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Sahihi M, Fayon P, Nauton L, Goujon F, Devémy J, Dequidt A, Hauret P, Malfreyt P. Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability. J Chem Inf Model 2024; 64:4112-4120. [PMID: 38703106 DOI: 10.1021/acs.jcim.4c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
Understanding the mechanisms influencing poly(ethylene terephthalate) (PET) biodegradation is crucial for developing innovative strategies to accelerate the breakdown of this persistent plastic. In this study, we employed all-atom molecular dynamics simulation to investigate the adsorption process of the LCC-ICCG cutinase enzyme onto the PET surface. Our results revealed that hydrophobic, π-π, and H bond interactions, specifically involving aliphatic, aromatic, and polar uncharged amino acids, were the primary driving forces for the adsorption of the cutinase enzyme onto PET. Additionally, we observed a negligible change in the enzyme's tertiary structure during the interaction with PET (RMSD = 1.35 Å), while its secondary structures remained remarkably stable. Quantitative analysis further demonstrated that there is about a 24% decrease in the number of enzyme-water hydrogen bonds upon adsorption onto the PET surface. The significance of this study lies in unraveling the molecular intricacies of the adsorption process, providing valuable insights into the initial steps of enzymatic PET degradation.
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Affiliation(s)
- Mehdi Sahihi
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Pierre Fayon
- CHU Clermont Ferrand, Clermont Auvergne INP, CNRS, ICCF, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Lionel Nauton
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Florent Goujon
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Julien Devémy
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Alain Dequidt
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Patrice Hauret
- Manufacture Francaise des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Clermont Auvergne INP, CNRS, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
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2
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Amalia L, Chang CY, Wang SSS, Yeh YC, Tsai SL. Recent advances in the biological depolymerization and upcycling of polyethylene terephthalate. Curr Opin Biotechnol 2024; 85:103053. [PMID: 38128200 DOI: 10.1016/j.copbio.2023.103053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Polyethylene terephthalate (PET) is favored for its exceptional properties and widespread daily use. This review highlights recent advancements that enable the development of biological tools for PET decomposition, transforming PET into valuable platform chemicals and materials in upcycling processes. Enhancing PET hydrolases' catalytic activity and efficiency through protein engineering strategies is a priority, facilitating more effective PET waste management. Efforts to create novel PET hydrolases for large-scale PET depolymerization continue, but cost-effectiveness remains challenging. Hydrolyzed monomers must add additional value to make PET recycling economically attractive. Valorization of hydrolysis products through the upcycling process is expected to produce new compounds with different values and qualities from the initial polymer, making the decomposed monomers more appealing. Advances in synthetic biology and enzyme engineering hold promise for PET upcycling. While biological depolymerization offers environmental benefits, further research is needed to make PET upcycling sustainable and economically feasible.
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Affiliation(s)
- Lita Amalia
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Chia-Yu Chang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Steven S-S Wang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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3
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Oda K, Wlodawer A. Development of Enzyme-Based Approaches for Recycling PET on an Industrial Scale. Biochemistry 2024. [PMID: 38285602 DOI: 10.1021/acs.biochem.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Pollution by plastics such as polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), polyurethane (PUR), polyamide (PA), polystyrene (PS), and poly(ethylene terephthalate) (PET) is now gaining worldwide attention as a critical environmental issue, closely linked to climate change. Among them, PET is particularly prone to hydrolysis, breaking down into its constituents, ethylene glycol (EG) and terephthalate (TPA). Biorecycling or bioupcycling stands out as one of the most promising methods for addressing PET pollution. For dealing with pollution by the macrosize PET, a French company Carbios has developed a pilot-scale plant for biorecycling waste PET beverage bottles into new bottles using derivatives of thermophilic leaf compost cutinase (LCC). However, this system still provides significant challenges in its practical implementation. For the micro- or nanosize PET pollution that poses significant human health risks, including cancer, no industrial-scale approach has been established so far, despite the need to develop such technologies. In this Perspective, we explore the enhancement of the low activity and thermostability of the enzyme PETase to match that of LCC, along with the potential application of microbes and enzymes for the treatment of waste PET as microplastics. Additionally, we discuss the shortcomings of the current biorecycling protocols from a life cycle assessment perspective, covering aspects such as the diversity of PET-hydrolyzing enzymes in nature, the catalytic mechanism for crystallized PET, and more. We also provide an overview of the Ideonella sakaiensis system, highlighting its ability to operate and grow at moderate temperatures, in contrast to high-temperature processes.
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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4
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Fonseca LP, Taipa MÂ. One-Step Purification of Recombinant Cutinase from an E. coli Extract Using a Stabilizing Triazine-Scaffolded Synthetic Affinity Ligand. Biomimetics (Basel) 2024; 9:57. [PMID: 38275454 PMCID: PMC10813525 DOI: 10.3390/biomimetics9010057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Cutinase from Fusarium solani pisi is an enzyme that bridges functional properties between lipases and esterases, with applications in detergents, food processing, and the synthesis of fine chemicals. The purification procedure of recombinant cutinase from E. coil extracts is a well-established but time-consuming process, which involves a sequence of two anionic exchange chromatography steps followed by dialysis. Affinity chromatography is the most efficient method for protein purification, the major limitation of its use being often the availability of a ligand selective for a given target protein. Synthetic affinity ligands that specifically recognize certain sites on the surface of proteins are highly desirable for affinity processes due to their cost-effectiveness, durability, and reusability across multiple cycles. Additionally, these ligands establish moderate affinity interactions with the target protein, making it possible to purify proteins under gentle conditions while maintaining high levels of activity recovery. This study aimed to develop a new method for purifying cutinase, utilizing triazine-scaffolded biomimetic affinity ligands. These ligands were previously screened from a biased-combinatorial library to ensure their binding ability to cutinase without compromising its biological function. A lead ligand, designated as 11/3', [4-({4-chloro-6-[(2-methylbutyl)amino]-1,3,5-triazin-2-yl}amino)benzoic acid], was chosen and directly synthesized onto agarose. Experiments conducted at different scales demonstrated that this ligand (with an affinity constant Ka ≈ 104 M-1) exhibited selectivity towards cutinase, enabling the purification of the enzyme from an E. coli crude production medium in a single step. Under optimized conditions, the protein and activity yields reached 25% and 90%, respectively, with a resulting cutinase purity of 85%.
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Affiliation(s)
- Luís P. Fonseca
- Department of Bioengineering, Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- Institute for Bioengineering and Biosciences (iBB), Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
| | - M. Ângela Taipa
- Department of Bioengineering, Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- Institute for Bioengineering and Biosciences (iBB), Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
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5
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Sui B, Wang T, Fang J, Hou Z, Shu T, Lu Z, Liu F, Zhu Y. Recent advances in the biodegradation of polyethylene terephthalate with cutinase-like enzymes. Front Microbiol 2023; 14:1265139. [PMID: 37849919 PMCID: PMC10577388 DOI: 10.3389/fmicb.2023.1265139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Polyethylene terephthalate (PET) is a synthetic polymer in the polyester family. It is widely found in objects used daily, including packaging materials (such as bottles and containers), textiles (such as fibers), and even in the automotive and electronics industries. PET is known for its excellent mechanical properties, chemical resistance, and transparency. However, these features (e.g., high hydrophobicity and high molecular weight) also make PET highly resistant to degradation by wild-type microorganisms or physicochemical methods in nature, contributing to the accumulation of plastic waste in the environment. Therefore, accelerated PET recycling is becoming increasingly urgent to address the global environmental problem caused by plastic wastes and prevent plastic pollution. In addition to traditional physical cycling (e.g., pyrolysis, gasification) and chemical cycling (e.g., chemical depolymerization), biodegradation can be used, which involves breaking down organic materials into simpler compounds by microorganisms or PET-degrading enzymes. Lipases and cutinases are the two classes of enzymes that have been studied extensively for this purpose. Biodegradation of PET is an attractive approach for managing PET waste, as it can help reduce environmental pollution and promote a circular economy. During the past few years, great advances have been accomplished in PET biodegradation. In this review, current knowledge on cutinase-like PET hydrolases (such as TfCut2, Cut190, HiC, and LCC) was described in detail, including the structures, ligand-protein interactions, and rational protein engineering for improved PET-degrading performance. In particular, applications of the engineered catalysts were highlighted, such as improving the PET hydrolytic activity by constructing fusion proteins. The review is expected to provide novel insights for the biodegradation of complex polymers.
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Affiliation(s)
- Beibei Sui
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Jingxiang Fang
- Rizhao Administration for Market Regulation, Rizhao, Shandong, China
| | - Zuoxuan Hou
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Ting Shu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Zhenhua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Youshuang Zhu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
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6
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Tournier V, Duquesne S, Guillamot F, Cramail H, Taton D, Marty A, André I. Enzymes' Power for Plastics Degradation. Chem Rev 2023; 123:5612-5701. [PMID: 36916764 DOI: 10.1021/acs.chemrev.2c00644] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.
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Affiliation(s)
- Vincent Tournier
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Sophie Duquesne
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Frédérique Guillamot
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Henri Cramail
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Daniel Taton
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Alain Marty
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
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7
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Kosiorowska KE, Moreno AD, Iglesias R, Leluk K, Mirończuk AM. Production of PETase by engineered Yarrowia lipolytica for efficient poly(ethylene terephthalate) biodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157358. [PMID: 35850328 DOI: 10.1016/j.scitotenv.2022.157358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
There has been a growing interest in poly(ethylene terephthalate) PET degradation studies in the last few years due to its widespread use and large-scale plastic waste accumulation in the environment. One of the most promising enzymatic methods in the context of PET degradation is the use of PETase from Ideonella sakaiensis, which has been reported to be an efficient enzyme for hydrolysing ester bonds in PET. In our study, we expressed a codon-optimized PETase gene in the yeast Yarrowia lipolytica. The obtained strain was tested for its ability to degrade PET directly in culture, and a screening of different supplements that might raise the level of PET hydrolysis was performed. We also carried out long-term cultures with PET film, the surface of which was examined by scanning electron microscopy. The efficiency of PET degradation was tested based on the concentration of degradation products released, and the results showed that supplementation of the culture with olive oil resulted in 66 % higher release of terephthalic acid into the medium compared to the mutant culture without supplementation. The results indicate the possibility of ethylene glycol uptake by both strains, and, additionally, the PETase produced by the newly engineered strain hydrolyses MHET. The structure of the PET film after culture with the modified strain, meanwhile, had numerous surface defects, cracks, and deformations.
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Affiliation(s)
- Katarzyna E Kosiorowska
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland.
| | - Antonio D Moreno
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Centre for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, 28040 Madrid, Spain.
| | - Raquel Iglesias
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Centre for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, 28040 Madrid, Spain.
| | - Karol Leluk
- Wroclaw University of Science and Technology, Faculty of Environmental Engineering, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Aleksandra M Mirończuk
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland.
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8
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Kosiorowska KE, Biniarz P, Dobrowolski A, Leluk K, Mirończuk AM. Metabolic engineering of Yarrowia lipolytica for poly(ethylene terephthalate) degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154841. [PMID: 35358523 DOI: 10.1016/j.scitotenv.2022.154841] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Polyethylene terephthalate (PET) is the most widely used plastic, whose global production scale causes serious problems due to it being highly non-biodegradable. The present work provides a novel approach to plastic degradation studies, which involves direct degradation of PET in the culture of a modified Y. lipolytica yeast strain extracellularly producing cutinase from Fusarium solani. In this study, we successfully accomplished a scale-up of the degradation process in culture, which is promising from the perspective of wider application of the developed method in the future. Additionally, we tested the effect of various supplements, which may increase the PET degradation efficiency in the culture of the Y. lipolytica pAD CUT_FS strain. The ability of PET decomposition was verified by the amount of the released degradation products, such as terephthalic acid (TPA) and mono-(2-hydroxyethyl)-terephthalic acid (MHET), during cultivation. We observed that the quantities of TPA and MHET released during the PET degradation process were increasing daily, and were 1.51 gL-1 and 0.45 gL-1, respectively after 240 h of the bioreactor fermentation. Analysis of the PET film by electron microscopy indicated that there was abundant damage on the surface of the material. This study also demonstrated that the engineered Y. lipolytica strain is able to degrade PET at 28 °C during fermentation. The results obtained in this study using amorphous PET powder provide a wide range of possibilities for application of the cutinase-secreting strain of Y. lipolytica on the more difficult to degrade highly crystalline PET films, PET bottles and PET melts.
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Affiliation(s)
- Katarzyna E Kosiorowska
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Piotr Biniarz
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Adam Dobrowolski
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland
| | - Karol Leluk
- Wroclaw University of Science and Technology, Faculty of Environmental Engineering, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Aleksandra M Mirończuk
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland.
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9
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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10
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Ahmaditabatabaei S, Kyazze G, Iqbal HMN, Keshavarz T. Fungal Enzymes as Catalytic Tools for Polyethylene Terephthalate (PET) Degradation. J Fungi (Basel) 2021; 7:931. [PMID: 34829219 PMCID: PMC8625934 DOI: 10.3390/jof7110931] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 02/05/2023] Open
Abstract
The ubiquitous persistence of plastic waste in diverse forms and different environmental matrices is one of the main challenges that modern societies are facing at present. The exponential utilization and recalcitrance of synthetic plastics, including polyethylene terephthalate (PET), results in their extensive accumulation, which is a significant threat to the ecosystem. The growing amount of plastic waste ending up in landfills and oceans is alarming due to its possible adverse effects on biota. Thus, there is an urgent need to mitigate plastic waste to tackle the environmental crisis of plastic pollution. With regards to PET, there is a plethora of literature on the transportation route, ingestion, environmental fate, amount, and the adverse ecological and human health effects. Several studies have described the deployment of various microbial enzymes with much focus on bacterial-enzyme mediated removal and remediation of PET. However, there is a lack of consolidated studies on the exploitation of fungal enzymes for PET degradation. Herein, an effort has been made to cover this literature gap by spotlighting the fungi and their unique enzymes, e.g., esterases, lipases, and cutinases. These fungal enzymes have emerged as candidates for the development of biocatalytic PET degradation processes. The first half of this review is focused on fungal biocatalysts involved in the degradation of PET. The latter half explains three main aspects: (1) catalytic mechanism of PET hydrolysis in the presence of cutinases as a model fungal enzyme, (2) limitations hindering enzymatic PET biodegradation, and (3) strategies for enhancement of enzymatic PET biodegradation.
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Affiliation(s)
- Seyedehazita Ahmaditabatabaei
- School of Life sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK; (S.A.); (G.K.)
| | - Godfrey Kyazze
- School of Life sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK; (S.A.); (G.K.)
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico;
| | - Tajalli Keshavarz
- School of Life sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK; (S.A.); (G.K.)
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11
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Gao R, Pan H, Lian J. Recent advances in the discovery, characterization, and engineering of poly(ethylene terephthalate) (PET) hydrolases. Enzyme Microb Technol 2021; 150:109868. [PMID: 34489027 DOI: 10.1016/j.enzmictec.2021.109868] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/28/2022]
Abstract
Poly(ethylene terephthalate) (PET) is a class of polyester plastic composed of terephthalic acid (TPA) and ethylene glycol (EG). The accumulation of large amount of PET waste has resulted in severe environmental and health problems. Microbial polyester hydrolases with the ability to degrade PET provide an economy- and environment-friendly approach for the treatment of PET waste. In recent years, many PET hydrolases have been discovered and characterized from various microorganisms and engineered for better performance under practical application conditions. Here, recent progress in the discovery, characterization, and enzymatic mechanism elucidation of PET hydrolases is firstly reviewed. Then, structure-guided protein engineering of PET hydrolases with increased enzymatic activities, expanded substrate specificity, as well as improved protein stability is summarized. In addition, strategies for efficient expression of recombinant PET hydrolases, including secretory expression and cell-surface display, are briefly introduced. This review is concluded with future perspectives in biodegradation and subsequent biotransformation of PET wastes to produce value-added compounds.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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12
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Zhu B, Wang D, Wei N. Enzyme Discovery and Engineering for Sustainable Plastic Recycling. Trends Biotechnol 2021; 40:22-37. [PMID: 33676748 DOI: 10.1016/j.tibtech.2021.02.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
The drastically increasing amount of plastic waste is causing an environmental crisis that requires innovative technologies for recycling post-consumer plastics to achieve waste valorization while meeting environmental quality goals. Biocatalytic depolymerization mediated by enzymes has emerged as an efficient and sustainable alternative for plastic treatment and recycling. A variety of plastic-degrading enzymes have been discovered from microbial sources. Meanwhile, protein engineering has been exploited to modify and optimize plastic-degrading enzymes. This review highlights the recent trends and up-to-date advances in mining novel plastic-degrading enzymes through state-of-the-art omics-based techniques and improving the enzyme catalytic efficiency and stability via various protein engineering strategies. Future research prospects and challenges are also discussed.
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Affiliation(s)
- Baotong Zhu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Dong Wang
- Department of Computer Science and Engineering, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA.
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13
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Li Y, Wei J, Yang H, Dai J, Ge X. Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity. PLoS One 2021; 16:e0247236. [PMID: 33606796 PMCID: PMC7894860 DOI: 10.1371/journal.pone.0247236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/03/2021] [Indexed: 11/19/2022] Open
Abstract
Berberine is a promising botanical pesticide against fungal plant pathogens. However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were partially inhibited in presence of berberine toward different substrates. Molecular dynamics simulation results suggested the rigidity of cutinase was decreased with berberine added into the system. Interestingly, aggregations of berberine to the catalytic center of cutinase were observed, and stronger hydrophobic interactions were detected between key residue His 208 and berberine with concentrations of berberine increased. More importantly, this hydrophobic interaction conferred conformational change of the imidazole ring of His 208, which swung out of the catalytic center to an inactive mode. In summary, we provided the molecular mechanism of the effect of berberine on cutinase from C. capsici.
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Affiliation(s)
- Ying Li
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Jinqing Wei
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Huizhen Yang
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Jing Dai
- Beijing Aerospace Petrochemical EC&EP Technology Co., Ltd, Beijing, China
| | - Xizhen Ge
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
- * E-mail:
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14
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Chen Z, Xiao Y, Weber G, Wei R, Wang Z. Yeast cell surface display of bacterial PET hydrolase as a sustainable biocatalyst for the degradation of polyethylene terephthalate. Methods Enzymol 2021; 648:457-477. [PMID: 33579416 DOI: 10.1016/bs.mie.2020.12.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Enzymatic hydrolysis of polyethylene terephthalate (PET) is considered to be an environmentally friendly method for the recycling of plastic waste. Recently, a bacterial enzyme named IsPETase was found in Ideonella sakaiensis with the ability to degrade amorphous PET at ambient temperature suggesting its possible use in recycling of PET. However, applying the purified IsPETase in large-scale PET recycling has limitations, i.e., a complicated production process, high cost of single-use, and instability of the enzyme. Yeast cell surface display has proven to be an effectual alternative for improving enzyme degradation efficiency and realizing industrial applications. This chapter deals with the construction and application of a whole-cell biocatalyst by displaying IsPETase on the surface of yeast (Pichia pastoris) cells.
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Affiliation(s)
- Zhuozhi Chen
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yunjie Xiao
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Gert Weber
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Ren Wei
- Junior Research Group Plastic Biodegradation, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin, China.
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15
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do Canto VP, Thompson CE, Netz PA. Computational studies of polyurethanases from Pseudomonas. J Mol Model 2021; 27:46. [PMID: 33484339 DOI: 10.1007/s00894-021-04671-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022]
Abstract
Polyurethanes (PU) are multifunctional polymers, used in automotive industry, in coatings, rigid and flexible foams, and also in biomimetic materials. In the same way as all plastic waste, the incorrect disposal of these materials leads to the accumulation of polyurethanes in the environment. To reduce the amount of waste as well as add value to degradation products, bioremediation methods have been studied for waste management of PU. Enzymes of the hydrolases class have been experimentally tested for enzymatic degradation of PU, with very promising results. In this work, two enzymes that can degrade polyurethanes were studied by molecular dynamics simulations: a protease and an esterase, both from Pseudomonas. From molecular dynamics simulations analysis, it was observed the stability of the structures, both in the simulations of the free enzymes and in the simulations of the complexes with a PU monomer. Hydrogen bonds were formed with the monomer and the enzymes throughout the simulation time, and the interaction free energy was found to be strongly negative, pointing to strong interactions in both cases.
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Affiliation(s)
- Vanessa Petry do Canto
- Grupo de Química Teórica, UFRGS - Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500. Bairro Agronomia., Porto Alegre, RS, 91501-970, Brazil.
| | - Claudia Elizabeth Thompson
- Departamento de Farmacociências, UFCSPA - Universidade Federal de Ciências da Saúde de Porto Alegre, Sarmento Leite 245, Porto Alegre, RS, 90050-170, Brazil
| | - Paulo Augusto Netz
- Grupo de Química Teórica, UFRGS - Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500. Bairro Agronomia., Porto Alegre, RS, 91501-970, Brazil
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16
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Tanimoto S, Tamura K, Hayashi S, Yoshida N, Nakano H. A computational method to simulate global conformational changes of proteins induced by cosolvent. J Comput Chem 2021; 42:552-563. [PMID: 33433010 DOI: 10.1002/jcc.26481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/09/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022]
Abstract
A computational method to investigate the global conformational change of a protein is proposed by combining the linear response path following (LRPF) method and three-dimensional reference interaction site model (3D-RISM) theory, which is referred to as the LRPF/3D-RISM method. The proposed method makes it possible to efficiently simulate protein conformational changes caused by either solutions of varying concentrations or the presence of cosolvent species by taking advantage of the LRPF and 3D-RISM. The proposed method is applied to the urea-induced denaturation of ubiquitin. The LRPF/3D-RISM trajectories successfully simulate the early stage of the denaturation process within the simulation time of 300 ns, whereas no significant structural change is observed even in the 1 μs standard MD simulation. The obtained LRPF/3D-RISM trajectories reproduce the mechanism of the urea denaturation of ubiquitin reported in previous studies, and demonstrate the high efficiency of the method.
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Affiliation(s)
- Shoichi Tanimoto
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Koichi Tamura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka, Japan
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17
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Chen Z, Wang Y, Cheng Y, Wang X, Tong S, Yang H, Wang Z. Efficient biodegradation of highly crystallized polyethylene terephthalate through cell surface display of bacterial PETase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:136138. [PMID: 31887523 DOI: 10.1016/j.scitotenv.2019.136138] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/13/2019] [Accepted: 12/14/2019] [Indexed: 05/16/2023]
Abstract
Polyethylene terephthalate (PET) is one of the most widely used plastics in the world. Accumulation of the discarded PET in the environment is creating a global environmental problem. Recently, a bacterial enzyme named PETase was found to have the novel ability to degrade the highly crystallized PET. However, the enzymatic activity of native PETase is still low limiting its possible use in recycling of PET. In this study, we developed a whole-cell biocatalyst by displaying PETase on the surface of yeast (Pichia pastoris) cell to improve its degradation efficiency. Our data shows that PETase could be functionally displayed on the yeast cell with enhanced pH and thermal stability. The turnover rate of the PETase-displaying yeast whole-cell biocatalyst towards highly crystallized PET dramatically increased about 36-fold compared with that of purified PETase. Furthermore, the whole-cell biocatalyst showed stable turnover rate after seven repeated use and under some chemical/solvent conditions, and its ability to degrade different commercial highly crystallized PET bottles. Our results reveal that PETase-displaying whole-cell biocatalyst affords a promising route for efficient biological recycling of PET.
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Affiliation(s)
- Zhuozhi Chen
- School of Life Sciences, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, China.
| | - Yanyan Wang
- School of Life Sciences, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, China.
| | - Yingying Cheng
- School of Life Sciences, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, China.
| | - Xue Wang
- School of Life Sciences, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Shanwei Tong
- School of Life Sciences, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, China.
| | - Haitao Yang
- School of Life Sciences, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, China.
| | - Zefang Wang
- School of Life Sciences, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, College of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, 300072, China; Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China.
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18
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Fecker T, Galaz-Davison P, Engelberger F, Narui Y, Sotomayor M, Parra LP, Ramírez-Sarmiento CA. Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase. Biophys J 2019; 114:1302-1312. [PMID: 29590588 DOI: 10.1016/j.bpj.2018.02.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/21/2022] Open
Abstract
Polyethylene terephthalate (PET) is one of the most-consumed synthetic polymers, with an annual production of 50 million tons. Unfortunately, PET accumulates as waste and is highly resistant to biodegradation. Recently, fungal and bacterial thermophilic hydrolases were found to catalyze PET hydrolysis with optimal activities at high temperatures. Strikingly, an enzyme from Ideonella sakaiensis, termed PETase, was described to efficiently degrade PET at room temperature, but the molecular basis of its activity is not currently understood. Here, a crystal structure of PETase was determined at 2.02 Å resolution and employed in molecular dynamics simulations showing that the active site of PETase has higher flexibility at room temperature than its thermophilic counterparts. This flexibility is controlled by a novel disulfide bond in its active site, with its removal leading to destabilization of the catalytic triad and reduction of the hydrolase activity. Molecular docking of a model substrate predicts that PET binds to PETase in a unique and energetically favorable conformation facilitated by several residue substitutions within its active site when compared to other enzymes. These computational predictions are in excellent agreement with recent mutagenesis and PET film degradation analyses. Finally, we rationalize the increased catalytic activity of PETase at room temperature through molecular dynamics simulations of enzyme-ligand complexes for PETase and other thermophilic PET-degrading enzymes at 298, 323, and 353 K. Our results reveal that both the binding pose and residue substitutions within PETase favor proximity between the catalytic residues and the labile carbonyl of the substrate at room temperature, suggesting a more favorable hydrolytic reaction. These results are valuable for enabling detailed evolutionary analysis of PET-degrading enzymes and for rational design endeavors aiming at increasing the efficiency of PETase and similar enzymes toward plastic degradation.
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Affiliation(s)
- Tobias Fecker
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Engelberger
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Yoshie Narui
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.
| | - Loreto P Parra
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Abstract
Cutinases are α/β hydrolases, and their role in nature is the degradation of cutin. Such enzymes are usually produced by phytopathogenic microorganisms in order to penetrate their hosts. The first focused studies on cutinases started around 50 years ago. Since then, numerous cutinases have been isolated and characterized, aiming at the elucidation of their structure–function relations. Our deeper understanding of cutinases determines the applications by which they could be utilized; from food processing and detergents, to ester synthesis and polymerizations. However, cutinases are mainly efficient in the degradation of polyesters, a natural function. Therefore, these enzymes have been successfully applied for the biodegradation of plastics, as well as for the delicate superficial hydrolysis of polymeric materials prior to their functionalization. Even though research on this family of enzymes essentially began five decades ago, they are still involved in many reports; novel enzymes are being discovered, and new fields of applications arise, leading to numerous related publications per year. Perhaps the future of cutinases lies in their evolved descendants, such as polyesterases, and particularly PETases. The present article reviews the biochemical and structural characteristics of cutinases and cutinase-like hydrolases, and their applications in the field of bioremediation and biocatalysis.
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20
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Gross C, Saponaro A, Santoro B, Moroni A, Thiel G, Hamacher K. Mechanical transduction of cytoplasmic-to-transmembrane-domain movements in a hyperpolarization-activated cyclic nucleotide-gated cation channel. J Biol Chem 2018; 293:12908-12918. [PMID: 29936413 PMCID: PMC6102142 DOI: 10.1074/jbc.ra118.002139] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 06/05/2018] [Indexed: 01/26/2023] Open
Abstract
Hyperpolarization-activated cyclic nucleotide–gated cation (HCN) channels play a critical role in the control of pacemaking in the heart and repetitive firing in neurons. In HCN channels, the intracellular cyclic nucleotide–binding domain (CNBD) is connected to the transmembrane portion of the channel (TMPC) through a helical domain, the C-linker. Although this domain is critical for mechanical signal transduction, the conformational dynamics in the C-linker that transmit the nucleotide-binding signal to the HCN channel pore are unknown. Here, we use linear response theory to analyze conformational changes in the C-linker of the human HCN1 protein, which couple cAMP binding in the CNBD with gating in the TMPC. By applying a force to the tip of the so-called “elbow” of the C-linker, the coarse-grained calculations recapitulate the same conformational changes triggered by cAMP binding in experimental studies. Furthermore, in our simulations, a displacement of the C-linker parallel to the membrane plane (i.e. horizontally) induced a rotational movement resulting in a distinct tilting of the transmembrane helices. This movement, in turn, increased the distance between the voltage-sensing S4 domain and the surrounding transmembrane domains and led to a widening of the intracellular channel gate. In conclusion, our computational approach, combined with experimental data, thus provides a more detailed understanding of how cAMP binding is mechanically coupled over long distances to promote voltage-dependent opening of HCN channels.
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Affiliation(s)
- Christine Gross
- Computational Biology and Simulation Group, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Andrea Saponaro
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Bina Santoro
- Department of Neuroscience, Columbia University, New York, New York 10032
| | - Anna Moroni
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Gerhard Thiel
- Membrane Biophysics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
| | - Kay Hamacher
- Computational Biology and Simulation Group, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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21
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Liu B, He L, Wang L, Li T, Li C, Liu H, Luo Y, Bao R. Protein Crystallography and Site‐Direct Mutagenesis Analysis of the Poly(ethylene terephthalate) Hydrolase PETase from
Ideonella sakaiensis. Chembiochem 2018; 19:1471-1475. [DOI: 10.1002/cbic.201800097] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Bing Liu
- Department of GastroenterologyWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
| | - Lihui He
- Center of Infectious DiseasesWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
| | - Liping Wang
- Department of GastroenterologyWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
| | - Tao Li
- Center of Infectious DiseasesWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
| | - Changcheng Li
- Center of Infectious DiseasesWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
| | - Huayi Liu
- Department of GastroenterologyWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
| | - Yunzi Luo
- Department of GastroenterologyWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
| | - Rui Bao
- Center of Infectious DiseasesWest China HospitalSichuan University and Collaborative Innovation Center of Biotherapy Chengdu 610041 China
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22
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Dombrowsky MJ, Jager S, Schiller B, Mayer BE, Stammler S, Hamacher K. StreaMD: Advanced analysis of molecular dynamics using R. J Comput Chem 2018; 39:1666-1674. [DOI: 10.1002/jcc.25197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/09/2018] [Accepted: 01/23/2018] [Indexed: 12/26/2022]
Affiliation(s)
| | - Sven Jager
- Computational Biology and Simulation, Department of Biology; TU Darmstadt Germany
| | - Benjamin Schiller
- Privacy and Data Security, Department of Computer Science; TU Dresden Germany
| | - Benjamin E. Mayer
- Computational Biology and Simulation, Department of Biology; TU Darmstadt Germany
| | - Sebastian Stammler
- Computational Biology and Simulation, Department of Biology; TU Darmstadt Germany
| | - Kay Hamacher
- Computational Biology and Simulation, Department of Biology; TU Darmstadt Germany
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23
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de Castro AM, Carniel A, Nicomedes Junior J, da Conceição Gomes A, Valoni É. Screening of commercial enzymes for poly(ethylene terephthalate) (PET) hydrolysis and synergy studies on different substrate sources. ACTA ACUST UNITED AC 2017; 44:835-844. [DOI: 10.1007/s10295-017-1942-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/31/2017] [Indexed: 11/30/2022]
Abstract
Abstract
Poly(ethylene terephthalate) (PET) is one of the most consumed plastics in the world. The development of efficient technologies for its depolymerization for monomers reuse is highly encouraged, since current recycling rates are still very low. In this study, 16 commercial lipases and cutinases were evaluated for their abilities to catalyze the hydrolysis of two PET samples. Humicola insolens cutinase showed the best performance and was then used in reactions on other PET sources, solely or in combination with the efficient mono(hydroxyethyl terephthalate)-converting lipase from Candida antarctica. Synergy degrees of the final titers of up to 2.2 (i.e., more than double of the concentration when both enzymes were used, as compared to their use alone) were found, with increased terephthalic acid formation rates, reaching a maximum of 59,989 µmol/L (9.36 g/L). These findings open up new possibilities for the conversion of post-consumer PET packages into their minimal monomers, which can be used as drop in at existing industrial facilities.
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Affiliation(s)
- Aline Machado de Castro
- 0000 0001 2192 4294 grid.423526.4 Biotechnology Division, Research and Development Center PETROBRAS Av. Horácio Macedo, 950. Ilha do Fundão 21941-915 Rio de Janeiro Brazil
| | - Adriano Carniel
- Falcão Bauer R. Aquinos111. Água Branca 05036-070 São Paulo Brazil
| | - José Nicomedes Junior
- 0000 0001 2192 4294 grid.423526.4 Biotechnology Division, Research and Development Center PETROBRAS Av. Horácio Macedo, 950. Ilha do Fundão 21941-915 Rio de Janeiro Brazil
| | - Absai da Conceição Gomes
- 0000 0001 2192 4294 grid.423526.4 Biotechnology Division, Research and Development Center PETROBRAS Av. Horácio Macedo, 950. Ilha do Fundão 21941-915 Rio de Janeiro Brazil
| | - Érika Valoni
- 0000 0001 2192 4294 grid.423526.4 Biotechnology Division, Research and Development Center PETROBRAS Av. Horácio Macedo, 950. Ilha do Fundão 21941-915 Rio de Janeiro Brazil
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