Structural Analysis of the Streptomyces avermitilis CYP107W1-Oligomycin A Complex and Role of the Tryptophan 178 Residue

Han, Songhee,Pham, Tan-Viet,Kim, Joo-Hwan,Lim, Young-Ran,Park, Hyoung-Goo,Cha, Gun-Su,Yun, Chul-Ho,Chun, Young-Jin,Kang, Lin-Woo,Kim, Donghak Korean Society for Molecular and Cellular Biology 2016 Molecules and cells Vol.39 No.3

CYP107W1 from Streptomyces avermitilis is a cytochrome P450 enzyme involved in the biosynthesis of macrolide oligomycin A. A previous study reported that CYP107W1 regioselectively hydroxylated C12 of oligomycin C to produce oligomycin A, and the crystal structure of ligand free CYP107W1 was determined. Here, we analyzed the structural properties of the CYP107W1-oligomycin A complex and characterized the functional role of the Trp178 residue in CYP107W1. The crystal structure of the CYP107W1 complex with oligomycin A was determined at a resolution of $2.6{\AA}$. Oligomycin A is bound in the substrate access channel on the upper side of the prosthetic heme mainly by hydrophobic interactions. In particular, the Trp178 residue in the active site intercalates into the large macrolide ring, thereby guiding the substrate into the correct binding orientation for a productive P450 reaction. A Trp178 to Gly mutation resulted in the distortion of binding titration spectra with oligomycin A, whereas binding spectra with azoles were not affected. The Gly178 mutant's catalytic turnover number for the 12-hydroxylation reaction of oligomycin C was highly reduced. These results indicate that Trp178, located in the open pocket of the active site, may be a critical residue for the productive binding conformation of large macrolide substrates.

Functional Characterization of Allelic Variants of Polymorphic Human Cytochrome P450 2A6 (CYP2A6*5, *7, *8, *18, *19, and *35)

Han, Songhee,Choi, Seunghye,Chun, Young-Jin,Yun, Chul-Ho,Lee, Chang Hoon,Shin, Hee Jung,Na, Han Sung,Chung, Myeon Woo,Kim, Donghak Pharmaceutical Society of Japan 2012 Biological & pharmaceutical bulletin Vol.35 No.3

<P>Cytochrome P450 2A6 (CYP2A6) catalyzes important metabolic reactions of many xenobiotic compounds, including coumarin, nicotine, cotinine, and clinical drugs. Genetic polymorphisms of CYP2A6 can influence its metabolic activities. This study analyzed the functional activities of six CYP2A6 allelic variants (CYP2A6*5, *7, *8, *18, *19, and *35) containing nonsynonymous single-nucleotide polymorphisms. Recombinant variant enzymes of CYP2A6*7, *8, *18, *19, and *35 were successfully expressed in <I>Escherichia coli</I> and purified. However, a P450 holoenzyme spectrum was not detected for the CYP2A6*5 allelic variant (G479V). Structural analysis shows that the G479V mutation may alter the interaction between the A helix and the F—G helices. Enzyme kinetic analyses indicated that the effects of mutations in CYP2A6 allelic variants on drug metabolism are dependent on the substrates. In the case of coumarin 7-hydroxylation, CYP2A6*8 and *35 displayed increased <I>K</I><SUB>m</SUB> values whereas CYP2A6*18 and *19 showed decreased <I>k</I><SUB>cat</SUB> values, which resulted in lower catalytic efficiencies (<I>k</I><SUB>cat</SUB>/<I>K</I><SUB>m</SUB>). In the case of nicotine 5-oxidation, the CYP2A6*19 variant exhibited an increased <I>K</I><SUB>m</SUB> value, whereas CYP2A6*18 and *35 showed much greater decreases in <I>k</I><SUB>cat</SUB> values. These results suggest that individuals carrying these allelic variants are likely to have different metabolisms for different CYP2A6 substrates. Functional characterization of these allelic variants of CYP2A6 can help determine the importance of CYP2A6 polymorphisms in the metabolism of many clinical drugs.</P>

Aromatic π–π interaction mediated by a metal atom: structure and ionization of the bis(η⁶-benzene)chromium–benzene cluster

Han, Songhee,Singh, N. Jiten,Kang, Tae Yeon,Choi, Kyo-Won,Choi, Sunyoung,Baek, Sun Jong,Kim, Kwang S.,Kim, Sang Kyu Royal Society of Chemistry 2010 Physical chemistry chemical physics Vol.12 No.27

<P>Aromatic π–π interaction in the presence of a metal atom has been investigated experimentally and theoretically with the model system of bis(η<SUP>6</SUP>-benzene)chromium–benzene cluster (Cr(Bz)<SUB>2</SUB>–Bz) in which a free solvating benzene is non-covalently attached to the benzene moiety of Cr(Bz)<SUB>2</SUB>. One-photon mass-analyzed threshold ionization (MATI) spectroscopy and first principles calculations are employed to identify the structure of Cr(Bz)<SUB>2</SUB>–Bz which adopts the parallel-displaced configuration. The decrease in ionization potential for Cr(Bz)<SUB>2</SUB>–Bz compared with Cr(Bz)<SUB>2</SUB>, resulting from the increase of the cation–π stabilization energy upon ionization, is consistent with the parallel-displaced structure of the cluster. Theoretical calculations give the detailed cluster structures with associated energetics, thus revealing the nature of π–π–metal or π–π–cation interactions at the molecular level.</P> <P>Graphic Abstract</P><P>The nature of the aromatic π–π interaction in the presence of a metal atom has been revealed by the combined study of ionization spectroscopy and first principles calculations for the model system of the Cr(C<SUB>6</SUB>H<SUB>6</SUB>)<SUB>2</SUB>–C<SUB>6</SUB>H<SUB>6</SUB> cluster. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b923929d'> </P>

One-photon ionization spectroscopy of jet-cooled oxazole and thiazole: the role of oxygen and sulfur in the π-conjugation of heterocyclic compounds

Han, Songhee,Kang, Tae Yeon,Choi, Sunyoung,Choi, Kyo-Won,Baek, Sun Jong,Lee, Sungyul,Kim, Sang Kyu Royal Society of Chemistry 2008 Physical chemistry chemical physics Vol.10 No.26

<P>One-photon mass-analyzed threshold ionization (MATI) spectroscopy of jet-cooled oxazole and thiazole has been carried out to give the precise adiabatic ionization energies of 9.5959 ± 0.0006 and 9.3633 ± 0.0009 eV, respectively. The structural change upon ionization has been revealed in the vibrationally resolved one-photon MATI spectra. Simulations based on the Franck–Condon analysis using the molecular structures calculated by the density functional theory reproduce the experiment very well for both molecules. The ionization-driven structural change of thiazole is quite different from that of oxazole in terms of the detailed geometrical shape, ascribed to the difference in the π-conjugation nature of two molecules. The role of oxygen and sulfur in the stabilization of heterocyclic systems is discussed through the inspection of the calculated molecular orbitals involved in the photoionization.</P> <P>Graphic Abstract</P><P>The intrinsic difference of sulfur and oxygen in the role of π-conjugation of the heterocyclic compounds is revealed as the difference in the structural change of two molecules upon ionization. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b719956b'> </P>

What Determines Korea’s Health Aid Allocation: Altruistic, Economic, or COVID-19 Motivations?

Songhee Han,Jisun Song 이화여자대학교 국제지역연구소 2022 Asian International Studies Review Vol.23 No.2

With the disproportionate impact of the global pandemic on developing countries, health aid has become crucial in improving people’s health and well-being more than ever. Reflecting developing countries’ needs, Korea, like other donors, made significant contributions to support the global COVID-19 response. Considering the increased amount and importance of the health sector in Korea’s foreign aid, this article aims to investigate the motivations of Korea’s total bilateral aid and bilateral health aid using panel data of 128 developing countries from 2006 to 2021 with the random-effects panel Tobit model. The time frame was divided into three periods, 2006–2009, 2010–2019 and 2020–2021, to test Korea’s aid determinants pre- and post-pandemic outbreak. No notable changes in Korea’s aid allocation pattern were found before and after the pandemic. Instead, Korea seemed to have mixed motives of donor interest and recipients’ needs in specific periods. However, a priority partner country was consistently identified as an influential factor in Korea’s aid.

Dynamic Role of the Intramolecular Hydrogen Bonding in Nonadiabatic Chemistry Revealed in the UV Photodissociation Reactions of 2-Fluorothiophenol and 2-Chlorothiophenol

Han, Songhee,You, Hyun Sik,Kim, So-Yeon,Kim, Sang Kyu American Chemical Society 2014 The Journal of physical chemistry A Vol.118 No.34

<P>The dynamic interplay between the intramolecular hydrogen bonding and intramolecular vibrational redistribution is found to be critical in nonadiabatic reaction dynamics. Herein, it has been demonstrated that the molecular planarity, directed by the intramolecular hydrogen bonding, plays an important role in the nonadiabatic passage of the reactive flux at the conical intersection in the photodissociation reactions of 2-fluorothiophenol and 2-chlorothiophenol. As the internal energy increases in the excited state, the intramolecular hydrogen bonding of 2-fluorothiophenol loosens. The floppiness brought into the molecular structure then modifies the dynamic path of the reactive flux, leading to the diminishment of the nonadiabatic transition probability at the conical intersection. On the contrary, for 2-chlorothiophenol having the relatively stronger intramolecular hydrogen bonding, the reactive flux seems to retain the molecular planarity even with the increase of the internal energy as manifested by the constant nonadiabatic transition probability over the wide range of the S<SUB>1</SUB> internal energy. The effect of the intramolecular hydrogen bonding on the molecular structure and its relation to the nonadiabatic dynamics along the tunneling path has been experimentally demonstrated.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcafh/2014/jpcafh.2014.118.issue-34/jp505699w/production/images/medium/jp-2014-05699w_0008.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jp505699w'>ACS Electronic Supporting Info</A></P>

Synthesis and characterization of novel astragalin galactosides using β-galactosidase from <i>Bacillus circulans</i>

Han, Songhee,Hanh Nguyen, Thi Thanh,Hur, Jaewon,Kim, Nahyun M.,Kim, Seong-Bo,Hwang, Kyeong-Hwan,Moon, Young-Hwan,Kang, Choongil,Chung, Byoungsang,Kim, Young-Min,Kim, Tae Sung,Park, Jun-Seong,Kim, Doma Elsevier 2017 Enzyme and microbial technology Vol.103 No.-

<P>Astragalin (kaempferol-3-O-beta-D-glucopyranoside, Ast) is a kind of flavonoid known to have anti-oxidant, anti-HIV, anti-allergic, and anti-inflammatory effects. It has low solubility in water. In this study, novel astragalin galactosides (Ast-Gals) were synthesized using beta-galactosidase from Bacillus circulans and reaction conditions were optimized to increase the conversion yield of astragallin. Purified Ast-Gal1 (11.6% of Ast used, w/w) and Ast-Gal2 (6.7% of Ast used, w/w) were obtained by medium pressure chromatography (MPLC) with silica C-18 column and open column packed with Sephadex LH-20. The structures of Ast-Gal1 and Ast-Gal2 were identified by nuclear magnetic resonance (NMR) to be kaempferol-3-O-beta-D-glucopyranosyl-(1 -> 6)-beta-D-galactopyranoside and kaempferol-3-O-beta-D-glucopyranosyl-(1 -> 6)-beta-D-galactopyranosyl-(1 -> 4)-beta-D-galactopyranoside, respectively. The water solubility of Ast, Ast-Gal1, and Ast-Gal2 were 28.2 +/- 1.2 mg/L, 38,300 +/- 3.5 mg/L, and 38,800 +/- 2.8 mg/L, respectively. The SC50 value (the concentration required to scavenge 50% of the ABTS.+) of Ast, Ast-Gal1, and Ast-Gal2 were 5.1 +/- 1.6 mu M, 6.5 +/- 0.4 mu M, and 4.9 +/- 1.1 mu M, respectively. The IC50 values (the half maximal inhibitory concentration) of Ast, Ast-Gal1, and Ast-Gal2 against angiotensin converting enzyme (ACE) were 171.0 +/- 1.2 mu M, 186.0 mu M, and 139.0 +/- 0.2 mu M, respectively.</P>

Synthesis and Characterization of Novel astragalin Galactosides Using b-Galactosidase from Bacillus circulans

Songhee HAN,Thi Thanh Hanh NGUYEN,Hee-Jung LIM,Jun-Seong PARK,Doman KIM 한국생물공학회 2017 한국생물공학회 학술대회 Vol.2017 No.4

Structural Analysis of the Streptomyces avermitilis CYP107W1-Oligomycin A Complex and Role of the Tryptophan 178 Residue

Songhee HAN,Tan-Viet Pham,Joo-Hwan Kim,임영란,Hyoung-Goo Park,Gun-Su Cha,Chul-Ho Yun,Young-Jin Chun,강린우,김동학 한국분자세포생물학회 2016 Molecules and cells Vol.39 No.3

CYP107W1 from Streptomyces avermitilis is a cytochrome P450 enzyme involved in the biosynthesis of macrolide oligomycin A. A previous study reported that CYP107W1 regioselectively hydroxylated C12 of oligomycin C to produce oligomycin A, and the crystal structure of ligand free CYP107W1 was determined. Here, we analyzed the structural properties of the CYP107W1-oligomycin A complex and characterized the functional role of the Trp178 residue in CYP107W1. The crystal structure of the CYP107W1 complex with oligomycin A was determined at a resolution of 2.6 Å. Oligomycin A is bound in the substrate access channel on the upper side of the prosthetic heme mainly by hydrophobic interactions. In particular, the Trp178 residue in the active site intercalates into the large macrolide ring, thereby guiding the substrate into the correct binding orientation for a productive P450 reaction. A Trp178 to Gly mutation resulted in the distortion of binding titration spectra with oligomycin A, whereas binding spectra with azoles were not affected. The Gly178 mutant’s catalytic turnover number for the 12-hydroxylation reaction of oligomycin C was highly reduced. These results indicate that Trp178, located in the open pocket of the active site, may be a critical residue for the productive binding conformation of large macrolide substrates.

Structural insights into the binding of lauric acid to CYP107L2 from <i>Streptomyces avermitilis</i>

Han, Songhee,Pham, Tan-Viet,Kim, Joo-Hwan,Lim, Young-Ran,Park, Hyoung-Goo,Jeong, Dabin,Yun, Chul-Ho,Chun, Young-Jin,Kang, Lin-Woo,Kim, Donghak Elsevier 2017 Biochemical and biophysical research communication Vol.482 No.4

<P><B>Abstract</B></P> <P> <I>Streptomyces avermitilis</I> is an actinobacterium known to produce clinically useful macrolides including avermectins. CYP107L2 from <I>S. avermitilis</I> shares a high sequence similarity with the PikC (CYP107L1) from <I>S. venezuelae</I>. To elucidate the structural features of CYP107L2, we conducted biochemical and structural characterization of CYP107L2 from <I>S. avermitilis</I>. The CYP107L2 gene was cloned, and its recombinant protein was expressed and purified. The CYP107L2 showed a low-spin state of heme, and the reduced form yielded the CO difference spectra with a maximal absorption at 449 nm. Binding of pikromycin and lauric acid yielded the typical type I spectra with <I>K</I> <SUB>d</SUB> values of 4.8 ± 0.3 and 111 ± 9 <I>μ</I>M, respectively. However, no metabolic product was observed in the enzyme reaction. X-ray crystal structures of the ligand-free CYP107L2 and its complex with lauric acid were determined at the resolution of 2.6 and 2.5 Å, respectively. CYP107L2 showed a well-conserved CYP structure with a wide-open substrate-binding cavity. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Glu-40 and Leu-382 residues in the CYP107L2 complex with lauric acid showed significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site.</P> <P><B>Highlights</B></P> <P> <UL> <LI> CYP107L2 from <I>S. avermitilis</I> shares a high sequence similarity with the PikC. </LI> <LI> Purified CYP107L2 yielded a typical type I binding spectra to pikromycin and lauric acid. </LI> <LI> Crystal structure of CYP107L2 complex with lauric acid was determined at 2.5 Å resolution. </LI> <LI> Laurate is bound mainly via hydrophobic interactions in the substrate binding cavity of CYP107L2. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>