Evolution of a designed retro-aldolase leads to complete active site remodeling
| Autor: | Sami Caner, Lars Giger, David Baker, Nenad Ban, Peter Kast, Donald Hilvert, Richard Obexer |
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| Rok vydání: | 2013 |
| Předmět: |
Models
Molecular Stereochemistry Lysine Protein design 010402 general chemistry Cleavage (embryo) complex mixtures 01 natural sciences Article 03 medical and health sciences Catalytic Domain Computer Simulation Molecular Biology 030304 developmental biology Aldehyde-Lyases 0303 health sciences biology Molecular Structure Aldolase A Active site Computational Biology Cell Biology Directed evolution Lyase 0104 chemical sciences Biochemistry biology.protein Biocatalysis bacteria Directed Molecular Evolution |
| Zdroj: | Nature chemical biology |
| DOI: | 10.1038/nchembio.1276 |
| Popis: | Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that dramatic molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400 fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate, and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes. |
| Databáze: | OpenAIRE |
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