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Computational Enzyme Design

Authors

  • Dr. Gert Kiss,

    1. Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles CA, 90095 (USA)
    2. Current address: Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
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  • Dr. Nihan Çelebi-Ölçüm,

    1. Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles CA, 90095 (USA)
    2. Current address: Yeditepe University, Department of Chemical Engineering, Istanbul (Turkey)
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  • Dr. Rocco Moretti,

    1. Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 (USA)
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  • Prof. Dr. David Baker,

    1. Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 (USA)
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  • Prof. Dr. Dr. K. N. Houk

    Corresponding author
    1. Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles CA, 90095 (USA)
    • Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles CA, 90095 (USA)

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Abstract

Recent developments in computational chemistry and biology have come together in the “inside-out” approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational “inside-out” design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.

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