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Review
. 2022 May;47(5):375-389.
doi: 10.1016/j.tibs.2021.08.008. Epub 2021 Sep 17.

Exploiting enzyme evolution for computational protein design

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Free article
Review

Exploiting enzyme evolution for computational protein design

Gaspar P Pinto et al. Trends Biochem Sci. 2022 May.
Free article

Abstract

Recent years have seen an explosion of interest in understanding the physicochemical parameters that shape enzyme evolution, as well as substantial advances in computational enzyme design. This review discusses three areas where evolutionary information can be used as part of the design process: (i) using ancestral sequence reconstruction (ASR) to generate new starting points for enzyme design efforts; (ii) learning from how nature uses conformational dynamics in enzyme evolution to mimic this process in silico; and (iii) modular design of enzymes from smaller fragments, again mimicking the process by which nature appears to create new protein folds. Using showcase examples, we highlight the importance of incorporating evolutionary information to continue to push forward the boundaries of enzyme design studies.

Keywords: conformational dynamics; directed evolution; enhanced sampling approaches; residue coevolution; structural bioinformatics.

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Conflict of interest statement

Declaration of interests No interests are declared.

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