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Kim DW, Lim ES, Lee GH, Son HF, Sung C, Jung JH, Park HJ, Gong G, Ko JK, Um Y, Han SO, Ahn JH. Biodegradation of oxidized low density polyethylene by Pelosinus fermentans lipase. BIORESOURCE TECHNOLOGY 2024; 403:130871. [PMID: 38782190 DOI: 10.1016/j.biortech.2024.130871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/28/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Polyethylene (PE) exhibits high resistance to degradation, contributing to plastic pollution. PE discarded into the environment is photo-oxidized by sunlight and oxygen. In this study, a key enzyme capable of degrading oxidized PE is reported for the first time. Twenty different enzymes from various lipase families were evaluated for hydrolytic activity using substrates mimicking oxidized PE. Among them, Pelosinus fermentans lipase 1 (PFL1) specifically cleaved the ester bonds within the oxidized carbon-carbon backbone. Moreover, PFL1 (6 μM) degraded oxidized PE film, reducing the weight average and number average molecular weights by 44.6 and 11.3 %, respectively, within five days. Finally, structural analysis and molecular docking simulations were performed to elucidate the degradation mechanism of PFL1. The oxidized PE-degrading enzyme reported here will provide the groundwork for advancing PE waste treatment technology and for engineering microbes to repurpose PE waste into valuable chemicals.
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Affiliation(s)
- Do-Wook Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Eui Seok Lim
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ga Hyun Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hyeoncheol Francis Son
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Changmin Sung
- Doping Control Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Hyun June Park
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jung Ho Ahn
- Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Daejeon 34113, Republic of Korea.
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Shehata M, Ünlü A, Iglesias-Fernández J, Osuna S, Sezerman OU, Timucin E. Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog. Phys Chem Chem Phys 2023; 25:2234-2247. [PMID: 36594810 DOI: 10.1039/d2cp05093e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Non-ionic surfactants were shown to stabilize the active conformation of thermoalkalophilic lipases by mimicking the lipid substrate while the catalytic interactions formed by anionic surfactants have not been well characterized. In this study, we combined μs-scale molecular dynamics (MD) simulations and lipase activity assays to analyze the effect of ionic surfactant, sodium dodecyl sulfate (SDS), on the structure and activity of thermoalkalophilic lipases. Both the open and closed lipase conformations that differ in geometry were recruited to the MD analysis to provide a broader understanding of the molecular effect of SDS on the lipase structure. Simulations at 298 K showed the potential of SDS for maintaining the active lipase through binding to the sn-1 acyl-chain binding pocket in the open conformation or transforming the closed conformation to an open-like state. Consistent with MD findings, experimental analysis showed increased lipase activity upon SDS incubation at ambient temperature. Notably, the lipase cores stayed intact throughout 2 μs regardless of an increase in the simulation temperature or SDS concentration. However, the surface structures were unfolded in the presence of SDS and at elevated temperature for both conformations. Simulations of the dimeric lipase were also carried out and showed reduced flexibility of the surface structures which were unfolded in the monomer, indicating the insulating role of dimer interactions against SDS. Taken together, this study provides insights into the possible substrate mimicry by the ionic surfactant SDS for the thermoalkalophilic lipases without temperature elevation, underscoring SDS's potential for interfacial activation at ambient temperatures.
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Affiliation(s)
- Mohamed Shehata
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Aişe Ünlü
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | | | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Department de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - O Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
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Kılınç E, Can Timucin A, Selim Cinaroglu S, Timucin E. Modeling and dynamical analysis of the full-length structure of factor XII with zinc. J Mol Model 2022; 28:129. [PMID: 35469101 DOI: 10.1007/s00894-022-05113-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/05/2022] [Indexed: 11/24/2022]
Abstract
Zinc (II), the second most abundant transition metal in blood, binds to the initiator of the contact pathway, factor XII (FXII). This binding induces conformational changes in the structure of FXII eventually leading to its activation. Despite many in vitro and in vivo studies on zinc-mediated activation of FXII, its molecular mechanism remains elusive mainly due to absence of a full-length structural model of FXII. To this end, this study investigated the role of zinc in the structure and dynamics of the full-length structure FXII that was obtained through molecular modeling. We have used four structural templates covering more than 70% of the FXII sequence and the remaining interconnecting regions were built by loop modeling. The resulting full-length structure of FXII contained disordered regions, but in comparison to the AlphaFold (AF) prediction, our full-length model represented a more realistic structure because of the disordered regions which were modeled to yield a more compact full-length structure in our model than the AF structure. Other than the disordered regions, our model and AF prediction were highly similar. The resulting full-length FXII structure was used to generate different systems representing the zinc-bound form (holo). Further to assess the contribution of the disulfide bridges, we also analyzed the apo and holo FXII structures with oxidized or reduced cysteine side-chains. Simulations suggested zinc binding conferred rigidity to the structure, particularly to the light chain of FXII. Zinc binding alone was sufficient to limit the backbone flexibility while 15 disulfide bonds, which were scattered throughout the structure, made a less significant contribution to the backbone rigidity. Altogether our results provide insights into the first realistic full-length structure of FXII focusing on the impact of structural zinc and disulfide bridges in the dynamics of this structure.
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Affiliation(s)
- Evren Kılınç
- Department of Biophysics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey
| | - Ahmet Can Timucin
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey
| | | | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey.
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4
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Buruaga-Ramiro C, Valenzuela SV, Pastor FIJ, Martínez J, Diaz P. Unexplored lipolytic activity of Escherichia coli: Implications for lipase cloning. Enzyme Microb Technol 2020; 139:109590. [PMID: 32732039 DOI: 10.1016/j.enzmictec.2020.109590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022]
Abstract
Recent investigations on cloned bacterial lipases performed in our laboratory revealed the presence of lipolytic activity that was not due to the cloned lipase-coding gene but was probably the result of an intrinsic activity of Escherichia coli itself. To confirm such a hypothesis, we assayed the activity of frequently used E. coli strains by fast paper tests, zymograms and spectrofluorometry. A band of Ca. 18-20 kDa showing activity on MUF-butyrate was detected in zymogram analysis of crude cell extracts in all E. coli strains assayed. Moreover, the spectrofluorometric results obtained confirmed the presence of low but significant lipolytic activity in E. coli, with strain BL21 showing the highest activity. Detailed characterization of such a lipolytic activity was performed using E. coli BL21 cell extracts, where preference for C7 substrates was found, although shorter substrates were also hydrolysed to a minor extent. Interestingly, E. coli lipolytic activity displays traits of a thermophilic enzyme, showing maximum activity at 50 °C and pH 8, an unexpected feature never described before. Kinetic and inhibition analysis were also performed showing that activity can be inhibited by several metal ions or by Triton X-100® and SDS, used in zymogram analysis. Such properties ‒ low activity, preference for medium chain-length substrates, and high operational temperature ‒ might justify why this activity had gone unexplored until now, even when many lipases and esterases have been cloned and expressed in E. coli strains in the past. From now on, lipase researchers should take into consideration the presence of such a basal lipolytic activity before starting their lipase cloning or expression experiments in E.coli.
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Affiliation(s)
- Carolina Buruaga-Ramiro
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - Susana V Valenzuela
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - F I J Pastor
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - Josefina Martínez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain
| | - Pilar Diaz
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Av. Diagonal 643, 08028 Barcelona Spain.
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5
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Shehata M, Timucin E, Venturini A, Sezerman OU. Understanding thermal and organic solvent stability of thermoalkalophilic lipases: insights from computational predictions and experiments. J Mol Model 2020; 26:122. [PMID: 32383051 DOI: 10.1007/s00894-020-04396-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/28/2020] [Indexed: 11/25/2022]
Abstract
Bacillus thermocatenulatus lipase (BTL2), a member of the isolated lipase family known as thermoalkalophilic lipases, carries potential for industrial applications owing to its ability to catalyze versatile reactions under extreme conditions. This study investigates the molecular effects of distinct solvents on the stability of BTL2 at different temperatures, aiming to contribute to lipase use in industrial applications. Initially, molecular dynamic (MD) simulations were carried out to address for the molecular impacts of distinct solvents on the structural stability of BTL2 at different temperatures. Two lipase conformations representing the active and inactive forms were simulated in 5 solvents including water, ethanol, methanol, cyclohexane, and toluene. Low temperature simulations showed that polar solvents led to enhanced lid fluctuations compared with non-polar solvents reflecting a more dynamic equilibrium between active and inactive lipase conformations in polar solvents including water, while the overall structure of the lipase in both forms became more rigid in non-polar solvents than they were in polar solvent. Notably, the native lipase fold was maintained in non-polar solvents even at high temperatures, indicating an enhancement of lipase's thermostability in non-polar organic solvents. Next, we conducted experiments for which BTL2 was expressed in a heterologous host and purified to homogeneity, and its thermostability in different solvents was assessed. Parallel to the computational findings, experimental results suggested that non-polar organic solvents contributed to BTL2's thermostability at concentrations as high as 70% (v/v). Altogether, this study provides beneficial insights to the lipase use under extreme conditions. Graphical Abstract.
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Affiliation(s)
- Mohamed Shehata
- Institute of Health Science, Department of Medical Biotechnology, Acibadem Mehmet Ali Aydınlar University, Atasehir, Istanbul, Turkey.
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydınlar University, Atasehir, Istanbul, Turkey
| | - Alessandro Venturini
- Institute of Organic Synthesis and Photoreactivity, National Research Council of Italy, Via P. Gobetti 101, 40129, Bologna, Italy
| | - Osman Uğur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydınlar University, Atasehir, Istanbul, Turkey
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Kitadokoro K, Tanaka M, Hikima T, Okuno Y, Yamamoto M, Kamitani S. Crystal structure of pathogenic Staphylococcus aureus lipase complex with the anti-obesity drug orlistat. Sci Rep 2020; 10:5469. [PMID: 32214208 PMCID: PMC7096528 DOI: 10.1038/s41598-020-62427-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/11/2020] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus lipase (SAL), a triacylglycerol esterase, is an important virulence factor and may be a therapeutic target for infectious diseases. Herein, we determined the 3D structure of native SAL, the mutated S116A inactive form, and the inhibitor complex using the anti-obesity drug orlistat to aid in drug development. The determined crystal structures showed a typical α/β hydrolase motif with a dimeric form. Fatty acids bound near the active site in native SAL and inactive S116A mutant structures. We found that orlistat potently inhibits SAL activity, and it covalently bound to the catalytic Ser116 residue. This is the first report detailing orlistat–lipase binding. It provides structure-based information on the production of potent anti-SAL drugs and lipase inhibitors. These results also indicated that orlistat can be repositioned to treat bacterial diseases.
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Affiliation(s)
- Kengo Kitadokoro
- Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Mutsumi Tanaka
- Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Takaaki Hikima
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo, 679-6148, Japan
| | - Yukiko Okuno
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masaki Yamamoto
- SR Life Science Instrumentation Team, Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo, 679-6148, Japan
| | - Shigeki Kamitani
- Graduate School of Comprehensive Rehabilitation, College of Health and Human Sciences, Osaka Prefecture University, 3-7-30 Habikino, Habikino, 583-8555, Osaka, Japan
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7
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Shift in Bacillus sp. JR3 esterase LipJ activity profile after addition of essential residues from family I.5 thermophilic lipases. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Timucin E, Sezerman OU. Thermostability of the PYL–PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants. J Chem Inf Model 2018; 58:661-672. [DOI: 10.1021/acs.jcim.7b00655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, 34752, Istanbul Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, 34752, Istanbul Turkey
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Biundo A, Steinkellner G, Gruber K, Spreitzhofer T, Ribitsch D, Guebitz GM. Engineering of the zinc-binding domain of an esterase from Clostridium botulinum towards increased activity on polyesters. Catal Sci Technol 2017. [DOI: 10.1039/c7cy00168a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Variants of the zinc-binding domain of Clostridium botulinum EstA (Cbotu_EstA) release more building blocks (Ta and BTa) from the aromatic/aliphatic copolyester poly(butylene adipate-co-terephthalate) (PBAT).
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Affiliation(s)
- Antonino Biundo
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
| | - Georg Steinkellner
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
| | - Karl Gruber
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
- Institute of Molecular Bioscience
- University of Graz
| | | | - Doris Ribitsch
- Austrian Centre for Industrial Biotechnology (ACIB)
- Tulln an der Donau
- Austria
- Institute of Environmental Biotechnology
- University of Natural Resources and Life Sciences (BOKU)
| | - Georg M. Guebitz
- Institute of Environmental Biotechnology
- University of Natural Resources and Life Sciences (BOKU)
- Tulln an der Donau
- Austria
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