Energy and conformation determine the enantioselectivity of enzyme

Gao, Bei; Jiang, Shuiqin; Wang, Liuzhu; Zhang, Lujia; Wei, Dongzhi

doi:10.1016/j.bej.2017.10.017

Cited by 8 publications

(2 citation statements)

References 35 publications

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“…The experimental results indicate that EstS and EstR exhibit excellent preference for the S -isomer and R -isomer, respectively. According to a previous study by Bei Gao et al , 19 the binding free energy and binding conformation may be two key factors that affect the enantioselectivity of enzymes. However, the study of the system of Bei Gao et al continues to be unclear, which necessitates elucidation of the chiral selectivity mechanism of esterase.…”

Section: Resultsmentioning

confidence: 98%

Sequential resolution of (S) and (R)-6-fluoro-chroman-2-carboxylic acid by two esterases in turn

Jiang

Liu

et al. 2022

Green Chem.

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Section: Resultsmentioning

confidence: 98%

Sequential resolution of (S) and (R)-6-fluoro-chroman-2-carboxylic acid by two esterases in turn

Jiang

Liu

et al. 2022

Green Chem.

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“…MD runs were performed for 100 ns with a time step of 2 fs at 300 K. The molecular docking of TrL17 with 4-nitrophenyl benzoate was carried out using Schrödinger software ( Godara et al, 2022 ), and the docking results were converted into PDB format using PyMOL. Discovery Studio 2019b (DS) was used to analyze the docking and virtual mutations ( Gao et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE

et al. 2023

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TrLipE is a thermophilic lipase that has potential commercial applications because of its catalytic ability under extreme conditions. Consistent with most lipases, the lid of TrLipE is located over the catalytic pocket, controls the substrate channel to the active center, and regulates the substrate specificity, activity, and stability of the enzyme through conformational changes. TrLipE from Thermomicrobium roseum has potential industrial applications, which is hindered by its weak enzymatic activity. Here, 18 chimeras (TrL1-TrL18) were reconstructed by N-terminal lid swapping between TrLipE and structurally similar enzymes. The results showed that the chimeras had a similar pH range and optimum pH as wild TrLipE but a narrower temperature range of 40–80°C, and TrL17 and the other chimeras showed lower optimum temperatures of 70°C and 60°C, respectively. In addition, the half-lives of the chimeras were lower than those of TrLipE under optimum temperature conditions. Molecular dynamics simulations indicated that chimeras had high RMSD, RMSF, and B-factor values. When p-nitrophenol esters with different chains were used as substrates, compared with TrLipE, most of the chimeras had a low Km and high kcat value. The chimeras TrL2, TrL3, TrL17, and TrL18 could specifically catalyze the substrate 4-nitrophenyl benzoate, with TrL17 showing the highest kcat/Km value of 363.88 ± 15.83 L⋅min–1⋅mmol–1. Mutants were then designed by investigating the binding free energies of TrL17 and 4-nitrophenyl benzoate. The results indicated that single, double, and triple substitution variants (M89W and I206N; E33W/I206M and M89W/I206M; and M89W/I206M/L21I and M89W/I206N/L21I, respectively) presented approximately 2- to 3-fold faster catalysis of 4-nitrophenyl benzoate than the wild TrL17. Our observations will facilitate the development of the properties and industrial applications of TrLipE.

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How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study

et al. 2020

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Expanding synthetic capabilities to routinely employ enzymes in organic solvents (OSs) is a dream for protein engineers and synthetic chemists. Despite significant advances in the field of protein engineering, general and transferable design principles to improve the OS resistance of enzymes are poorly understood. Herein, we report a combined computational and directed evolution study of Bacillus subtlis lipase A (BSLA) in three OSs (i. e., 1,4‐dioxane, dimethyl sulfoxide, 2,2,2‐trifluoroethanol) to devise a rational strategy to guide engineering OS resistant enzymes. Molecular dynamics simulations showed that OSs reduce BSLA activity and resistance in OSs by (i) stripping off essential water molecules from the BLSA surface mainly through H‐bonds binding; and (ii) penetrating the substrate binding cleft leading to inhibition and conformational change. Interestingly, integration of computational results with “BSLA‐SSM” variant library (3439 variants; all natural diversity with amino acid exchange) revealed two complementary rational design strategies: (i) surface charge engineering, and (ii) substrate binding cleft engineering. These strategies are most likely applicable to stabilize other lipases and enzymes and assist experimentalists to design organic solvent resistant enzymes with reduced time and screening effort in lab experiments.

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Energy and conformation determine the enantioselectivity of enzyme

Cited by 8 publications

References 35 publications

Sequential resolution of (S) and (R)-6-fluoro-chroman-2-carboxylic acid by two esterases in turn

Sequential resolution of (S) and (R)-6-fluoro-chroman-2-carboxylic acid by two esterases in turn

N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE

How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study

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