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. 2011;6(5):e19230.
doi: 10.1371/journal.pone.0019230. Epub 2011 May 16.

De novo enzyme design using Rosetta3

Florian Richter  1 , Andrew Leaver-Fay, Sagar D Khare, Sinisa Bjelic, David Baker
Affiliations

De novo enzyme design using Rosetta3

Florian Richter et al. PLoS One. 2011.

Abstract

The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest. The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Isomerization of DiDihydroxy-acetone-phosphate (DHAP) to Glyceraldehyde-3-phosphate (GAP).
Figure 2
Figure 2. Flowchart of the enzyme design protocol, colored according to the different stages.
Stage 1: light green; Stage 2: green; Stage 3: cyan; Stage 4: blue.
Figure 3
Figure 3. Theozyme geometries.
Top left: Interaction 1; top right: Interaction 3; bottom: Interaction 2; Color scheme: distanceAB: blue, angle_A: purple, angle_B: yellow, torsion_A: cyan, torsion_AB: orange, torsion_B: ligt brown.
Figure 4
Figure 4. Crystal structure of S. cerevisiae TIM with substrate and the three most critical catalytic residues shown in stick representation.
Figure 5
Figure 5. Proposed reaction mechanism of the DHAP to GAP isomerization as catalyzed by S. cerevisiae TIM.
In the top left panel, substrate atoms are labeled according to their label in the theozyme model.
See this image and copyright information in PMC

References

    1. Siegel JustinB, et al. “Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction,” . Science. 2010;329, no.5989:309–313. (New York, N.Y.) - PMC - PubMed
    1. Röthlisberger Daniela, et al. “Kemp elimination catalysts by computational enzyme design,”. Nature. 2008;453, no.7192:190–195. - PubMed
    1. Lin Jiang, et al. “De novo computational design of retro-aldol enzymes,” . Science. 2008;319, no.5868:1387–1391. (New York, N.Y.) - PMC - PubMed
    1. Garcia-Viloca Mireia, et al. “How enzymes work: analysis by modern rate theory and computer simulations,”. Science. 2004;303, no.5655:186–195. (New York, N.Y.) - PubMed
    1. Tantillo DJ, Chen J, Houk KN. “Theozymes and compuzymes: theoretical models for biological catalysis,” . Current Opinion in Chemical Biology. 1998;2, no.6:743–750. - PubMed

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