Hyungdon Yun

Konkuk University, Sŏul, Seoul, South Korea

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Publications (82)

  • Pradeepraj Durairaj · Jae-Seoun Hur · Hyungdon Yun
    [Show abstract] [Hide abstract] ABSTRACT: Cytochrome P450 (CYP) monooxygenases, the nature’s most versatile biological catalysts have unique ability to catalyse regio-, chemo-, and stereospecific oxidation of a wide range of substrates under mild reaction conditions, thereby addressing a significant challenge in chemocatalysis. Though CYP enzymes are ubiquitous in all biological kingdoms, the divergence of CYPs in fungal kingdom is manifold. The CYP enzymes play pivotal roles in various fungal metabolisms starting from housekeeping biochemical reactions, detoxification of chemicals, and adaptation to hostile surroundings. Considering the versatile catalytic potentials, fungal CYPs has gained wide range of attraction among researchers and various remarkable strategies have been accomplished to enhance their biocatalytic properties. Numerous fungal CYPs with multispecialty features have been identified and the number of characterized fungal CYPs is constantly increasing. Literature reveals ample reviews on mammalian, plant and bacterial CYPs, however, modest reports on fungal CYPs urges a comprehensive review highlighting their novel catalytic potentials and functional significances. In this review, we focus on the diversification and functional diversity of fungal CYPs and recapitulate their unique and versatile biocatalytic properties. As such, this review emphasizes the crucial issues of fungal CYP systems, and the factors influencing efficient biocatalysis.
    Article · Dec 2016 · Microbial Cell Factories
  • [Show abstract] [Hide abstract] ABSTRACT: Bacterial cytochrome P450 enzymes in cytochrome P450 (CYP)153 family were recently reported as fatty acid ω-hydroxylase. Among them, CYP153As from Marinobacter aquaeolei VT8 (CYP153A33), Alcanivorax borkumensis SK2 (CYP153A13), and Gordonia alkanivorans (CYP153A35) were selected, and their specific activities and product yields of ω-hydroxy palmitic acid based on whole cell reactions toward palmitic acid were compared. Using CamAB as redox partner, CYP153A35 and CYP153A13 showed the highest product yields of ω-hydroxy palmitic acid in whole cell and in vitro reactions, respectively. Artificial self-sufficient CYP153A35-BMR was constructed by fusing it to the reductase domain of CYP102A1 (i.e., BM3) from Bacillus megaterium, and its catalytic activity was compared with CYP153A35 and CamAB systems. Unexpectedly, the system with CamAB resulted in a 1.5-fold higher yield of ω-hydroxy palmitic acid than that using A35-BMR in whole cell reactions, whereas the electron coupling efficiency of CYP153A35-BM3 reductase was 4-fold higher than that of CYP153A35 and CamAB system. Furthermore, various CamAB expression systems according to gene arrangements of the three proteins and promoter strength in their gene expression were compared in terms of product yields and productivities. Tricistronic expression of the three proteins in the order of putidaredoxin (CamB), CYP153A35, and putidaredoxin reductase (CamA), i.e., A35-AB2, showed the highest product yield from 5 mM palmitic acid for 9 h in batch reaction owing to the concentration of CamB, which is the rate-limiting factor for the activity of CYP153A35. However, in fed-batch reaction, A35-AB1, which expressed the three proteins individually using three T7 promoters, resulted with the highest product yield of 17.0 mM (4.6 g/L) ω-hydroxy palmitic acid from 20 mM (5.1 g/L) palmitic acid for 30 h.
    Article · Jun 2016 · Applied Microbiology and Biotechnology
  • Sam Mathew · Saravanan Prabhu Nadarajan · Taeowan Chung · [...] · Hyungdon Yun
    [Show abstract] [Hide abstract] ABSTRACT: An (S)-ω-transaminase from the thermophilic eubacterium Sphaerobacter thermophilus was expressed and functionally characterized. The enzyme showed good stability at high temperature and in the presence of various substrates. Substrate specificity analysis showed that the enzyme had activity towards a broad range of substrates including amines, β- and γ-amino acids. The purified enzyme showed a specific activity of 3.3 U/mg towards rac-β-phenylalanine at 37 °C. The applicability of this enzyme as an attractive biocatalyst was demonstrated by synthesizing optically pure β- and γ-amino acids. Among the various beta and gamma amino acids produced via asymmetric synthesis, (S)-4-amino-4-(4-methoxyphenyl)-butanoic acid showed highest analytical yield (82%) with excellent enantiomeric excess (>99%).
    Article · Jun 2016 · Enzyme and Microbial Technology
  • Sam Mathew · Kanagavel Deepankumar · Giyoung Shin · [...] · Hyungdon Yun
    [Show abstract] [Hide abstract] ABSTRACT: A novel thermostable ω-transaminase from Thermomicrobium roseum which showed broad substrate specificity and high enantioselectivity was identified, expressed and biochemically characterized. The advantage of this enzyme to remove volatile inhibitory by-products was demonstrated by performing asymmetric synthesis and kinetic resolution at high temperature.
    Article · Jan 2016 · RSC Advances
  • [Show abstract] [Hide abstract] ABSTRACT: Bacterial Light-Oxygen-Voltage sensing photoreceptor derived Flavin mononucleotide-based fluorescent proteins act as a promising distinct class of fluorescent proteins utilized for various biomedical and biotechnological applications. The key property of its independency towards oxygen for its chromophore maturation has greatly helped this protein to outperform the other fluorescent proteins such as GFP and DsRed for anaerobic applications. Here we describe the feasibility of FMN containing fluorescent protein FbFP as a metal sensing probe by measuring the fluorescence emission changes of a protein with respect to the concentration of metal ions. In the present study, we demonstrated the mercury sensing ability of FbFP protein and the possible amino acids responsible for metal binding. Ratiometric approach was employed here in order to exploit the fluorescence changes observed at two different emission maxima with respect to Hg(2+) at micromolar concentration. The engineered variant FbFPC56I shows high sensitivity towards Hg(2+) and followed a good linear relationship from 0.1 µM to until 3 µM of Hg(2+). So, further engineering with rational approach would enable the FbFP to be developed as a novel and highly selective and sensitive biosensor for other toxic heavy metal ions as well.
    Article · Dec 2015 · Journal of Microbiology and Biotechnology
  • Sam Mathew · Seong-Su Jeong · Taeowan Chung · [...] · Hyungdon Yun
    [Show abstract] [Hide abstract] ABSTRACT: Synthesized aromatic β-amino acids have recently attracted considerable attention for their application as precursors in many pharmacologically relevant compounds. Previous studies on asymmetric synthesis of aromatic β-amino acids using ?-transaminases could not be done efficiently due to the instability of β-keto acids. In this study, a strategy to circumvent the instability problem of β-keto acids was utilized to generate β-amino acids efficiently via asymmetric synthesis. In this work, thermodynamically stable β-ketoesters were initially converted to β-keto acids using lipase, and the β-keto acids were subsequently aminated using ?-transaminase. By optimizing the lipase concentration, we successfully overcame the instability problem of β-keto acids and enhanced the production of β-amino acids. This strategy can be used as a general approach to efficiently generate β-amino acids from β-keto esters.
    Article · Oct 2015 · Biotechnology Journal
  • [Show abstract] [Hide abstract] ABSTRACT: The bioprocess engineering with biocatalysts broadly spans its development and actual application of enzymes in an industrial context. Recently, both the use of bioprocess engineering and the development and employment of enzyme engineering techniques have been increasing rapidly. Importantly, engineering techniques that incorporate unnatural amino acids (UAAs) in vivo has begun to produce enzymes with greater stability and altered catalytic properties. Despite the growth of this technique, its potential value in bioprocess applications remains to be fully exploited. In this review, we explore the methodologies involved in UAA incorporation as well as ways to synthesize these UAAs. In addition, we summarize recent efforts to increase the yield of UAA engineered proteins in Escherichia coli and also the application of this tool in enzyme engineering. Furthermore, this protein engineering tool based on the incorporation of UAA can be used to develop immobilized enzymes that are ideal for bioprocess applications. Considering the potential of this tool and by exploiting these engineered enzymes, we expect the field of bioprocess engineering to open up new opportunities for biocatalysis in the near future.
    Article · Sep 2015 · Biotechnology Journal
  • Dataset · Jul 2015
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    [Show abstract] [Hide abstract] ABSTRACT: For the construction of an efficient copper waste treatment system, a cell surface display strategy was employed. The copper adsorption ability of recombinant bacterial strains displaying three different copper binding peptides were evaluated in LB Luria–Bertani medium (LB), artificial wastewater, and copper phthalocyanine containing textile dye industry wastewater samples. Structural characteristics of the three peptides were also analyzed by similarity-based structure modeling. The best binding peptide was chosen for the construction of a dimeric peptide display and the adsorption ability of the monomeric and dimeric peptide displayed strains were compared. The dimeric peptide displayed strain showed superior copper adsorption in all three tested conditions (LB, artificial wastewater, and textile dye industry wastewater). When the strains were exposed to copper phthalocyanine dye polluted wastewater, the dimeric pep-tide display [543.27 lmol/g DCW dry cell weight (DCW)] showed higher adsorption of copper when compared with the monomeric strains (243.53 lmol/g DCW).
    Full-text Article · Jul 2015 · Bioprocess and Biosystems Engineering
  • [Show abstract] [Hide abstract] ABSTRACT: Traditional enzyme engineering relies on substituting one amino acid by one of the other 19 natural amino acids to change the functional properties of an enzyme. However, incorporation of unnatural amino acids (UAAs) has been harnessed to engineer efficient enzymes for biocatalysis. Residue-specific and site-specific in vivo incorporation methods are becoming the preferred approach for producing enzymes with altered or improved functions. We describe the contribution of in vivo UAA incorporation methodologies to enzyme engineering as well as the future prospects for the field, including the integration of UAAs with other new advances in enzyme engineering. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Article · Jun 2015 · Trends in Biotechnology
  • [Show abstract] [Hide abstract] ABSTRACT: The iLOV protein belongs to a family of blue-light photoreceptor proteins containing a lightoxygen- voltage sensing domain with a noncovalently bound flavin mononucleotide (FMN) as its chromophore. Owing to advantages such as its small size, oxygen-independent nature, and pH stability, iLOV is an ideal candidate over other reporter fluorescent proteins such as GFP and DsRed. Here, for the first time, we describe the feasibility of applying LOV domain-based fluorescent iLOV as a metal sensor by measuring the fluorescence quenching of a protein with respect to the concentration of metal ions. In the present study, we demonstrated the inherent copper sensing property of the iLOV protein and identified the possible amino acids responsible for metal binding. The fluorescence quenching upon exposure to Cu2++ was highly sensitive and exhibited reversibility upon the addition of the metal chelator EDTA. The copper binding constant was found to be 4.72 ± 0.84 μM. In addition, Cu2+-bound iLOV showed high fluorescence quenching at near physiological pH. Further computational analysis yielded a better insight into understanding the possible amino acids responsible for Cu2++ binding with the iLOV protein. © 2015 by The Korean Society for Microbiology and Biotechnology.
    Article · Apr 2015 · Journal of Microbiology and Biotechnology
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    [Show abstract] [Hide abstract] ABSTRACT: Omega hydroxy fatty acids (ω-OHFAs) are multifunctional compounds that act as the basis for the production of various industrial products with broad commercial and pharmaceutical implications. However, the terminal oxygenation of saturated or unsaturated fatty acids for the synthesis of ω-OHFAs is intricate to accomplish through chemocatalysis, due to the selectivity and controlled reactivity in C-H oxygenation reactions. Cytochrome P450, the ubiquitous enzyme is capable of catalyzing the selective terminal omega hydroxylation naturally in biological kingdom. To gain a deep insight on the biochemical role of fungal P450s towards the production of omega hydroxy fatty acids, two cytochrome P450 monooxygenases from Fusarium oxysporum (FoCYP), FoCYP539A7 and FoCYP655C2; were identified, cloned, and heterologously expressed in Saccharomyces cerevisiae. For the efficient production of ω-OHFAs, the S. cerevisiae was engineered to disrupt the acyl-CoA oxidase enzyme and the β-oxidation pathway inactivated (ΔPox1) S. cerevisiae mutant was generated. To elucidate the significance of the interaction of redox mechanism, FoCYPs were reconstituted with the heterologous and homologous reductase systems - S. cerevisiae CPR (ScCPR) and F. oxysporum CPR (FoCPR). To further improve the yield, the effect of pH was analyzed and the homologous FoCYP-FoCPR system efficiently hydroxylated caprylic acid, capric acid and lauric acid into their respective ω-hydroxy fatty acids with 56%, 79% and 67% conversion. Furthermore, based on computational simulations, we identified the key residues (Asn106 of FoCYP539A7 and Arg235 of FoCYP655C2) responsible for the recognition of fatty acids and demonstrated the structural insights of the active site of FoCYPs. Fungal CYP monooxygenases, FoCYP539A7 and FoCYP655C2 with its homologous redox partner, FoCPR constitutes a promising catalyst due to its high regio- and stereo-selectivity in the hydroxylation of fatty acids and in the substantial production of industrially valuable ω-hydroxy fatty acids.
    Full-text Article · Apr 2015 · Microbial Cell Factories
  • [Show abstract] [Hide abstract] ABSTRACT: Genetically encoded fluorescent proteins are extensively utilized for labeling and imaging proteins, organelles, cell tissues, and whole organisms. In this study, we explored the feasibility of mRFP1 and its variants for measuring intracellular temperature. A linear relationship was observed between the temperature and fluorescence intensity of mRFP1 and its variants. Temperature sensitivities of E. coli expressing mRFP1, mRFP-P63A and mRFP-P63A[(4R)-FP] were −1.27%, −1.26% and −0.77%/°C, respectively. Finally, we demonstrated the potentiality of mRFP1 and its variants as an in vivo temperature sensor.
    Article · Mar 2015 · Biotechnology and Bioprocess Engineering
  • Sam Mathew · Hanseop Bea · Nadarajan Saravanan Prabhu · [...] · Hyungdon Yun
    [Show abstract] [Hide abstract] ABSTRACT: Optically pure β-amino acids are of high pharmacological significance since they are used as key ingredients in many physiologically active compounds. Despite a number of enzymatic routes to these compounds, an efficient synthesis of β-amino acids continues to pose a major challenge for researchers. ω-transaminase has emerged as an important class of enzymes for generating amine compounds. However, only a few ω-transaminases have been reported so far which show activity towards aromatic β-amino acids. In this study, (S)-ω-transaminase from Burkholderia graminis C4D1M has been functionally characterized and used for the production of chiral aromatic β-amino acids via kinetic resolution. The enzyme showed a specific activity of 3.1 U/mg towards rac-β-phenylalanine at 37°C. The Km and Kcat values of this enzyme towards rac-β-phenylalanine with pyruvate as the amino acceptor were 2.88mM and 91.57min(-1) respectively. Using this enzyme, racemic β-amino acids were kinetically resolved to produce (R)-β-amino acids with an excellent enantiomeric excess (>99%) and ∼50% conversion. Additionally, kinetic resolution of aromatic β-amino acids was performed using benzaldehyde as a cheap amino acceptor. Copyright © 2015. Published by Elsevier B.V.
    Article · Jan 2015 · Journal of Biotechnology
  • Pradeepraj Durairaj · Eunok Jung · Hyun Ho Park · [...] · Hyungdon Yun
    [Show abstract] [Hide abstract] ABSTRACT: FoCYP53A19, a novel cytochrome P450 capable of performing benzoate hydroxylation, was identified and characterized from the ascomycete Fusarium oxysporum f.sp. lycopersici. Comparative functional analysis of FoCYP53A19 with the heterologous and homologous cytochrome P450 reductases (CPR) such as Saccharomyces cerevisiae (ScCPR), Candida albicans (CaCPR) and F. oxysporum (FoCPR) revealed novel catalytic properties. The catalytic efficiency and substrate specificity of FoCYP53A19 was significantly influenced and altered by the source of the reductase employed. The yeast reconstitution system of FoCYP53A19 with ScCPR performed the hydroxylation of benzoic acid (BA) and demethylation of 3-methoxybenzoic acid (3-MBA); but when reconstituted with CaCPR, FoCYP53A19 performed only the essential hydroxylation of fungal benzoate catabolism. Remarkably, FoCYP53A19 with its homologous reductase FoCPR, not only demonstrated the improved conversion rates of BA and 3-MBA, but also exhibited activity towards the hydroxylation of 3-hydroxybenzoic acid. The electron transfer compatibility and the coupling efficiency between the homologous FoCYP-FoCPR system is significant and it favored enhanced monooxygenase activity with broader substrate specificity.
    Article · Dec 2014 · Enzyme and Microbial Technology
  • [Show abstract] [Hide abstract] ABSTRACT: In general, conventional enzyme engineering utilizes 20 canonical amino acids to alter and improve the functional properties of proteins such as stability, and activity. In this study, we utilized the noncanonical amino acid incorporation technique to enhance the functional properties of ω-transaminase (ω-TA). Herein, we enhanced the stability of ω-TA by residue-specific incorporation of (4R)-fluoroproline [(4R)-FP] and successfully immobilized onto chitosan or polystyrene (PS) beads with site-specifically incorporated L-3,4-dihydroxyphenylalanine (DOPA) moiety. The immobilization of ω-TAdopa and ω-TAdp[(4R)-FP] onto PS beads showed excellent reusability for 10 cycles in the kinetic resolution of chiral amines. Compared to the ω-TAdopa, the ω-TAdp[(4R)-FP] immobilized onto PS beads exerted more stability that can serve as suitable biocatalyst for the asymmetric synthesis of chiral amines.
    Article · Dec 2014 · ChemCatChem
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    Byeongseon Yang · Niraikulam Ayyadurai · Hyungdon Yun · [...] · Hyung Joon Cha
    [Show abstract] [Hide abstract] ABSTRACT: Misaminoacylation of 3,4-dihydroxyphenylalanine (Dopa) molecules to tRNATyr by endogenous tyrosyl-tRNA synthetase allowed the quantitative replacement of tyrosine residues with a yield of over 90 % by an in vivo residue-specific incorporation strategy, to create, for the first time, engineered mussel adhesive proteins (MAPs) in Escherichia coli with a very high Dopa content, close to that of natural MAPs. The Dopa-incorporated MAPs exhibited a superior surface adhesion and water resistance ability by assistance of Dopa-mediated interactions including the oxidative Dopa cross-linking, and furthermore, showed underwater adhesive properties comparable to those of natural MAPs. These results propose promising use of Dopa-incorporated engineered MAPs as bioglues or adhesive hydrogels for practical underwater applications.
    Full-text Article · Dec 2014 · Angewandte Chemie
  • [Show abstract] [Hide abstract] ABSTRACT: Lead is one of the most hazardous metals ubiquitous in the environment, causing serious health hazards to organisms. Recently, fluorescent proteins such as GFP and Dsred were utilized for the development of reagent-less rapid metal sensors. Here, we demonstrate the development of a lead-sensing GFP that is highly sensitive to lead in micro molar concentrations
    Article · Nov 2014 · Chemical Communications
  • [Show abstract] [Hide abstract] ABSTRACT: The iLOV protein belongs to a family of blue-light photoreceptor proteins containing a light-oxygen-voltage sensing domain with a non-covalently bound flavin mononucleotide (FMN) as its chromophore. Due to advantages such as small size, oxygen-independent nature, and pH stability, iLOV is an ideal candidate over other reporter fluorescent proteins such as GFP and DsRed. Here, for the first time, we describe the feasibility of applying LOV domain-based fluorescent iLOV as a metal sensor by measuring the fluorescence quenching of a protein with respect to the concentration of metal ions. In the present study, we demonstrate the inherent copper sensing property of the iLOV protein and identify the possible amino acids responsible for metal binding. The fluorescence quenching upon exposure to Cu(2+) was highly sensitive and exhibited reversibility upon the addition of the metal chelator EDTA. The copper binding constant was found to be 4.72 ± 0.84 µM. In addition, Cu(2+)-bound iLOV showed high fluorescence quenching at near physiological pH. Further computational analysis yielded a better insight into understanding the possible amino acids responsible for Cu(2+) binding with the iLOV protein.
    Article · Oct 2014 · Journal of Microbiology and Biotechnology
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    Minsu Shon · Ramachandran Shanmugavel · Giyoung Shin · [...] · Hyungdon Yun
    [Show abstract] [Hide abstract] ABSTRACT: In this study, we successfully synthesized enantiomerically pure (R)- and (S)-γ-amino acids (>99% ee) using ω- transaminase (ω-TA) through kinetic resolution and asymmetric synthesis respectively. The present study demonstrates the high potentiality of ω-TA reaction for the production of chiral γ-amino acids.
    Full-text Article · Aug 2014 · Chemical Communications