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De novo computational design of retro-aldol enzymes.

Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D
Science 319 1387-91 (2008)
Cited: 559 times
EuropePMC logo PMID: 18323453

Abstract

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.

Articles - 3b5l mentioned but not cited (2)

  1. De novo computational design of retro-aldol enzymes. Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D. Science 319 1387-1391 (2008)
  2. A score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness. Martínez-Castilla LP, Rodríguez-Sotres R. PLoS One 5 e12483 (2010)


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