Solvent induced conformational changes for the altered activity of laccase: A molecular dynamics study

Radhakrishnan, Rokesh; Manna, Bharat; Ghosh, Amit

doi:10.1016/j.jhazmat.2021.127123

Cited by 11 publications

(2 citation statements)

References 51 publications

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“…MD simulation provides insights into molecular mechanism at nanosecond scale with improved accuracy (Dodson & Verma, 2006; Radhakrishnan et al, 2022; Rezaei et al, 2007). To explore the mechanism of solvent‐tolerance variants, 100 ns MD simulations of Kp ADH and its variants (V231D and S237G) were performed three times (Figures S2–S5).…”

Section: Resultsmentioning

confidence: 99%

Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance

Zhang,

Dai,

Rong

et al. 2024

Protein Science

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Alcohol dehydrogenases (ADHs) are synthetically important biocatalysts for the asymmetric synthesis of chiral alcohols. The catalytic performance of ADHs in the presence of organic solvents is often important since most prochiral ketones are highly hydrophobic. Here, the organic solvent tolerance of KpADH from Kluyveromyces polyspora was semi‐rationally evolved. Using tolerant variants obtained, meticulous experiments and computational studies were conducted to explore properties including stability, activity and kinetics in the presence of various organic solvents. Compared with WT, variant V231D exhibited 1.9‐fold improvement in ethanol tolerance, while S237G showed a 6‐fold increase in catalytic efficiency, a higher , as well as 15% higher tolerance in 7.5% (v/v) ethanol. Based on 3 × 100 ns MD simulations, the increased tolerance of V231D and S237G against ethanol may be ascribed to their enhanced ability in retaining water molecules and repelling ethanol molecules. Moreover, 6.3‐fold decreased KM value of V231D toward hydrophilic ketone substrate confirmed its capability of retaining hydration shell. Our results suggest that retaining hydration shell surrounding KpADH is critical for its tolerance to organic solvents, as well as catalytic performance. This study provides useful guidance for engineering organic solvent tolerance of KpADH and other ADHs.

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Section: Resultsmentioning

confidence: 99%

Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance

Zhang,

Dai,

Rong

et al. 2024

Protein Science

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“…Acetonitrile can also form a strong hydrogen bond interaction with the amino acid residues at the catalytic site of laccase, which affects the catalysis of the substrate. In addition, acetonitrile may also change the tertiary structure of laccase, resulting in the decrease in laccase stability [39].…”

Section: Enzymatic Properties Of Lac-4 Laccasementioning

confidence: 99%

Degradation and Detoxification of Chlorophenols with Different Structure by LAC-4 Laccase Purified from White-Rot Fungus Ganoderma lucidum

Deng

Zhao

Yang

2022

IJERPH

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A laccase named LAC-4 was purified from Ganoderma lucidum. Firstly, the enzymatic properties of purified LAC-4 laccase, and the degradation of three chlorophenol pollutants 2,6-dichlorophenol (2,6-DCP), 2,3,6-trichlorophenol (2,3,6-TCP) and 3-chlorophenol (3-CP) by LAC-4 were systematically studied. LAC-4 had a strong ability for 2,6-DCP and 2,3,6-TCP degradation. The degradation ability of LAC-4 to 3-CP was significantly lower than that of 2,6-DCP and 2,3,6-TCP. LAC-4 also had a good degradation effect on the chlorophenol mixture (2,6-DCP + 2,3,6-TCP). The results of kinetics of degradation of chlorophenols by LAC-4 suggested that the affinity of LAC-4 for 2,6-DCP was higher than 2,3,6-TCP. The catalytic efficiency and the catalytic rate of LAC-4 on 2,6-DCP were also significantly higher than 2,3,6-TCP. During degradation of 2,6-DCP and 2,3,6-TCP, LAC-4 had a strong tolerance for high concentrations of different metal salts (such as MnSO4, ZnSO4, Na2SO4, MgSO4, CuSO4, K2SO4) and organic solvents (such as ethylene glycol and glycerol). Next, detoxification of chlorophenols by LAC-4 was also systematically explored. LAC-4 treatment had a strong detoxification ability and a good detoxification effect on the phytotoxicity of individual chlorophenols (2,6-DCP, 2,3,6-TCP) and chlorophenol mixtures (2,6-DCP + 2,3,6-TCP). The phytotoxicities of 2,6-DCP, 2,3,6-TCP and chlorophenol mixtures (2,6-DCP + 2,3,6-TCP) treated with LAC-4 were considerably reduced or eliminated. Finally, we focused on the degradation mechanisms and pathways of 2,6-DCP and 2,3,6-TCP degradation by LAC-4. The putative transformation pathway of 2,6-DCP and 2,3,6-TCP catalyzed by laccase was revealed for the first time. The free radicals formed by LAC-4 oxidation of 2,6-DCP and 2,3,6-TCP produced dimers through polymerization. LAC-4 catalyzed the polymerization of 2,6-DCP and 2,3,6-TCP, forming dimer products. LAC-4 catalyzed 2,6-DCP into two main products: 2,6-dichloro-4-(2,6-dichlorophenoxy) phenol and 3,3′,5,5′-tetrachloro-4,4′-dihydroxybiphenyl. LAC-4 catalyzed 2,3,6-TCP into two main products: 2,3,6-trichloro-4-(2,3,6-trichlorophenoxy) phenol and 2,2′,3,3′,5,5′-hexachloro-[1,1′-biphenyl]-4,4′-diol.

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Copper formate–lysine nanoparticles with polyphenol oxidase-like activity for the detection of epinephrine

Sun,

Zhou,

Qiu

et al. 2023

Anal Bioanal Chem

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Solvent induced conformational changes for the altered activity of laccase: A molecular dynamics study

Cited by 11 publications

References 51 publications

Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance

Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance

Degradation and Detoxification of Chlorophenols with Different Structure by LAC-4 Laccase Purified from White-Rot Fungus Ganoderma lucidum

Copper formate–lysine nanoparticles with polyphenol oxidase-like activity for the detection of epinephrine

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