GRAPE, a greedy accumulated strategy for computational protein engineering.
| Autor: | Sun J; CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China., Cui Y; CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China., Wu B; CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. Electronic address: wub@im.ac.cn. |
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| Jazyk: | angličtina |
| Zdroj: | Methods in enzymology [Methods Enzymol] 2021; Vol. 648, pp. 207-230. Date of Electronic Publication: 2021 Feb 01. |
| DOI: | 10.1016/bs.mie.2020.12.026 |
| Abstrakt: | Nature harbors fascinating enzymatic catalysts with high efficiency, chemo-, regio- and stereoselectivity. However, the insufficient stability of the enzymes often prevents their widespread utilization for industrial processes. Not content with the finite repertoire of naturally occurring enzymes, protein engineering holds promises to extend the applications of the improved enzymes with desired physical and catalytic properties. Herein, we devised a computational strategy (greedy accumulated strategy for protein engineering, GRAPE) to enhance the thermostability of enzymes. Through scanning of all point mutations of the structural and evolutionary consensus analysis, a library containing fewer than 100 mutations was established for characterization. After preliminary experimental verification, effective mutations are clustered in a multidimensional physical property space and then accumulated via the greedy algorithm to produce the final designed enzyme. Using the recently reported IsPETase from Ideonella sakaiensis that decomposes PET under ambient temperatures as a starting point, we adopted the GRAPE strategy to come up with a DuraPETase (T (© 2021 Elsevier Inc. All rights reserved.) |
| Databáze: | MEDLINE |
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