De novo computational design of retro-aldol enzymes

Science

Volumn 319, Issue 5868, 2008, Pages 1387-1391

  Jiang, Lin ^a,b   Althoff, Eric A ^a   Clemente, Fernando R ^c   Doyle, Lindsey ^d   Röthlisberger, Daniela ^a   Zanghellini, Alexandre ^a,b   Gallaher, Jasmine L ^a   Betker, Jamie L ^a   Tanaka, Fujie ^e   Barbas III, Carlos F ^e   Hilvert, Donald ^f   Houk, Kendall N ^c   Stoddard, Barry L ^d   Baker, David ^a,b  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Fred Hutchinson Cancer Research Center   (United States)

^e SCRIPPS RESEARCH INSTITUTE   (United States)

^f ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; FRUCTOSE BISPHOSPHATE ALDOLASE; PROTON; WATER;

ALGORITHM; CATALYSIS; COMPUTER AIDED DESIGN; CRYSTAL STRUCTURE; ENZYME ACTIVITY; EXPERIMENTAL STUDY; PROTEOMICS; X-RAY SPECTROSCOPY;

ACCURACY; ARTICLE; CHEMICAL BOND; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SYNTHESIS; MATHEMATICAL COMPUTING; MOLECULE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN MOTIF; X RAY CRYSTALLOGRAPHY;

ALDEHYDE-LYASES; ALGORITHMS; BINDING SITES; CATALYSIS; CATALYTIC DOMAIN; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; HYDROPHOBICITY; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN ENGINEERING;

EID: 40449116114     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1152692     Document Type: Article

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26. Kinetic parameters of the designs reported here were determined at the University of Washington. For selected designs, the kinetic parameters were confirmed by independent experiments performed at the Scripps Research Institute. We thank R. Fuller for technical assistance. Thorough testing of the four catalytic motifs was made possible through gene synthesis by Codon Devices. We thank Rosetta@Home participants for their valuable contributions of computer time. E.A.A. is funded by a Ruth L. Kirschstein National Research Service Award. This work was supported by the Defense Advanced Research Projects Agency and HHMI. Coordinates and structure factors for the crystal structures of RA22 variant S210A and RA61 variant M48K were deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank (PDB) under the accession numbers 3B5V and 3B5L, respectively. The xyz coordinates of the designs RA22, RA34, RA45, RA46, RA60, and RA61 are included with the SOM as a zipped archive.