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Le, Quang Anh Tuan,Joo, Jeong Chan,Yoo, Young Je,Kim, Yong Hwan John Wiley & Sons 2012 Biotechnology and Bioengineering Vol. No.
<P><B>Abstract</B></P><P>Lipase B from <I>Candida antarctica</I> (CalB) is a versatile biocatalyst for various bioconversions. In this study, the thermostability of CalB was improved through the introduction of a new disulfide bridge. Analysis of the B‐factors of residue pairs in CalB wild type (CalB‐WT) followed by simple flexibility analysis of residues in CalB‐WT and its designated mutants using FIRST server were newly proposed to enhance the selective power of two computational tools (MODIP and DbD v1.20) to predict the possible disulfide bonds in proteins for the enhancement of thermostability. Five residue pairs (A162‐K308, N169‐F304, Q156<SUB>‐</SUB>L163, S50‐A273, and S239C‐D252C) were chosen and the respective amino acid residues were mutated to cysteine. In the results, CalB A162C‐K308C showed greatly improved thermostability while maintaining its catalytic efficiency compared to that of CalB‐WT. Remarkably, the temperature at which 50% of its activity remained after 60‐min incubation (<I>T</I> 5060<IMG src='/wiley-blackwell_img/equation/tex2gif-stack-1.gif' alt ='math image'/>) of CalB A162C_K308C was increased by 8.5°C compared to that of CalB‐WT (55 and 46.5°C, respectively). Additionally, the half‐life at 50°C of CalB A162C‐K308C was 4.5‐fold higher than that of CalB‐WT (220 and 49 min, respectively). The improvement of thermostability of CalB A162C‐K308C was elucidated at the molecular level by molecular dynamics (MD) simulation. Biotechnol. Bioeng. 2012; 109:867–876. © 2011 Wiley Periodicals, Inc.</P>
Rational design of paraoxonase 1 (PON1) for the efficient hydrolysis of organophosphates
Le, Quang Anh Tuan,Chang, Rakwoo,Kim, Yong Hwan The Royal Society of Chemistry 2015 Chemical communications Vol.51 No.77
<P>A rational design of paraoxonase 1 based on molecular docking discovered H115W/T332S and I74F/H115W/T332S mutants exhibited a 40-fold increase in catalytic efficiency (<I>k</I><SUB>cat</SUB>/<I>K</I><SUB>m</SUB>) toward the hydrolysis of two toxic and popular organophosphates (diethyl-paraoxon and dimethyl-paraoxon). Moreover, the conversion of the paraoxons (741.3–825.6 mg L<SUP>−1</SUP>) by the evolved mutants was 42–60-fold faster than that by the wild type.</P> <P>Graphic Abstract</P><P>Discovered paraoxonase 1 mutants through rational design exhibited dramatically improved catalytic efficiency for the hydrolysis of toxic organophosphates (diethyl-paraoxons and dimethyl-paraoxons). <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c5cc05857k'> </P>
Le, Quang Anh Tuan,Kim, Seonghoon,Chang, Rakwoo,Kim, Yong Hwan American Chemical Society 2015 The Journal of physical chemistry B Vol.119 No.30
<P>Serum paraoxonase 1 (PON1) is a versatile enzyme for the hydrolysis of various substrates (e.g., lactones, phosphotriesters) and for the formation of a promising chemical platform γ-valerolactone. Elucidation of the PON1-catalyzed lactonase reaction mechanism is very important for understanding the enzyme function and for engineering this enzyme for specific applications. Kinetic study and hybrid quantum mechanics/molecular mechanics (QM/MM) method were used to investigate the PON1-catalyzed lactonase reaction of γ-butyrolactone (GBL) and (<I>R</I>)-γ-valerolactone (GVL). The activation energies obtained from the QM/MM calculations were in good agreement with the experiments. Interestingly, the QM/MM energy barriers at MP2/3-21G(d,p) level for the lactonase of GVL and GBL were respectively 14.3–16.2 and 11.5–13.1 kcal/mol, consistent with the experimental values (15.57 and 14.73 kcal/mol derived from respective <I>k</I><SUB>cat</SUB> values of 36.62 and 147.21 s<SUP>–1</SUP>). The QM/MM energy barriers at MP2/6-31G(d) and MP2/6-31G(d,p) levels were also in relatively good agreements with the experiments. Importantly, the difference in the QM/MM energy barriers at MP2 level with all investigated basis sets for the lactonase of GVL and GBL were in excellent agreement with the experiments (0.9–3.1 and 0.8 kcal/mol, respectively). A detailed mechanism for the PON1-catalyzed lactonase reaction was also proposed in this study.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2015/jpcbfk.2015.119.issue-30/acs.jpcb.5b03184/production/images/medium/jp-2015-03184p_0019.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jp5b03184'>ACS Electronic Supporting Info</A></P>
Le, Quang Anh Tuan,Kim, Hee Gon,Kim, Yong Hwan Elsevier 2018 Enzyme and microbial technology Vol.116 No.-
<P><B>Abstract</B></P> <P>The electro-biocatalytic conversion of CO<SUB>2</SUB> into formic acid using whole-cell and isolated biocatalysts is useful as an alternative route for CO<SUB>2</SUB> sequestration. In this study, <I>Shewanella oneidensis</I> MR-1 (<I>S. oneidensis</I> MR-1), a facultative aerobic bacterium that has been extensively studied for its utility as biofuel cells as well as for the detoxification of heavy metal oxides (i.e., MnO<SUB>2</SUB>, uranium), has been applied for the first time as a whole-cell biocatalyst for formic acid synthesis from gaseous CO<SUB>2</SUB> and electrons supplied from an electrode. <I>S. oneidensis</I> MR-1, when aerobically grown in Luria-Bertani (LB) medium, exhibited its ability as a whole-cell biocatalyst for the conversion of CO<SUB>2</SUB> into formic acid with moderate productivity of 0.59 mM h<SUP>−1</SUP> for 24 h. In addition, an optimization of growth conditions of <I>S. oneidensis</I> MR-1 resulted in a remarkable increase in productivity. The CO<SUB>2</SUB> reduction reaction catalyzed by <I>S. oneidensis</I> MR-1, when anaerobically grown in newly optimized LB medium supplemented with fumarate and nitrate, exhibited 3.2-fold higher productivity (1.9 mM h<SUP>−1</SUP> for 72 h) compared to that grown aerobically in only LB medium. Furthermore, the average conversion rate of formic acid synthesis catalyzed by <I>S. oneidensis</I> MR-1 when grown in the optimal medium over a period of 72 h was 3.8 mM h<SUP>−1</SUP> g<SUP>−1</SUP> wet-cell, which is 9.6-fold higher than that catalyzed by <I>Methylobacterium extorquens</I> AM1 whole-cells in our previous study.</P> <P><B>Highlights</B></P> <P> <UL> <LI> <I>Shewanella oneidensis</I> MR-1 microbial has shown capability to reduce CO<SUB>2</SUB> to formate by using electrons supplied from cathode. </LI> <LI> Anaerobically grown microbial in newly optimized LB medium supplemented with fumarate and nitrate exhibited 3.2-fold higher productivity. </LI> <LI> Maximum formate concentration produced by whole cell approached about 150 mM in 72 h. </LI> </UL> </P>