 5:895-903.
8. Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15:2785-2794. (Pubitemid 44833759)
9. Tantillo DJ, Jiangang C, Houk KN (1998) Theozymes and compuzymes: theoretical models for biological catalysis. Curr Opin Chem Biol 2:743-750.
10. Zhang X, DeChancie J, Gunaydin H, Chowdry A, Clemente FR, Smith AJ, Handel T, Houk KN (2008) Quantum mechanical design of enzyme active sites. J Org Chem 73:889-899. (Pubitemid 351198732)
11. Zanghellini A, Jiang L, Cheng G, Althoff EA, Röthlisberger D, Wollacott AM, Meiler J, Baker D (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15:2785-2794. (Pubitemid 44833759)
12. Berman HM, Henrick K, Nakamura H (2003) Announcing the worldwide protein data bank. Nat Struct Biol 10:980.
13. Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D (2008) Kemp elimination catalysts by computational enzyme design. Nature 453:190-195.
14. Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Takana F, Barbas CF, III, Hilvert D, Houk KN, Stoddart BL, Baker D (2008) De novo computational design of retro-aldol enzymes. Science 319:1387-1391.
15. Zhang X, Houk KN (2005) Why enzymes are proficient catalysts: beyond the Pauling paradigm. Acc Chem Res 38:379-385.
16. Khersonsky O, Röthlisberger D, Dym O, Albeck S, Jackson CJ, Baker D, Tawfik DS (2010) Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. J Mol Biol 396: 1025-1042.
17. Casey ML, Kemp DS, Paul KG, Cox DD (1973) Physical organic chemistry of benzisoxazoles. I. Mechanism of the base-catalyzed decomposition of benzisoxazoles. J Org Chem 38:2294-2301.
18. Kemp DS, Casey ML (1973) Physical organic chemistry of benzisoxazoles. II. Linearity of the Broensted free energy relation for the base-catalyzed decomposition of benzisoxazoles. J Am Chem Soc 95:6670-6680.
19. Hu Y, Houk KN, Kikuchi K, Hotta K, Hilvert D (2004) 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. (Pubitemid 38878965)
20. Kikuchi K, Thorn SN, Hilvert D (1996) Large rate accelerations in antibody catalysis by strategic use of haptenic charge. J Am Chem Soc 118:8184-8185.
21. Hollfelder F, Kirby AJ, Tawfik DS (2001) Off-the-shelf proteins that rival tailor-made antibodies as catalysts. J Org Chem 66:5866-5874.
22. Perez-Juste J, Hollfelder F, Kirby AJ, Engberts JBFN (2000) Vesicles accelerate proton transfer from carbon up to 850-fold. Org Lett 2:127-130.
23. Shulman H, Keinan E (2000) Catalysis of the Kemp elimination by natural coals. Org Lett 2:3747-3750.
24. Gunaydin H, Houk KN (2008) Molecular dynamics prediction of the mechanism of ester hydrolysis in water. J Am Chem Soc 130:15232-15233.
25. Eigen M, de Maeyer LZ (1955) Untersuchungen ueber die kinetik der neutralisation 1. Z Electrochem59:986-993.
26. Luz Z, Meiboom S (1964) The activation energies of proton transfer reactions in water. J Am Chem Soc 86: 4768-4769.
27. Kemp DS, Cox DD, Paul KG (1975) Physical organic chemistry of benzisoxazoles. IV. Origins and catalytic nature of the solvent rate acceleration for the decarboxylation of 3-carboxybenzisoxazoles. J Am Chem Soc 97: 7312-7318.
28. Kirby AJ (1997) Efficiency of proton transfer catalysis in models and enzymes. Acc Chem Res 30:290-296.
29. Radzicka A, Wolfenden R (1995) A proficient enzyme. Science 267:90-93.
30. Wolfenden R, Ridgway C, Young G (1998) Spontaneous hydrolysis of ionized phosphate monoesters and diesters and the proficiencies of phosphatases and phosphodiesterases as catalysts. J Am Chem Soc 120:833-834. (Pubitemid 28081969)
31. Miller BG, Wolfenden R (2002) Catalytic proficiency: the unusual case of OMP decarboxylase. Annu Rev Biochem 71:847-885.
32. Kemp DS (1995) How to promote proton transfer. Nature 373:196-197.
33. Siegbahn PEM, Himo F (2009) Recent developments of the quantum chemical cluster approach for modeling enzyme reactions. J Biol Inorg Chem 14:643-651.
34. Svensson M, Humbel S, Froese RDJ, Matsubara T, Sieber S, Morokuma K (1996) ONIOM: a multilayered integrated MO+MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)(3))(2)+H-2 oxidative addition. J Phys Chem 100:19357-19363.
35. Alexandrova AN, Röthlisberger D, Baker D, Jorgensen WL (2008) Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. J Am Chem Soc 130:15907-15915.
36. Guimarães CRW, Udier-Blagović M, Jorgensen WL (2005) Macrophomate synthase: QM/MM simulations address the Diels-Alder versus Michael-Aldol reaction mechanism. J Am Chem Soc 127:3577-3588. (Pubitemid 40365296)
37. Tubert-Brohman I, Acevedo O, Jorgensen WL (2006) Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations. J Am Chem Soc 128:16904-16913. (Pubitemid 46032766)
38. Roca M, Vardi-Kilshtain A, Warshel A (2009) Toward accurate screening in computer-aided enzyme design. Biochemistry 48:3046-3056.
39. Steiner T (2002) The hydrogen bond in the solid state. Angew Chem Intl Ed 41:48-76.
40. Kroon J, Kanters JA (1974) Non-linearity of hydrogen bonds in molecular crystals. Nature 248:667-669.
41. Steiner T, Mason SA (2000) Short N+-H center dot center dot center dot Ph hydrogen bonds in ammonium tetraphenylborate characterized by neutron diffraction. Acta Crystallogr B 56:254-260.
42. Jeffrey GA (1997) An introduction to hydrogen bonding. Oxford: Oxford University Press.
43. Bossard MJ, Tomaszek TA, Thompson SK, Amegadzie BY, Hanning CR, Jones C, Kurdyla JT, McNulty DE, Drake FH, Gowen M, Levy MA (1996) Proteolytic activity of human osteoclast cathepsin K: Expression, purification, activation, and substrate identification. J Biol Chem 271:12517-12524.
44. Thompson SK, Halbert SM, Bossard MJ, Tomaszek TA, Levy MA, Zhao B, Smith WW, Abdel-Meguid SS, Janson CA, D'Alessio KJ, McQueney MS, Amegadzie BY, Hanning CR, DesJarlais RL, Briand J, Sarkar SK, Huddleston MJ, Ijames CF, Carr SA, Garnes KT, Shu A, Heys JR, Bradbeer J, Zembryki D, Lee-Rykaczewski L, James IE, Lark MW, Drake FH, Gowen M, Gleason JG, Veber D (1997) Design of potent and selective human cathepsin K inhibitors that span the active site. Proc Natl Acad Sci USA 94:14249-14254.
45. Ruscio JZ, Kohn JE, Ball KA, Head-Gordon T (2009) The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc 131: 14111-14115.
46. Hedstrom L (2002) Serine protease mechanism and specificity. Chem Rev 102:4501-4524.
47. Siegel JB, Zanghellini A, Lovick H, Kiss G, Lambert A, St. Clair J, Gallaher JL, Hilvert D, Gelb M, Stoddard B, Forrest M, Houk KN, Baker D (2010) Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction. Science 329:309-313.
48. Debler EW, Ito S, Seebeck FP, Heine A, Hilvert D, Wilson IA (2005) Structural origins of efficient proton abstraction from carbon by a catalytic antibody. Proc Natl Acad Sci USA 102:4984-4989.
49. Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Crowley M, Walker RC, Zhang W, Merz KM, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Mathews DH, Seetin MG, Sagui C, Babin V, Kollman PA (2008) AMBER 10. San Francisco: University of California.