Computational design of catalytic dyads and oxyanion holes for ester hydrolysis

Richter, Florian; Blomberg, Rebecca; Khare, Sagar D.; Kiss, Gert; Kuzin, Alexandre P.; Smith, Adam J. T.; Gallaher, Jasmine; Pianowski, Zbigniew; Helgeson, Roger C.; Grjasnow, Alexej; Xiao, Rong; Seetharaman, Jayaraman; Su, Min; Vorobiev, Sergey; Lew, Scott; Forouhar, Farhad; Kornhaber, Gregory J.; Hunt, John F.; Montelione, Gaetano T.; Tong, Liang; Houk, K. N.; Hilvert, Donald; Baker, David

doi:10.1021/ja3037367

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	Computational design of catalytic dyads and oxyanion holes for ester hydrolysis
Authors:	Richter, Florian Blomberg, Rebecca Khare, Sagar D. Kiss, Gert Kuzin, Alexandre P. Smith, Adam J. T. Gallaher, Jasmine Pianowski, Zbigniew Helgeson, Roger C. Grjasnow, Alexej Xiao, Rong Seetharaman, Jayaraman Su, Min Vorobiev, Sergey Lew, Scott Forouhar, Farhad Kornhaber, Gregory J. Hunt, John F. Montelione, Gaetano T. Tong, Liang Houk, K. N. Hilvert, Donald Baker, David
DOI:	10.1021/ja3037367
Published in:	Journal of the American Chemical Society
Volume(Issue):	134
Issue:	39
Page(s):	16197
Pages to:	16206
Issue Date:	2012
Publisher / Ed. Institution:	American Chemical Society
ISSN:	0002-7863 1520-5126
Language:	English
Subjects:	Catalytic domain; Esterases; Esters; Hydrogen bonding; Hydrolysis; Kinetics; Biocatalysis; Drug design; Molecular models
Subject (DDC):	540: Chemistry
Abstract:	Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.
URI:	https://digitalcollection.zhaw.ch/handle/11475/9665
Fulltext version:	Published version
License (according to publishing contract):	Licence according to publishing contract
Departement:	Life Sciences and Facility Management
Appears in collections:	Publikationen Life Sciences und Facility Management

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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., Xiao, R., Seetharaman, J., Su, M., Vorobiev, S., Lew, S., Forouhar, F., Kornhaber, G. J., Hunt, J. F., Montelione, G. T., et al. (2012). Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Journal of the American Chemical Society, 134(39), 16197–16206. https://doi.org/10.1021/ja3037367

Richter, F. et al. (2012) ‘Computational design of catalytic dyads and oxyanion holes for ester hydrolysis’, Journal of the American Chemical Society, 134(39), pp. 16197–16206. Available at: https://doi.org/10.1021/ja3037367.

F. Richter et al., “Computational design of catalytic dyads and oxyanion holes for ester hydrolysis,” Journal of the American Chemical Society, vol. 134, no. 39, pp. 16197–16206, 2012, doi: 10.1021/ja3037367.

RICHTER, Florian, Rebecca BLOMBERG, Sagar D. KHARE, Gert KISS, Alexandre P. KUZIN, Adam J. T. SMITH, Jasmine GALLAHER, Zbigniew PIANOWSKI, Roger C. HELGESON, Alexej GRJASNOW, Rong XIAO, Jayaraman SEETHARAMAN, Min SU, Sergey VOROBIEV, Scott LEW, Farhad FOROUHAR, Gregory J. KORNHABER, John F. HUNT, Gaetano T. MONTELIONE, Liang TONG, K. N. HOUK, Donald HILVERT und David BAKER, 2012. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Journal of the American Chemical Society. 2012. Bd. 134, Nr. 39, S. 16197–16206. DOI 10.1021/ja3037367

Richter, Florian, Rebecca Blomberg, Sagar D. Khare, Gert Kiss, Alexandre P. Kuzin, Adam J. T. Smith, Jasmine Gallaher, et al. 2012. “Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis.” Journal of the American Chemical Society 134 (39): 16197–206. https://doi.org/10.1021/ja3037367.

Richter, Florian, et al. “Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis.” Journal of the American Chemical Society, vol. 134, no. 39, 2012, pp. 16197–206, https://doi.org/10.1021/ja3037367.