From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics

Chaturvedi, Shobhit S.; Bím, Daniel; Christov, Christo Z.; Alexandrova, Anastassia N.

doi:10.1039/d3sc02982d

Cited by 5 publications

(5 citation statements)

References 127 publications

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“…Now, we pivot toward analyzing if the electric fields generated by the studied enzyme changes, and its link to protoglobin reactivity. Enzyme catalysis is often attributed to electrostatic preorganization and dynamics, ,− occasionally put in contradiction with each other . We have previously observed that the reactivity of Fe-heme oxidoreductases is strongly regulated by the electric field form the protein scaffold, in addition to the regulation by the axial ligand to Fe .…”

Section: Resultsmentioning

confidence: 99%

Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

Chaturvedi,

Vargas,

Ajmera

et al. 2024

J. Am. Chem. Soc.

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To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory evolution of protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that the previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field in the entire active site is tracked through protein dynamics, clustered using the affinity propagation algorithm, and subjected to principal component analysis. This analysis reveals notable changes in the electric field with DE, where distinct field topologies influence transition state energetics and mechanism. A chemically meaningful field component emerges and takes the lead during DE and facilitates crossing the barrier to carbene transfer. Our findings underscore intrinsic electric field dynamic's influence on enzyme function, the ability of the field to switch mechanisms within the same protein, and the crucial role of the field in enzyme design.

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Section: Resultsmentioning

confidence: 99%

Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

Chaturvedi,

Vargas,

Ajmera

et al. 2024

J. Am. Chem. Soc.

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show abstract

“…License: CC BY-NC 4.0 Now, we pivot towards analyzing if the electric fields generated by the studied enzyme changes, and its link to Protoglobin reactivity. Enzyme catalysis is often attributed to electrostatic preorganization and dynamics, [20][21][22][23][24] occasionally put in contradiction with each other. 25 We have previously observed that the reactivity of Fe-heme oxidoreductases is strongly regulated by the electric field form the protein scaffold, in addition to the regulation by the axial ligand to Fe.…”

Section: Electric Field Evolution During Directed Evolutionmentioning

confidence: 99%

Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field

Chaturvedi,

Vargas,

Ajmera

et al. 2024

Preprint

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To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory evolution of Protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that the previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field in the entire active site is tracked through protein dynamics, clustered using the affinity propagation algorithm, and subjected to principal component analysis. This analysis reveals notable changes in the electric field with DE, where distinct field topologies influence transition state energetics and mechanism. A chemically meaningful field component emerges and takes the lead during DE and facilitates crossing the barrier to carbene transfer. Our findings underscore intrinsic electric field dynamic's influence on enzyme function, the ability of the field to switch mechanisms within the same protein, and the crucial role of the field in enzyme design.

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“…An important aspect of enzyme catalysis lies in the self-folding protein structure, which plays a pivotal role in forming the active site of an enzyme. 1 Therefore, the three-dimensional conformation of enzymes is finely tuned, facilitating a specific reaction at the active site through the interaction with versatile substrate molecules at the binding pocket. Moreover, metal cofactors further contribute to the catalytic prowess of enzymes, serving as essential components that orchestrate precise chemical transformations.…”

Section: Introductionmentioning

confidence: 99%