Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis

Ma, Dong; Cheng, Zhongyi; Pepłowski, Łukasz; Han, Laichuang; Xia, Yuanyuan; Hou, Xiaodong; Guo, Junling; Yin, Dejing; Rao, Yijian; Zhou, Zhemin

doi:10.1039/d2sc02319a

Cited by 16 publications

(6 citation statements)

References 48 publications

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“…To further explore the changes introduced by reshaping the binding pocket, the dynamic cross-correlation map (DCCM) analysis was used to assess enzyme system motion during the whole simulation, particularly on the Cα atom positions . Correlated motion is another indicator of improved enzyme structure rigidity.…”

Section: Resultsmentioning

confidence: 99%

“…34 To further explore the changes introduced by reshaping the binding pocket, the dynamic cross-correlation map (DCCM) analysis was used to assess enzyme system motion during the whole simulation, particularly on the Cα atom positions. 31 Correlated motion is another indicator of improved enzyme structure rigidity. As shown in Figure 4, the correlated motion (two residues move to the same direction) and the anticorrelated motion (two residues move to the opposite direction) are represented as red and blue regions, respectively, while white regions have a low correlation.…”

Section: Evolution Of a Dynamical Networkmentioning

confidence: 99%

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Simultaneously Enhanced Catalytic Activity and Thermostability of a Baeyer–Villiger Monooxygenase from Oceanicola granulosus by Reshaping the Binding Pocket

Du,

Lv,

Feng

et al. 2024

J. Agric. Food Chem.

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Enzymatic oxygenation of various cyclic ketones into lactones via Baeyer−Villiger monooxygenases (BVMOs) could provide a promising route for synthesizing fragrances and pharmaceutical ingredients. However, unsatisfactory catalytic activity and thermostability restricted their applications in the pharmaceutical and food industries. In this study, we successfully improved the catalytic activity and thermostability of a Baeyer−Villiger monooxygenase (OgBVMO) from Oceanicola granulosus by reshaping the binding pocket. As a result, mutant OgBVMO-Re displayed a 1.0-to 6.4-fold increase in the activity toward branched cyclic ketones tested, accompanied by a 3 °C higher melting point, and a 2-fold longer half-life time (t 1/2 (45 °C)). Molecular dynamics simulations revealed that reshaping the binding pocket achieved strengthened motion correlation between amino acid residues, appropriate size of the substrate-binding pocket, beneficial surface characteristics, lower energy barriers, and shorter nucleophilic distance. This study well demonstrated the trade-off between the enzyme activity and thermostability by reshaping the substrate-binding pocket, paving the way for further engineering other enzymes.

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Section: Resultsmentioning

confidence: 99%

Section: Evolution Of a Dynamical Networkmentioning

confidence: 99%

Simultaneously Enhanced Catalytic Activity and Thermostability of a Baeyer–Villiger Monooxygenase from Oceanicola granulosus by Reshaping the Binding Pocket

Du,

Lv,

Feng

et al. 2024

J. Agric. Food Chem.

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show abstract

“…S3, ESI †) show that the structure is preserved during the MD simulations and the time evolution is very similar to other studies. 14,15,[18][19][20] Since the heterotetramer model was simulated in each simulation, we could analyze two dimers, each interacting with the ligand, and thus our statistics are twice better.…”

Section: Resultsmentioning

confidence: 99%

Highly efficient biosynthesis of isonicotinamide through a substrate access tunnel engineered nitrile hydratase from Carbonactinospora thermoautotrophicus

Guo¹,

Cheng²,

Pepłowski³

et al. 2023

New J. Chem.

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“…It has a buried active site so that the nitrile substrate should pass through a tunnel to access it. Recently, Zhou and his team successfully broadened the substrate scope of nitrile hydratase through mutation of two tunnel entrance residues, which also provided dynamic evidence for insight into enzyme substrate scope broadening . The details of tunnel engineering will be specified in the following, including the identification and modification methods of tunnels.…”

Section: Tunnel Engineering Of Lipasementioning

confidence: 99%

Computer-Aided Tunnel Engineering: A Promising Strategy for Improving Lipase Applications in Esterification Reactions

Chong,

Qi,

et al. 2023

ACS Catal.

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Esterification is one of the most important reactions in organic synthesis and industrial applications. The applications of lipases in esterification are increasingly widespread and have high cumulative values. Mostly, in the catalytic cycle of lipases, the tunnel connecting the active site to the surface of a protein plays a significant role in ligand transport. As a unique conformational structure of a protein, the tunnel could regulate the catalytic performance of lipases via ligand transportation. Therefore, the tunnel of lipase can be designed accordingly to speed up the transportation of the ligand, also highlighting the importance of tunnel engineering in the industrial application of enzymatic esterification reactions. This article reviewed the characterizations of the tunnel structure and focused on the strategies of tunnel engineering, such as rational design and directed evolution. Additionally, tunnel engineering using computer-aided design techniques (e.g., CAVER, Molecular Dynamics simulations) to improve the catalytic functions of lipases, such as activity, substrate specificity, and stability, was also discussed in depth. Finally, this review provides future perspectives about tunnel-engineered lipases as biocatalysts in esterification reactions.

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Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis

Abstract: Mutations of two gating residues at the substrate access tunnel entrance direct the substrate scope of NHases.

Cited by 16 publications

References 48 publications

Simultaneously Enhanced Catalytic Activity and Thermostability of a Baeyer–Villiger Monooxygenase from Oceanicola granulosus by Reshaping the Binding Pocket

Simultaneously Enhanced Catalytic Activity and Thermostability of a Baeyer–Villiger Monooxygenase from Oceanicola granulosus by Reshaping the Binding Pocket

Highly efficient biosynthesis of isonicotinamide through a substrate access tunnel engineered nitrile hydratase from Carbonactinospora thermoautotrophicus

Computer-Aided Tunnel Engineering: A Promising Strategy for Improving Lipase Applications in Esterification Reactions

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