23 results on '"Ly Thi Huong Luu Le"'
Search Results
2. Self‐Aggregating Tau Fragments Recapitulate Pathologic Phenotypes and Neurotoxicity of Alzheimer's Disease in Mice
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Ly Thi Huong Luu Le, Jeeyoung Lee, Dongjoon Im, Sunha Park, Kyoung‐Doo Hwang, Jung Hoon Lee, Yanxialei Jiang, Yong‐Seok Lee, Young Ho Suh, Hugh I. Kim, and Min Jae Lee
- Subjects
aggregation ,Alzheimer's disease ,axon initial segment ,phosphorylation ,tau ,Science - Abstract
Abstract In tauopathy conditions, such as Alzheimer's disease (AD), highly soluble and natively unfolded tau polymerizes into an insoluble filament; however, the mechanistic details of this process remain unclear. In the brains of AD patients, only a minor segment of tau forms β‐helix‐stacked protofilaments, while its flanking regions form disordered fuzzy coats. Here, it is demonstrated that the tau AD nucleation core (tau‐AC) sufficiently induced self‐aggregation and recruited full‐length tau to filaments. Unexpectedly, phospho‐mimetic forms of tau‐AC (at Ser324 or Ser356) show markedly reduced oligomerization and seeding propensities. Biophysical analysis reveal that the N‐terminus of tau‐AC facilitates the fibrillization kinetics as a nucleation motif, which becomes sterically shielded through phosphorylation‐induced conformational changes in tau‐AC. Tau‐AC oligomers are efficiently internalized into cells via endocytosis and induced endogenous tau aggregation. In primary hippocampal neurons, tau‐AC impaired axon initial segment plasticity upon chronic depolarization and is mislocalized to the somatodendritic compartments. Furthermore, it is observed significantly impaired memory retrieval in mice intrahippocampally injected with tau‐AC fibrils, which corresponds to the neuropathological staining and neuronal loss in the brain. These findings identify tau‐AC species as a key neuropathological driver in AD, suggesting novel strategies for therapeutic intervention.
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- 2023
- Full Text
- View/download PDF
3. Feruloyl Esterase (LaFae) from Lactobacillus acidophilus: Structural Insights and Functional Characterization for Application in Ferulic Acid Production
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Sangeun Jeon, Jisub Hwang, Hackwon Do, Ly Thi Huong Luu Le, Chang Woo Lee, Wanki Yoo, Min Ju Lee, Seung Chul Shin, Kyeong Kyu Kim, Han-Woo Kim, and Jun Hyuck Lee
- Subjects
crystal structure ,LaFae ,ferulic acid ,feruloyl esterase ,X-ray crystallography ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Ferulic acid and related hydroxycinnamic acids, used as antioxidants and preservatives in the food, cosmetic, pharmaceutical and biotechnology industries, are among the most abundant phenolic compounds present in plant biomass. Identification of novel compounds that can produce ferulic acid and hydroxycinnamic acids, that are safe and can be mass-produced, is critical for the sustainability of these industries. In this study, we aimed to obtain and characterize a feruloyl esterase (LaFae) from Lactobacillus acidophilus. Our results demonstrated that LaFae reacts with ethyl ferulate and can be used to effectively produce ferulic acid from wheat bran, rice bran and corn stalks. In addition, xylanase supplementation was found to enhance LaFae enzymatic hydrolysis, thereby augmenting ferulic acid production. To further investigate the active site configuration of LaFae, crystal structures of unliganded and ethyl ferulate-bound LaFae were determined at 2.3 and 2.19 Å resolutions, respectively. Structural analysis shows that a Phe34 residue, located at the active site entrance, acts as a gatekeeper residue and controls substrate binding. Mutating this Phe34 to Ala produced an approximately 1.6-fold increase in LaFae activity against p-nitrophenyl butyrate. Our results highlight the considerable application potential of LaFae to produce ferulic acid from plant biomass and agricultural by-products.
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- 2023
- Full Text
- View/download PDF
4. Biodiesel and flavor compound production using a novel promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from the psychrophilic bacterium Halocynthiibacter arcticus
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Ly Thi Huong Luu Le, Wanki Yoo, Sangeun Jeon, Changwoo Lee, Kyeong Kyu Kim, Jun Hyuck Lee, and T. Doohun Kim
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HaSGNH1 ,Halocynthiibacter arcticus ,Immobilization ,SGNH-type lipase ,Substrate specificity ,Biodiesel ,Fuel ,TP315-360 ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract Background Biodiesel and flavor compound production using enzymatic transesterification by microbial lipases provides mild reaction conditions and low energy cost compared to the chemical process. SGNH-type lipases are very effective catalysts for enzymatic transesterification due to their high reaction rate, great stability, relatively small size for convenient genetic manipulations, and ease of immobilization. Hence, it is highly important to identify novel SGNH-type lipases with high catalytic efficiencies and good stabilities. Results A promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from Halocynthiibacter arcticus was catalytically characterized and functionally explored. HaSGNH1 displayed broad substrate specificity that included tert-butyl acetate, glucose pentaacetate, and p-nitrophenyl esters with excellent stability and high efficiency. Important amino acids (N83, M86, R87, F131, and I173F) around the substrate-binding pocket were shown to be responsible for catalytic activity, substrate specificity, and reaction kinetics. Moreover, immobilized HaSGNH1 was used to produce high yields of butyl and oleic esters. Conclusions This work provides a molecular understanding of substrate specificities, catalytic regulation, immobilization, and industrial applications of a promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from H. arcticus. This is the first analysis on biodiesel and flavor synthesis using a cold-adapted halophilic SGNH-type lipase from a Halocynthiibacter species.
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- 2020
- Full Text
- View/download PDF
5. Structural and functional characterization of a novel cold-active S-formylglutathione hydrolase (SfSFGH) homolog from Shewanella frigidimarina, a psychrophilic bacterium
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Chang Woo Lee, Wanki Yoo, Sun-Ha Park, Ly Thi Huong Luu Le, Chang-Sook Jeong, Bum Han Ryu, Seung Chul Shin, Han-Woo Kim, Hyun Park, Kyeong Kyu Kim, T. Doohun Kim, and Jun Hyuck Lee
- Subjects
Crystal structure ,S-Formylglutathione hydrolase ,Substrate specificity ,Shewanella frigidimarina ,Mutagenesis ,Microbiology ,QR1-502 - Abstract
Abstract Background S-Formylglutathione is hydrolyzed to glutathione and formate by an S-formylglutathione hydrolase (SFGH) (3.1.2.12). This thiol esterase belongs to the esterase family and is also known as esterase D. SFGHs contain highly conserved active residues of Ser-Asp-His as a catalytic triad at the active site. Characterization and investigation of SFGH from Antarctic organisms at the molecular level is needed for industrial use through protein engineering. Results A novel cold-active S-formylglutathione hydrolase (SfSFGH) from Shewanella frigidimarina, composed of 279 amino acids with a molecular mass of ~ 31.0 kDa, was characterized. Sequence analysis of SfSFGH revealed a conserved pentapeptide of G-X-S-X-G found in various lipolytic enzymes along with a putative catalytic triad of Ser148-Asp224-His257. Activity analysis showed that SfSFGH was active towards short-chain esters, such as p-nitrophenyl acetate, butyrate, hexanoate, and octanoate. The optimum pH for enzymatic activity was slightly alkaline (pH 8.0). To investigate the active site configuration of SfSFGH, we determined the crystal structure of SfSFGH at 2.32 Å resolution. Structural analysis shows that a Trp182 residue is located at the active site entrance, allowing it to act as a gatekeeper residue to control substrate binding to SfSFGH. Moreover, SfSFGH displayed more than 50% of its initial activity in the presence of various chemicals, including 30% EtOH, 1% Triton X-100, 1% SDS, and 5 M urea. Conclusions Mutation of Trp182 to Ala allowed SfSFGH to accommodate a longer chain of substrates. It is thought that the W182A mutation increases the substrate-binding pocket and decreases the steric effect for larger substrates in SfSFGH. Consequently, the W182A mutant has a broader substrate specificity compared to wild-type SfSFGH. Taken together, this study provides useful structure–function data of a SFGH family member and may inform protein engineering strategies for industrial applications of SfSFGH.
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- 2019
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- View/download PDF
6. Formation of Non-Nucleoplasmic Proteasome Foci during the Late Stage of Hyperosmotic Stress
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Jeeyoung Lee, Ly Thi Huong Luu Le, Eunkyoung Kim, and Min Jae Lee
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proteasome ,hyperosmotic stress ,nuclear foci ,insulator body ,nuclear pore complex ,phase separation ,Cytology ,QH573-671 - Abstract
Cellular stress induces the formation of membraneless protein condensates in both the nucleus and cytoplasm. The nucleocytoplasmic transport of proteins mainly occurs through nuclear pore complexes (NPCs), whose efficiency is affected by various stress conditions. Here, we report that hyperosmotic stress compartmentalizes nuclear 26S proteasomes into dense nuclear foci, independent of signaling cascades. Most of the proteasome foci were detected between the condensed chromatin mass and inner nuclear membrane. The proteasome-positive puncta were not colocalized with other types of nuclear bodies and were reversibly dispersed when cells were returned to the isotonic medium. The structural integrity of 26S proteasomes in the nucleus was slightly affected under the hyperosmotic condition. We also found that these insulator-body-like proteasome foci were possibly formed through disrupted nucleus-to-cytosol transport, which was mediated by the sequestration of NPC components into osmostress-responding stress granules. These data suggest that phase separation in both the nucleus and cytosol may be a major cell survival mechanism during hyperosmotic stress conditions.
- Published
- 2021
- Full Text
- View/download PDF
7. Pentaminomycins C–E: Cyclic Pentapeptides as Autophagy Inducers from a Mealworm Beetle Gut Bacterium
- Author
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Sunghoon Hwang, Ly Thi Huong Luu Le, Shin-Il Jo, Jongheon Shin, Min Jae Lee, and Dong-Chan Oh
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insect ,mealworm ,gut bacteria ,OSMAC ,cyclic peptides ,biosynthetic pathway ,Biology (General) ,QH301-705.5 - Abstract
Pentaminomycins C–E (1–3) were isolated from the culture of the Streptomyces sp. GG23 strain from the guts of the mealworm beetle, Tenebrio molitor. The structures of the pentaminomycins were determined to be cyclic pentapeptides containing a modified amino acid, N5-hydroxyarginine, based on 1D and 2D NMR and mass spectroscopic analyses. The absolute configurations of the amino acid residues were assigned using Marfey’s method and bioinformatics analysis of their nonribosomal peptide biosynthetic gene cluster (BGC). Detailed analysis of the BGC enabled us to propose that the structural variations in 1–3 originate from the low specificity of the adenylation domain in the nonribosomal peptide synthetase (NRPS) module 1, and indicate that macrocyclization can be catalyzed noncanonically by penicillin binding protein (PBP)-type TE. Furthermore, pentaminomycins C and D (1 and 2) showed significant autophagy-inducing activities and were cytoprotective against oxidative stress in vitro.
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- 2020
- Full Text
- View/download PDF
8. Molecular Characterization of a Novel Cold-Active Hormone-Sensitive Lipase (HaHSL) from Halocynthiibacter Arcticus
- Author
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Ly Thi Huong Luu Le, Wanki Yoo, Changwoo Lee, Ying Wang, Sangeun Jeon, Kyeong Kyu Kim, Jun Hyuck Lee, and T. Doohun Kim
- Subjects
hormone-sensitive lipase ,substrate specificity ,enantioselectivity ,immobilization ,halocynthiibacter arcticus ,Microbiology ,QR1-502 - Abstract
Bacterial hormone-sensitive lipases (bHSLs), which are homologous to the catalytic domains of human HSLs, have received great interest due to their uses in the preparation of highly valuable biochemicals, such as drug intermediates or chiral building blocks. Here, a novel cold-active HSL from Halocynthiibacter arcticus (HaHSL) was examined and its enzymatic properties were investigated using several biochemical and biophysical methods. Interestingly, HaHSL acted on a large variety of substrates including tertiary alcohol esters and fish oils. Additionally, this enzyme was highly tolerant to high concentrations of salt, detergents, and glycerol. Furthermore, immobilized HaHSL retained its activity for up to six cycles of use. Homology modeling suggested that aromatic amino acids (Trp23, Tyr74, Phe78, Trp83, and Phe245) in close proximity to the substrate-binding pocket were important for enzyme activity. Mutational analysis revealed that Tyr74 played an important role in substrate specificity, thermostability, and enantioselectivity. In summary, the current study provides an invaluable insight into the novel cold-active HaHSL from H. arcticus, which can be efficiently and sustainably used in a wide range of biotechnological applications.
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- 2019
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9. N-recognins UBR1 and UBR2 as central ER stress sensors in mammals.
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Ly Thi Huong Luu Le, Seoyoung Park, Jung Hoon Lee, Yun Kyung Kim, and Min Jae Lee
- Abstract
In eukaryotes, a primary protein quality control (PQC) process involves the destruction of conformationally misfolded proteins through the ubiquitin-proteasome system. Because approximately one-third of eukaryotic proteomes fold and assemble within the endoplasmic reticulum (ER) before being sent to their destinations, the ER plays a crucial role in PQC. The specific functions and biochemical roles of several E3 ubiquitin ligases involved in ER-associated degradation in mammals, on the other hand, are mainly unknown. We identified 2 E3 ligases, ubiquitin protein ligase E3 component Nrecognin 1 (UBR1) and ubiquitin protein ligase E3 component N-recognin 2 (UBR2), which are the key N-recognins in the Ndegron pathway and participate in the ER stress response in mammalian cells by modulating their stability. Cells lacking UBR1 and UBR2 are hypersensitive to ER stress-induced apoptosis. Under normal circumstances, these proteins are polyubiquitinated through Lys48-specific linkages and are then degraded by the 26S proteasome. In contrast, when cells are subjected to ER stress, UBR1 and UBR2 exhibit greater stability, potentially as a cellular adaptive response to stressful conditions. Although the precise mechanisms underlying these findings require further investigation, our findings show that cytoplasmic UBR1 and UBR2 have anti-ER stress activities and contribute to global PQC in mammals. These data also reveal an additional level of complexity within the mammalian ER-associated degradation system, implicating potential involvement of the N-degron pathway. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
- View/download PDF
10. Feruloyl Esterase (LaFae) from Lactobacillus acidophilus: Structural Insights and Functional Characterization for Application in Ferulic Acid Production
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Lee, Sangeun Jeon, Jisub Hwang, Hackwon Do, Ly Thi Huong Luu Le, Chang Woo Lee, Wanki Yoo, Min Ju Lee, Seung Chul Shin, Kyeong Kyu Kim, Han-Woo Kim, and Jun Hyuck
- Subjects
crystal structure ,LaFae ,ferulic acid ,feruloyl esterase ,X-ray crystallography - Abstract
Ferulic acid and related hydroxycinnamic acids, used as antioxidants and preservatives in the food, cosmetic, pharmaceutical and biotechnology industries, are among the most abundant phenolic compounds present in plant biomass. Identification of novel compounds that can produce ferulic acid and hydroxycinnamic acids, that are safe and can be mass-produced, is critical for the sustainability of these industries. In this study, we aimed to obtain and characterize a feruloyl esterase (LaFae) from Lactobacillus acidophilus. Our results demonstrated that LaFae reacts with ethyl ferulate and can be used to effectively produce ferulic acid from wheat bran, rice bran and corn stalks. In addition, xylanase supplementation was found to enhance LaFae enzymatic hydrolysis, thereby augmenting ferulic acid production. To further investigate the active site configuration of LaFae, crystal structures of unliganded and ethyl ferulate-bound LaFae were determined at 2.3 and 2.19 Å resolutions, respectively. Structural analysis shows that a Phe34 residue, located at the active site entrance, acts as a gatekeeper residue and controls substrate binding. Mutating this Phe34 to Ala produced an approximately 1.6-fold increase in LaFae activity against p-nitrophenyl butyrate. Our results highlight the considerable application potential of LaFae to produce ferulic acid from plant biomass and agricultural by-products.
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- 2023
- Full Text
- View/download PDF
11. Dual functional roles of a novel bifunctional β-lactamase/esterase from Lactococcus garvieae
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Ly Thi Huong Luu, Le, Wanki, Yoo, Ying, Wang, Sangeun, Jeon, Kyeong Kyu, Kim, Han-Woo, Kim, and T Doohun, Kim
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Structural Biology ,Lactococcus ,Esterases ,Amino Acid Sequence ,Cefotaxime ,General Medicine ,Molecular Biology ,Biochemistry ,beta-Lactamases ,Anti-Bacterial Agents - Abstract
A novel bifunctional β-lactamase/esterase (LgLacI), which is capable of hydrolyzing β-lactam-containing antibiotics including ampicillin, oxacillin, and cefotaxime as well as synthesizing biodiesels, was cloned from Lactococcus garvieae. Unlike most bacterial esterases/lipases that have G-x-S-x-G motif, LgLacI, which contains S-x-x-K catalytic motif, has sequence similarities to bacterial family VIII esterase as well as β-lactamases. The catalytic properties of LgLacI were explored using a wide range of biochemical methods including spectroscopy, assays, structural modeling, mutagenesis, and chromatography. We confirmed the bifunctional property of LgLacI hydrolyzing both esters and β-lactam antibiotics. This study provides novel perspectives into a bifunctional enzyme from L. garvieae, which can degrade β-lactam antibiotics with high esterase activity.
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- 2022
12. Formation of Non-Nucleoplasmic Proteasome Foci during the Late Stage of Hyperosmotic Stress
- Author
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Eunkyoung Kim, Ly Thi Huong Luu Le, Min Jae Lee, and Jee Young Lee
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Cytoplasm ,Proteasome Endopeptidase Complex ,QH301-705.5 ,Nuclear Envelope ,Active Transport, Cell Nucleus ,stress granule ,Article ,Protein Aggregates ,Stress granule ,Osmotic Pressure ,Stress, Physiological ,Cell Line, Tumor ,nuclear pore complex ,medicine ,Inner membrane ,Humans ,Biology (General) ,Nuclear pore ,Cell Nucleus ,nucleocytoplasmic transport ,Chemistry ,Proteins ,liquid droplet ,General Medicine ,Chromatin ,Cell biology ,Cytosol ,medicine.anatomical_structure ,proteasome ,Proteasome ,nuclear foci ,Nucleocytoplasmic Transport ,hyperosmotic stress ,Nuclear Pore ,insulator body ,phase separation ,Nucleus - Abstract
Cellular stress induces the formation of membraneless protein condensates in both the nucleus and cytoplasm. The nucleocytoplasmic transport of proteins mainly occurs through nuclear pore complexes (NPCs), whose efficiency is affected by various stress conditions. Here, we report that hyperosmotic stress compartmentalizes nuclear 26S proteasomes into dense nuclear foci, independent of signaling cascades. Most of the proteasome foci were detected between the condensed chromatin mass and inner nuclear membrane. The proteasome-positive puncta were not colocalized with other types of nuclear bodies and were reversibly dispersed when cells were returned to the isotonic medium. The structural integrity of 26S proteasomes in the nucleus was slightly affected under the hyperosmotic condition. We also found that these insulator-body-like proteasome foci were possibly formed through disrupted nucleus-to-cytosol transport, which was mediated by the sequestration of NPC components into osmostress-responding stress granules. These data suggest that phase separation in both the nucleus and cytosol may be a major cell survival mechanism during hyperosmotic stress conditions.
- Published
- 2021
13. A novel enantioselective SGNH family esterase (NmSGNH1) from Neisseria meningitides: Characterization, mutational analysis, and ester synthesis
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Kyeong Kyu Kim, T. Doohun Kim, Jun Hyuck Lee, Wanki Yoo, and Ly Thi Huong Luu Le
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Models, Molecular ,Meningitides ,02 engineering and technology ,Meningitis, Meningococcal ,Neisseria meningitidis ,Esterase ,Substrate Specificity ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Enzyme Stability ,Humans ,Point Mutation ,Amino Acid Sequence ,Molecular Biology ,030304 developmental biology ,Thermostability ,chemistry.chemical_classification ,0303 health sciences ,biology ,Esterases ,Fatty acid ,Esters ,Stereoisomerism ,Cell Biology ,021001 nanoscience & nanotechnology ,biology.organism_classification ,Enzyme ,chemistry ,Biochemistry ,Neisseria ,Peptidoglycan ,0210 nano-technology ,Butyl acetate ,Sequence Alignment - Abstract
In Neisseria sp., SGNH family esterases are involved in bacterial pathogenesis as well as cell wall peptidoglycan maturation. Here, a novel enantioselective SGNH family esterase (NmSGNH1) from Neisseria meningitidis, which has sequence similarity to carbohydrate esterase (CE3) family, was catalytically characterized and functionally explored. NmSGNH1 exhibited a wide range of substrate specificities including naproxol acetate, tert-butyl acetate, glucose pentaacetate as well as p-nitrophenyl esters. Deletion of C-terminal residues (NmSGNH1Δ11) led to the altered substrate specificity, reduced catalytic activity, and increased thermostability. Furthermore, a hydrophobic residue of Leu92 in the substrate-binding pocket was identified to be critical in catalytic activity, thermostability, kinetics, and enantioselectivity. Interestingly, immobilization of NmSGNH1 by hybrid nanoflowers (hNFs) and crosslinked enzyme aggregates (CLEAs) showed increased level of activity, recycling property, and enhanced stability. Finally, synthesis of butyl acetate, oleic acid esters, and fatty acid methyl esters (FAMEs) were verified. In summary, this work provides a molecular understanding of substrate specificities, catalytic regulation, immobilization, and industrial applications of a novel SGNH family esterase from Neisseria meningitidis.
- Published
- 2019
14. Characterization, immobilization, and mutagenesis of a novel cold-active acetylesterase (EaAcE) from Exiguobacterium antarcticum B7
- Author
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Wanki Yoo, Kyeong Kyu Kim, Chang Woo Lee, Ly Thi Huong Luu Le, Jun Hyuck Lee, T. Doohun Kim, and Ying Wang
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Models, Molecular ,Protein Conformation ,Mutagenesis (molecular biology technique) ,02 engineering and technology ,Biochemistry ,Esterase ,Substrate Specificity ,03 medical and health sciences ,Acetic acid ,chemistry.chemical_compound ,Structural Biology ,Enzyme Stability ,Amino Acid Sequence ,Homology modeling ,Lipase ,Psychrophile ,Bacillaceae ,Molecular Biology ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,Computational Biology ,General Medicine ,Acetylesterase ,Enzymes, Immobilized ,021001 nanoscience & nanotechnology ,Cold Temperature ,Kinetics ,Enzyme ,chemistry ,Mutagenesis ,biology.protein ,0210 nano-technology - Abstract
Cold-active enzymes with distinctive properties from a psychrophilic Exiguobacterium antarcticum B7 could be excellent biocatalysts in industrial and biotechnological processes. Here, the characterization, immobilization, and site-directed mutagenesis of a novel cold-active acetylesterase (EaAcE) from E. antarcticum B7 is reported. EaAcE does not belong to any currently known lipase/esterase family, although there are some sequence similarities with family III and V members. Biochemical characterization of EaAcE was carried out using activity staining, mass spectrometry analysis, circular dichroism spectra, freeze-thaw experiments, kinetic analysis, acetic acid release assays, and enantioselectivity determination. Furthermore, immobilization of EaAcE using four different approaches was explored to enhance its thermal stability and recyclability. Based on a homology model of EaAcE, four mutations (F45A, S118A, S141A, and T216A) within the substrate-binding pocket were investigated to elucidate their roles in EaAcE catalysis and substrate specificity. This work has provided invaluable information on the properties of EaAcE, which can now be used to understand the acetylesterase enzyme family.
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- 2019
15. Modulating α-synuclein fibril formation using DNA tetrahedron nanostructures
- Author
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Kyoung-Ran Kim, Kyeong Kyu Kim, Bum Han Ryu, Ly Thi Huong Luu Le, Dae-Ro Ahn, Gergely Toth, Wan Ki Yoo, Ying Wang, T. Doohun Kim, and Jun Hyuck Lee
- Subjects
0301 basic medicine ,Amyloid ,Nanostructure ,Light ,Biophysics ,macromolecular substances ,Microscopy, Atomic Force ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Microscopy, Electron, Transmission ,mental disorders ,Humans ,Scattering, Radiation ,Benzothiazoles ,Cytotoxicity ,Molecular Biology ,Alpha-synuclein ,Synucleinopathies ,Parkinson Disease ,DNA ,Nanostructures ,nervous system diseases ,030104 developmental biology ,chemistry ,Chromatography, Gel ,alpha-Synuclein ,Nucleic acid ,Nucleic Acid Conformation ,Thioflavin ,030217 neurology & neurosurgery - Abstract
The small presynaptic protein α-synuclein (α-syn) is involved in the etiology of Parkinson's disease owing to its abnormal misfolding. To date, little information is known on the role of DNA nanostructures in the formation of α-syn amyloid fibrils. Here, the effects of DNA tetrahedrons on the formation of α-syn amyloid fibrils were investigated using various biochemical and biophysical methods such as thioflavin T fluorescence assay, atomic force microscopy, light scattering, transmission electron microscopy, and cell-based cytotoxicity assay. It has been shown that DNA tetrahedrons decreased the level of oligomers and increased the level of amyloid fibrils, which corresponded to decreased cellular toxicity. The ability of DNA tetrahedron to facilitate the formation of α-syn amyloid fibrils demonstrated that structured nucleic acids such as DNA tetrahedrons could modulate the process of amyloid fibril formation. Our study suggests that DNA tetrahedrons could be used as an important facilitator toward amyloid fibril formation of α-synuclein, which may be of significance in finding therapeutic approaches to Parkinson's disease and related synucleinopathies.
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- 2019
16. Pentaminomycins C–E: Cyclic Pentapeptides as Autophagy Inducers from a Mealworm Beetle Gut Bacterium
- Author
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Jongheon Shin, Min Jae Lee, Dong-Chan Oh, Ly Thi Huong Luu Le, Shin-Il Jo, and Sunghoon Hwang
- Subjects
Microbiology (medical) ,Mealworm ,gut bacteria ,Penicillin binding proteins ,autophagy inducer ,mealworm ,010402 general chemistry ,OSMAC ,01 natural sciences ,Microbiology ,Streptomyces ,Article ,Nonribosomal peptide ,Virology ,Gene cluster ,lcsh:QH301-705.5 ,Adenylylation ,chemistry.chemical_classification ,biology ,010405 organic chemistry ,cyclic peptides ,biology.organism_classification ,biosynthetic pathway ,Cyclic peptide ,0104 chemical sciences ,Amino acid ,lcsh:Biology (General) ,chemistry ,Biochemistry ,insect - Abstract
Pentaminomycins C&ndash, E (1&ndash, 3) were isolated from the culture of the Streptomyces sp. GG23 strain from the guts of the mealworm beetle, Tenebrio molitor. The structures of the pentaminomycins were determined to be cyclic pentapeptides containing a modified amino acid, N5-hydroxyarginine, based on 1D and 2D NMR and mass spectroscopic analyses. The absolute configurations of the amino acid residues were assigned using Marfey&rsquo, s method and bioinformatics analysis of their nonribosomal peptide biosynthetic gene cluster (BGC). Detailed analysis of the BGC enabled us to propose that the structural variations in 1&ndash, 3 originate from the low specificity of the adenylation domain in the nonribosomal peptide synthetase (NRPS) module 1, and indicate that macrocyclization can be catalyzed noncanonically by penicillin binding protein (PBP)-type TE. Furthermore, pentaminomycins C and D (1 and 2) showed significant autophagy-inducing activities and were cytoprotective against oxidative stress in vitro.
- Published
- 2020
17. Biodiesel and flavor compound production using a novel promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from the psychrophilic bacterium Halocynthiibacter arcticus
- Author
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Chang Woo Lee, Wanki Yoo, Ly Thi Huong Luu Le, T. Doohun Kim, Sangeun Jeon, Jun Hyuck Lee, and Kyeong Kyu Kim
- Subjects
0106 biological sciences ,Substrate specificity ,lcsh:Biotechnology ,Triacylglycerol lipase ,HaSGNH1 ,Management, Monitoring, Policy and Law ,01 natural sciences ,Applied Microbiology and Biotechnology ,lcsh:Fuel ,Catalysis ,Immobilization ,03 medical and health sciences ,lcsh:TP315-360 ,lcsh:TP248.13-248.65 ,010608 biotechnology ,Organic chemistry ,Lipase ,Psychrophile ,Flavor ,030304 developmental biology ,SGNH-type lipase ,chemistry.chemical_classification ,0303 health sciences ,Biodiesel ,biology ,Renewable Energy, Sustainability and the Environment ,Chemistry ,Transesterification ,Amino acid ,General Energy ,biology.protein ,Halocynthiibacter arcticus ,Biotechnology - Abstract
Background Biodiesel and flavor compound production using enzymatic transesterification by microbial lipases provides mild reaction conditions and low energy cost compared to the chemical process. SGNH-type lipases are very effective catalysts for enzymatic transesterification due to their high reaction rate, great stability, relatively small size for convenient genetic manipulations, and ease of immobilization. Hence, it is highly important to identify novel SGNH-type lipases with high catalytic efficiencies and good stabilities. Results A promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from Halocynthiibacter arcticus was catalytically characterized and functionally explored. HaSGNH1 displayed broad substrate specificity that included tert-butyl acetate, glucose pentaacetate, and p-nitrophenyl esters with excellent stability and high efficiency. Important amino acids (N83, M86, R87, F131, and I173F) around the substrate-binding pocket were shown to be responsible for catalytic activity, substrate specificity, and reaction kinetics. Moreover, immobilized HaSGNH1 was used to produce high yields of butyl and oleic esters. Conclusions This work provides a molecular understanding of substrate specificities, catalytic regulation, immobilization, and industrial applications of a promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from H. arcticus. This is the first analysis on biodiesel and flavor synthesis using a cold-adapted halophilic SGNH-type lipase from a Halocynthiibacter species.
- Published
- 2020
18. Characterization and Immobilization of a Novel SGNH Family Esterase (
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Ly Thi Huong Luu, Le, Wanki, Yoo, Sangeun, Jeon, Kyeong Kyu, Kim, and T Doohun, Kim
- Subjects
LaSGNH1 ,Binding Sites ,Communication ,Enzymes, Immobilized ,Substrate Specificity ,Lactobacillus acidophilus ,Bacterial Proteins ,Phospholipases ,Enzyme Stability ,immobilization ,crosslinked enzyme aggregates ,SGNH family esterases ,Conserved Sequence ,Protein Binding - Abstract
The SGNH family esterases are highly effective biocatalysts due to their strong catalytic efficiencies, great stabilities, relatively small sizes, and ease of immobilization. Here, a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus NCFM, which has homologues in many Lactobacillus species, was identified, characterized, and immobilized. LaSGNH1 is highly active towards acetate- or butyrate-containing compounds, such as p-nitrophenyl acetate or 1-naphthyl acetate. Enzymatic properties of LaSGNH1, including thermal stability, optimum pH, chemical stability, and urea stability, were investigated. Interestingly, LaSGNH1 displayed a wide range of substrate specificity that included glyceryl tributyrate, tert-butyl acetate, and glucose pentaacetate. Furthermore, immobilization of LaSGNH1 by crosslinked enzyme aggregates (CLEAs) showed enhanced thermal stability and efficient recycling property. In summary, this work paves the way for molecular understandings and industrial applications of a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus.
- Published
- 2019
19. Molecular Characterization of a Novel Cold-Active Hormone-Sensitive Lipase (HaHSL) from Halocynthiibacter Arcticus
- Author
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Wanki Yoo, Chang Woo Lee, Sangeun Jeon, T. Doohun Kim, Jun Hyuck Lee, Ying Wang, Kyeong Kyu Kim, and Ly Thi Huong Luu Le
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0106 biological sciences ,0301 basic medicine ,Models, Molecular ,substrate specificity ,Molecular Conformation ,lcsh:QR1-502 ,Hormone-sensitive lipase ,01 natural sciences ,Biochemistry ,Article ,lcsh:Microbiology ,Catalysis ,03 medical and health sciences ,chemistry.chemical_compound ,Fish Oils ,Bacterial Proteins ,010608 biotechnology ,enantioselectivity ,Glycerol ,Aromatic amino acids ,Homology modeling ,Cloning, Molecular ,Rhodobacteraceae ,Molecular Biology ,Thermostability ,chemistry.chemical_classification ,Binding Sites ,biology ,food and beverages ,Esters ,Sterol Esterase ,Enzymes, Immobilized ,Enzyme assay ,030104 developmental biology ,Enzyme ,chemistry ,hormone-sensitive lipase ,Structural Homology, Protein ,halocynthiibacter arcticus ,Mutation ,immobilization ,biology.protein ,Tyrosine ,Halocynthiibacter arcticus - Abstract
Bacterial hormone-sensitive lipases (bHSLs), which are homologous to the catalytic domains of human HSLs, have received great interest due to their uses in the preparation of highly valuable biochemicals, such as drug intermediates or chiral building blocks. Here, a novel cold-active HSL from Halocynthiibacter arcticus (HaHSL) was examined and its enzymatic properties were investigated using several biochemical and biophysical methods. Interestingly, HaHSL acted on a large variety of substrates including tertiary alcohol esters and fish oils. Additionally, this enzyme was highly tolerant to high concentrations of salt, detergents, and glycerol. Furthermore, immobilized HaHSL retained its activity for up to six cycles of use. Homology modeling suggested that aromatic amino acids (Trp23, Tyr74, Phe78, Trp83, and Phe245) in close proximity to the substrate-binding pocket were important for enzyme activity. Mutational analysis revealed that Tyr74 played an important role in substrate specificity, thermostability, and enantioselectivity. In summary, the current study provides an invaluable insight into the novel cold-active HaHSL from H. arcticus, which can be efficiently and sustainably used in a wide range of biotechnological applications.
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- 2019
20. Biodiesel and flavor compound production using a novel promiscuous cold-adapted SGNH-type lipase (
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Ly Thi Huong Luu, Le, Wanki, Yoo, Sangeun, Jeon, Changwoo, Lee, Kyeong Kyu, Kim, Jun Hyuck, Lee, and T Doohun, Kim
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SGNH-type lipase ,Immobilization ,Research ,Substrate specificity ,HaSGNH1 ,Biodiesel ,Halocynthiibacter arcticus - Abstract
Background Biodiesel and flavor compound production using enzymatic transesterification by microbial lipases provides mild reaction conditions and low energy cost compared to the chemical process. SGNH-type lipases are very effective catalysts for enzymatic transesterification due to their high reaction rate, great stability, relatively small size for convenient genetic manipulations, and ease of immobilization. Hence, it is highly important to identify novel SGNH-type lipases with high catalytic efficiencies and good stabilities. Results A promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from Halocynthiibacter arcticus was catalytically characterized and functionally explored. HaSGNH1 displayed broad substrate specificity that included tert-butyl acetate, glucose pentaacetate, and p-nitrophenyl esters with excellent stability and high efficiency. Important amino acids (N83, M86, R87, F131, and I173F) around the substrate-binding pocket were shown to be responsible for catalytic activity, substrate specificity, and reaction kinetics. Moreover, immobilized HaSGNH1 was used to produce high yields of butyl and oleic esters. Conclusions This work provides a molecular understanding of substrate specificities, catalytic regulation, immobilization, and industrial applications of a promiscuous cold-adapted SGNH-type lipase (HaSGNH1) from H. arcticus. This is the first analysis on biodiesel and flavor synthesis using a cold-adapted halophilic SGNH-type lipase from a Halocynthiibacter species.
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- 2019
21. Structural and functional characterization of a novel cold-active S-formylglutathione hydrolase (SfSFGH) homolog from Shewanella frigidimarina, a psychrophilic bacterium
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Seung Chul Shin, Wanki Yoo, Kyeong Kyu Kim, Han-Woo Kim, S. H. Park, Chang-Sook Jeong, Jun Hyuck Lee, Ly Thi Huong Luu Le, Chang Woo Lee, Hyun Park, Bum Han Ryu, and T. Doohun Kim
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Models, Molecular ,Shewanella frigidimarina ,Shewanella ,Formates ,Protein Conformation ,Substrate specificity ,lcsh:QR1-502 ,Bioengineering ,Applied Microbiology and Biotechnology ,Esterase ,lcsh:Microbiology ,Catalytic Domain ,Catalytic triad ,Hydrolase ,Escherichia coli ,Cloning, Molecular ,chemistry.chemical_classification ,Sequence Homology, Amino Acid ,biology ,Research ,Crystal structure ,Active site ,S-Formylglutathione hydrolase ,Protein engineering ,Hydrogen-Ion Concentration ,Glutathione ,Amino acid ,Kinetics ,Enzyme ,Biochemistry ,chemistry ,Mutagenesis ,biology.protein ,Thiolester Hydrolases ,Biotechnology - Abstract
Background S-Formylglutathione is hydrolyzed to glutathione and formate by an S-formylglutathione hydrolase (SFGH) (3.1.2.12). This thiol esterase belongs to the esterase family and is also known as esterase D. SFGHs contain highly conserved active residues of Ser-Asp-His as a catalytic triad at the active site. Characterization and investigation of SFGH from Antarctic organisms at the molecular level is needed for industrial use through protein engineering. Results A novel cold-active S-formylglutathione hydrolase (SfSFGH) from Shewanella frigidimarina, composed of 279 amino acids with a molecular mass of ~ 31.0 kDa, was characterized. Sequence analysis of SfSFGH revealed a conserved pentapeptide of G-X-S-X-G found in various lipolytic enzymes along with a putative catalytic triad of Ser148-Asp224-His257. Activity analysis showed that SfSFGH was active towards short-chain esters, such as p-nitrophenyl acetate, butyrate, hexanoate, and octanoate. The optimum pH for enzymatic activity was slightly alkaline (pH 8.0). To investigate the active site configuration of SfSFGH, we determined the crystal structure of SfSFGH at 2.32 Å resolution. Structural analysis shows that a Trp182 residue is located at the active site entrance, allowing it to act as a gatekeeper residue to control substrate binding to SfSFGH. Moreover, SfSFGH displayed more than 50% of its initial activity in the presence of various chemicals, including 30% EtOH, 1% Triton X-100, 1% SDS, and 5 M urea. Conclusions Mutation of Trp182 to Ala allowed SfSFGH to accommodate a longer chain of substrates. It is thought that the W182A mutation increases the substrate-binding pocket and decreases the steric effect for larger substrates in SfSFGH. Consequently, the W182A mutant has a broader substrate specificity compared to wild-type SfSFGH. Taken together, this study provides useful structure–function data of a SFGH family member and may inform protein engineering strategies for industrial applications of SfSFGH. Electronic supplementary material The online version of this article (10.1186/s12934-019-1190-1) contains supplementary material, which is available to authorized users.
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- 2019
22. Structural and functional analysis of a dimeric fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum
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B.W. Kim, Jun Hyuck Lee, Wanki Yoo, Han-Woo Kim, Kyeong Kyu Kim, Ly Thi Huong Luu Le, T. Doohun Kim, Seung Chul Shin, Chang Woo Lee, and S. H. Park
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0301 basic medicine ,Models, Molecular ,Circular dichroism ,Stereochemistry ,Hydrolases ,Protein Conformation ,Size-exclusion chromatography ,Biophysics ,Crystallography, X-Ray ,Biochemistry ,Substrate Specificity ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Bacterial Proteins ,Catalytic Domain ,Hydrolase ,Aromatic amino acids ,Magnesium ,Carboxylate ,Amino Acid Sequence ,Molecular Biology ,Bacillaceae ,Phylogeny ,biology ,Chemistry ,Hydrolysis ,Active site ,Native Polyacrylamide Gel Electrophoresis ,Cell Biology ,030104 developmental biology ,030220 oncology & carcinogenesis ,biology.protein ,Fumarylacetoacetate hydrolase ,Protein Multimerization ,Sequence Alignment - Abstract
Fumarylacetoacetate hydrolase (FAH) is essential for the degradation of aromatic amino acids as well as for the cleavage of carbon-carbon bonds in metabolites or small organic compounds. Here, the X-ray crystal structure of EaFAH, a dimeric fumarylacetoacetate hydrolase from Exiguobacterium antarcticum, was determined, and its functional properties were investigated using biochemical methods. EaFAH adopts a mixed β-sandwich roll fold with a highly flexible lid region (Val73-Leu94), and an Mg2+ ion is bound at the active site by coordinating to the three carboxylate oxygen atoms of Glu124, Glu126, and Asp155. The hydrolytic activity of EaFAH toward various substrates, including linalyl acetate was investigated using native polyacrylamide gel electrophoresis, activity staining, gel filtration, circular dichroism spectroscopy, fluorescence, and enzyme assays.
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- 2018
23. Characterization and Immobilization of a Novel SGNH Family Esterase (LaSGNH1) from Lactobacillus acidophilus NCFM
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Kyeong Kyu Kim, Ly Thi Huong Luu Le, Wanki Yoo, Sangeun Jeon, and T. Doohun Kim
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0301 basic medicine ,chemistry.chemical_classification ,030106 microbiology ,Organic Chemistry ,General Medicine ,Esterase ,Catalysis ,Computer Science Applications ,Inorganic Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Enzyme ,Lactobacillus acidophilus ,Biochemistry ,chemistry ,Urea ,Chemical stability ,Thermal stability ,Physical and Theoretical Chemistry ,Lactobacillus species ,Molecular Biology ,Spectroscopy - Abstract
The SGNH family esterases are highly effective biocatalysts due to their strong catalytic efficiencies, great stabilities, relatively small sizes, and ease of immobilization. Here, a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus NCFM, which has homologues in many Lactobacillus species, was identified, characterized, and immobilized. LaSGNH1 is highly active towards acetate- or butyrate-containing compounds, such as p-nitrophenyl acetate or 1-naphthyl acetate. Enzymatic properties of LaSGNH1, including thermal stability, optimum pH, chemical stability, and urea stability, were investigated. Interestingly, LaSGNH1 displayed a wide range of substrate specificity that included glyceryl tributyrate, tert-butyl acetate, and glucose pentaacetate. Furthermore, immobilization of LaSGNH1 by crosslinked enzyme aggregates (CLEAs) showed enhanced thermal stability and efficient recycling property. In summary, this work paves the way for molecular understandings and industrial applications of a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus.
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- 2019
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