De novo computational design of retro-aldol enzymes

被引：870

作者：

Jiang, Lin ^{[1
,2
]}

Althoff, Eric A. ^{[1
]}

Clemente, Fernando R. ^{[4
]}

Doyle, Lindsey ^{[5
]}

Rothlisberger, Daniela ^{[1
]}

Zanghellini, Alexandre ^{[1
,2
]}

Gallaher, Jasmine L. ^{[1
]}

Betker, Jamie L. ^{[1
]}

Tanaka, Fujie ^{[6
,7
,8
]}

Barbas, Carlos F., III ^{[6
,7
,8
]}

Hilvert, Donald ^{[9
]}

Houk, Kendall N. ^{[4
]}

Stoddard, Barry L. ^{[5
]}

Baker, David ^{[1
,2
,3
]}

机构：

[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA

[2] Univ Washington, Biomol Struct & Design Program, Seattle, WA 98195 USA

[3] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA

[4] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA

[5] Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98109 USA

[6] Scripps Res Inst, Skaggs Inst Chem Biol, La Jolla, CA 92037 USA

[7] Scripps Res Inst, Dept Chem, La Jolla, CA 92037 USA

[8] Scripps Res Inst, Dept Biol Mol, La Jolla, CA 92037 USA

[9] ETH, Organ Chem Lab, CH-8093 Zurich, Switzerland

来源：

SCIENCE | 2008年 / 319卷 / 5868期

关键词：

D O I：

10.1126/science.1152692

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro- aldolases that use four different catalytic motifs to catalyze the breaking of a carbon- carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side- chain networks. The atomic accuracy of the design process was confirmed by the x- ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.

引用

页码：1387 / 1391

页数：5

共 23 条

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