Harnessing Conformational Plasticity to Generate Designer Enzymes

Crean, Rory; Gardner, Jasmine M.; Kamerlin, Shina Caroline Lynn

doi:10.1021/jacs.0c04924

Cited by 100 publications

(128 citation statements)

References 250 publications

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“…Small geometry changes in the protein will produce slight changes in the electric field and, so, in its catalytic effect. Recently, the role of conformational dynamics in the emergence of new enzymes has been emphasized [44] . In particular, the flexibility of the protein being used in the design of a new Kemp eliminase has been studied [45,46] …”

Section: Resultsmentioning

confidence: 99%

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Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

et al. 2020

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The effect of solvent reaction fields and oriented electric fields on the Kemp elimination reaction between methylamine or imidazole and 5-nitrobenzisoxazole has been theoretically studied. The Kemp reaction is the most widely used for the design of new enzymes. Our results, using the SMD continuous model for solvents, are in quite good agreement with the experimental fact that the rate of the analogous reaction with butylamine is one order of magnitude smaller in water than in acetonitrile. In the case of external electric fields, our results show that they can increase or decrease the energy barrier depending on the magnitude and orientation of the field. A duly oriented electric field may have a notable catalytic effect on the reaction. So, external electric fields and reaction fields due to the medium can contribute to the design of new enzymes. Several factors that must be taken into account to increase the catalytic effect are discussed.

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Section: Resultsmentioning

confidence: 99%

“…Recently, the role of conformational dynamics in the emergence of new enzymes has been emphasized. [44] In particular, the flexibility of the protein being used in the design of a new Kemp eliminase has been studied. [45,46]…”

Section: Implications In the De Novo Design Of A Kemp Eliminasementioning

confidence: 99%

Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

et al. 2020

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“…It also evidences that conformational heterogeneity and, in particular, the use of ancestral conformationally-rich scaffolds corresponds to a successful strategy for designing desired enzymatic functions. 41,45…”

Section: Discussionmentioning

confidence: 99%

Rational Prediction of Distal Activity-Enhancing Mutations in Tryptophan Synthase

Maria-Solano¹,

Kinateder²,

Iglésias-Fernández³

et al. 2021

Preprint

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Allostery is a central mechanism for the regulation of multi-enzyme complexes. The mechanistic basis that drives allosteric regulation is poorly understood, but harbors key information for enzyme engineering. In the present study, we focus on the tryptophan synthase complex that is composed of TrpA and TrpB subunits, which allosterically activate each other. Specifically, we develop a rational approach for identifying key amino acid residues of TrpB distal from the active site. In particular, we predict positions crucial for shifting the inefficient conformational ensemble of the isolated TrpB to a productive ensemble through intra-subunit allosteric effects. The experimental validation of the new conformationally-driven TrpB design demonstrates its superior stand-alone activity in the absence of TrpA, comparable to those enhancements obtained after multiple rounds of experimental laboratory evolution. Our work evidences that the current challenge of distal active site prediction for enhanced function in computational enzyme design can be ultimately addressed.

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“…In an apparently conflicting observation, highly disordered proteins can also exhibit high evolutionary rates ( 27 ), potentially because mutations have little influence on their ability to function and therefore have high innovability, as depicted in Figure 2 B . Furthermore, conformational plasticity and dynamics, rather than rigidity, is correlated with functional promiscuity, another feature thought to enable innovability ( 28 , 29 , 30 , 31 ). These disparate concepts have raised the question of whether there exists a structural order–disorder paradox ( 20 ).…”

Section: Factors That Drive Evolution and The Diversification Of Funcmentioning

confidence: 99%

Linking molecular evolution to molecular grafting

Wang

Craik

2021

Journal of Biological Chemistry

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Harnessing Conformational Plasticity to Generate Designer Enzymes

Cited by 100 publications

References 250 publications

Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

Rational Prediction of Distal Activity-Enhancing Mutations in Tryptophan Synthase

Linking molecular evolution to molecular grafting

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