Atomistic insight into the binding mode and self-regulation mechanism of <i>Is</i>PETase towards PET substrates with different polymerization degrees

Chen, Linyu; Fan, Fangfang; Yang, Mingliang; Wang, Linquan; Bai, Y.; Qiu, Shuai; Lyu, Changjiang; Huang, Jun

doi:10.1039/d3cp01700a

Cited by 5 publications

(2 citation statements)

References 63 publications

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“…To assess the binding affinity of DHC within the active sites of the wild-type and m5 variant MPH enzymes, data from the final 50 ns MM MD simulations were utilized for MM/GBSA calculations . The predicted binding affinity of DHC in the m5 variant (−20.7 kcal/mol) is slightly higher than that in wild-type MPH (−17.1 kcal/mol).…”

Section: Resultsmentioning

confidence: 99%

Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations

Fu,

Yu,

Fan

et al. 2024

J. Phys. Chem. B

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Methyl-parathion hydrolase (MPH), which evolved from dihydrocoumarin hydrolase, offers one of the most efficient enzymes for the hydrolysis of methyl-parathion. Interestingly, the substrate preference of MPH shifts from the methyl-parathion to the lactone dihydrocoumarin (DHC) after its mutation of five specific residues (R72L, L273F, L258H, T271I, and S193Δ, m5-MPH). Here, extensive QM/MM calculations and MM MD simulations have been used to delve into the structure−function relationship of MPH enzymes and plausible mechanisms for the chemical and nonchemical steps, including the transportation and binding of the substrate DHC to the active site, the hydrolysis reaction, and the product release. The results reveal that the five mutations remodel the active pocket and reposition DHC within the active site, leading to stronger enzyme−substrate interactions. The MM/GBSA-estimated binding free energies are about −20.7 kcal/mol for m5-MPH and −17.1 kcal/mol for wild-type MPH. Furthermore, this conformational adjustment of the protein may facilitate the chemical step of DHC hydrolysis and the product release, although there is a certain influence on the substrate transport. The hydrolytic reaction begins with the nucleophilic attack of the bridging OH − with the energy barriers of 22.0 and 18.0 kcal/mol for the wild-type and m5-MPH enzymes, respectively, which is rate-determining for the entire process. Unraveling these mechanistic intricacies may help in the understanding of the natural evolution of enzymes for diverse substrates and establish the enzyme structure−function relationship.

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Section: Resultsmentioning

confidence: 99%

Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations

Fu,

Yu,

Fan

et al. 2024

J. Phys. Chem. B

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“…Improper disposal of waste PET poses a significant threat, leading to resource depletion and wastage. 8,9 Extensive efforts have been made to find effective strategies for addressing the challenges associated with PET recycling 10–12 and upcycling. 13–15…”

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confidence: 99%

Metal-free recycling of waste polyethylene terephthalate mediated by TBD protic ionic salts: the crucial role of anionic ligands

Zhu,

Yang,

Chen

et al. 2023

Phys. Chem. Chem. Phys.

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Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases

Xu,

Huo,

Chu

2024

J. Chem. Inf. Model.

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The accumulation of polyethylene terephthalate (PET), a widely used polyester plastic in packaging and textiles, has led to a global environmental crisis. Biodegradation presents a promising strategy for PET recycling, with PET hydrolases (PETase) undertaking the task at the molecular level. Unfortunately, PETase operates only at ambient temperatures with low efficiency, limiting its industrial application. Current engineering efforts focus on enhancing the thermostability of PETase, but increased stability can reduce the structural dynamics needed for substrate binding, potentially slowing enzymatic activity. To elucidate the balance between stability and flexibility in optimizing PETase catalytic activity, we performed theoretical investigations on both wild-type PETase (WT-PETase) and a thermophilic variant (Thermo-PETase) using molecular dynamics simulations and frustration analysis. Despite being initially designed to stabilize the native structure of the enzyme, our findings reveal that Thermo-PETase exhibits an unprecedented increase in structural flexibility at the PET-binding and catalytic sites, beneficial for substrate recruitment and product release, compared to WT-PETase. Upon PET binding, we observed that the structural dynamics of Thermo-PETase is largely quenched, favoring the proximity between the catalytic residues and the carbonyl of the PET substrate. This may potentially contribute to a higher probability of a catalytic reaction occurring in Thermo-PETase compared to WT-PETase. We suggest that Thermo-PETase can exhibit higher PET-degradation performance than WT-PETase across a broad temperature range by leveraging stability and flexibility at high and low temperatures, respectively. Our findings provide valuable insights into how PETase optimizes its enzymatic performance by balancing stability and flexibility, which may contribute to future PETase design strategies.

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Atomistic insight into the binding mode and self-regulation mechanism of IsPETase towards PET substrates with different polymerization degrees

Abstract: Poly(ethylene terephthalate) (PET) is one of the most widely used synthetic polyesters, while its extensive use becomes a long-term environmental burden. Unlike traditional recycling methods, biodegradation is a sustainable strategy....

Cited by 5 publications

References 63 publications

Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations

Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations

Metal-free recycling of waste polyethylene terephthalate mediated by TBD protic ionic salts: the crucial role of anionic ligands

Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases

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