Crystal structure and biochemical properties of <i>msed</i>_0281, the citrate synthase from <i>Metallosphaera sedula</i>

Lee, Seul Hoo,Kim, Kyung-Jin Elsevier 2019 Biochemical and biophysical research communication Vol.509 No.3

<P><B>Abstract</B></P> <P> <I>Metallosphaera sedula</I> is a thermoacidophilic archaeon that has carbon fixation ability using the 3-hydroxypropionate/4-hydroxybutyrate(3-HP/4-HB) cycle, and has an incomplete TCA cycle to produce necessary biosynthetic precursors. The citrate synthase from <I>M. sedula</I> (<I>Ms</I>CS) is an enzyme involved in the first step of the incomplete TCA cycle, catalyzing the conversion of oxaloacetate and acetyl-CoA into citrate and coenzyme A. To investigate the molecular mechanism of <I>Ms</I>CS, we determined its crystal structure at 1.8 Å resolution. As other known CSs, <I>Ms</I>CS functions as a dimer, and each monomer consists of two domains, a large domain and a small domain. We also determined the structure of the complex with acetyl-CoA and revealed the acetyl-CoA binding mode of <I>Ms</I>CS. Structural comparison of <I>Ms</I>CS with another CS in complex with oxaloacetate enabled us to predict the oxaloacetate binding site. Moreover, we performed inhibitory kinetic analyses of <I>Ms</I>CS, and showed that the protein is inhibited by citrate and ATP by competitive and non-competitive inhibition modes, respectively, but not by NADH. Based on these results, we suggest that <I>Ms</I>CS belongs to the type-I CS with structural and biochemical properties similar to those of CSs involved in the conventional TCA cycle.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The crystal structure of archaeal citrate synthase from <I>Metallosphaera sedula</I> (<I>Ms</I>CS) was determined. </LI> <LI> The cofactor binding mode of <I>Ms</I>CS was confirmed and inhibition properties of <I>Ms</I>CS was elucidated. </LI> <LI> <I>Ms</I>CS belongs to type I with structural and biochemical properties similar to those of CSs involved in the TCA cycle. </LI> </UL> </P>

Structure-based Bioengineering with Enhanced Regiospecificity of Catechol O-methyltransferase from Niastella koreensis

Seul Hoo LEE,Mijeong KIM,Kyung-Jin KIM 한국생물공학회 2022 한국생물공학회 학술대회 Vol.2022 No.9

Structural Insight for Production of Catechol Derivatives at Acidic pH by Tyrosinase from Burkholderia thailandensis

Seul Hoo LEE,Mi Jeong KIM,Hogyun SEO,Kyung-Jin KIM 한국생물공학회 2023 한국생물공학회 학술대회 Vol.2023 No.4

Purification, crystallization, and X-ray crystallographic analysis terephthalic acid binding protein from Ideonella sakaiensis

Seul Hoo Lee,Dongwoo Ki,Kyung-Jin Kim 한국구조생물학회 2023 Biodesign Vol.11 No.1

Periplasmic terephthalic acid binding protein (TBP) from Ideonella sakaiensis (IsTBP) is a periplasmic protein that imports TPA to the cytoplasm interacting with the TTT-transport system. In this study, we overexpressed IsTBP and purified the protein to homogeneity by Ni-NTA affinity and size-exclusion chromatography. The IsTBP protein was crystallized using hanging-drop vapor-diffusion method in the presence of 20% PEG3350 and 0.2 M Ammonium iodide at 20°C. X-ray diffraction data were collected to a maximum resolution of 1.02 Å. The IsTBP crystals belonged to the space group P21 with unit cell parameters a = 46.2 Å, b = 54.1 Å, c = 50.6 Å. With one molecule of IsTBP per asymmetric unit, the crystal volume per unit of protein mass was 2.32 Å3 Da–1, which corresponds to a solvent content was approximately 47.00%.

Functional and Structural Determination of an Auxiliary Domain-containing PET Hydrolase from Burkholderiales Bacterium

Seul Hoo LEE,Dongwoo KI,Mi Jeong KIM,Kyung-Jin KIM 한국생물공학회 2022 한국생물공학회 학술대회 Vol.2022 No.4

인터넷 개인방송 BJ의 노동 과정에 대한 탐색

이동후(Dong-Hoo Lee),이설희(Seul-Hi Lee) 한국언론학회 2017 한국언론학보 Vol.61 No.2

This study examines the labor processes of user content production and value creation through a case study of so-called Broadcasting Jockeys (BJ), Internet personal broadcasters who have attracted significant public attention. The purpose of this study is to investigate how these labor processes are carried out within the users’ concrete experiences, considering the structural ambivalence in both participatory digital-media usage and exploitative free labor. In-depth interviews were conducted with fourteen BJs who work at AfreecaTV as Best or Partner BJs. The results show that the imagined affordances of AfreecaTV are associated with the BJs’ perceived and creative motivation; the cognitive, communicative, and communal characteristics of their labor; the dynamics of producing labor value based on byeolpungseon (star balloon); the valorization process of labor power; and the self-branding mechanism in these unstable labor practices. This study finds that Internet personal broadcasting has emerged as a new media industry, with a labor process of a complex and ambivalent nature.

게임 스트리밍 공간의 여성 스트리머 경험 연구 : 심층인터뷰를 중심으로

이동후(Dong-Hoo, Lee),홍남희(Namhee, Hong),이설희(Seul-hi, Lee) 한국언론학회 2021 한국언론학보 Vol.65 No.5

This study attempts to look at how women become game streamers, how they build their identity as streamers, and how those practices are shaped by the social-technical affordances of streaming platforms and gendered culture. For this investigation, in-depth interviews were conducted with women game streamers. The findings show that platforms’ affordances, in conjunction with existing gendered conventions, affect the ways in which women game streamers present themselves and have relationships with their viewers. Webcam’s visualism induces women to be concerned about their looks and femininity, and platforms’ social affordances facilitate their performativity to vie for viewers’ attention, which tends to make them vulnerable to gender discriminatory and toxic culture. In addition, women game streamers constantly negotiate with the revenue affordances of platforms that allow their affective labor to be monetized, and try to pave their way for self-employed entrepreneurism, but only with short-term visions. Based on their experiences, the study shows that women game streamers have limited autonomy and that their entrepreneurial practices are constrained by the given social-technological affordances.

소아 영양 및 유아식 응용을 위한 신바이오틱스의 잠재력: 총설

정후길 ( Hoo Kil Jung ),김선진 ( Sun Jin Kim ),석민정 ( Min Jeong Seok ),차현아 ( Hyun Ah Cha ),윤슬기 ( Seul Ki Yoon ),이나현 ( Nah Hyun Lee ),강경진 ( Kyung Jin Kang ) 한국유가공기술과학회 2015 Journal of Dairy Science and Biotechnology (JMSB) Vol.33 No.2

프로바이오틱스, 프리바이오틱스 및 신바이오틱스 등의 물질과 미생물을 조제분유에 강화하여 건강증진 기능성 유산균, 특히 비피더스균과 유산간균의 성장을 선택적으로 자극함으로써 장내균총에 유익한 효과를 나타내고자 하는 노력이 경주되고 있다. 지난 10년 동안, 모유 수유가 장내균총에 미치는 유용 효과를 도모하기 위해서 프로바이오틱스와 프리바이오틱스를 함유하는 새로운 신바이오틱 조제분유가 제안되었다. 새로운 신바이오틱스는 상승 효과로 인해서 프로바이오틱스 및 프리바이오틱스를 개별적으로 사용하는 경우보다 더 도움이 되는 것으로 기대된다. 한편, 조제분유 및 건조 제품의 제조에 사용되는 가공 기술 및 저장 조건 등이 프로바이오틱스의 생존에 악영향을 미치게 된다. 충분한 유산균수(108 cfu/g)로 장내 예정된 부위에 도달하여 숙주에 긍정적인 효과를 나타내기 위해서는 식품제조공정 및 위장관 통과 시 프로바이오틱스의 생존성을 유지하는 것이 가장 중요한 요소이다. 일반적으로 안전하다고 인정되며, 높은 생물학적 가치를 가지고 있는 물질을 이용하여 적절하고 비용 효율적인 마이크로캡슐화 기술이 개발되면 조제분유의 품질 향상이 가능하게 된다. 프로바이오틱스는 복합적인 효과를 나타낸다. 하나는 살아 있는 생균체가 장내균총에 유익하게 영향을 미쳐 면역조절 효과를 보여주는 것이며, 다른 하나는 사균체가 항-염증반응을 나타내는 것이다. 최근에, 사균체 또는 정제되지 않은 미생물 분획물이 건강에 긍정적인 영향을 미친다는 것을 명확하게 정의할 새로운 용어에 대한 필요성이 대두되었다. 그결과, 충분한 양을 경구 또는 국소적으로 투여했을 때 인간과 동물에게 이로운 작용을 하는 사균체(손상되지 않거나 또는 파손된)나 정제되지 않은 세포 추출물(즉, 복잡한 화학적 조성)을 정의하기 위해 paraprobiotics라는 용어가 제안되었다. 프로바이오틱 균주 또는 프리바이오틱스를 조제분유에 강화했을 때 조제분유 수유아의 분변 미생물균총이 조정된다. 즉, 비피더스균 및 유산간균과 같은 건강 유익한 세균을 증가시킴으로써, 프리바이오틱스는 분변 미생물균총의 조성을 변경하고, 이에 따라서 면역계의 활성을 조절한다. 따라서, 품질 향상을 위한 조제분유의 개발은 토착 장내균총의 대사 활성과 증식을 선택적으로 자극하는 비피더스균 등의 특정 프로바이오틱스 및 이눌린과 올리고당 등의 프리바이오틱스를 사용하여, 모유의 건강 유용 효과와 유사하게 접근하는 것에 초점을 맞추고 있다. Probiotic, prebiotic, and synbiotic substances as well as microorganisms were added to infant formula in an attempt to influence the intestinal microflora with an aim to stimulate the growth of lactic acid bacteria, especially bifidobacteria and lactobacilli. Over the last 10 years, new synbiotic infant formulas containing probiotics and prebiotics have been proposed in order to simulate the effect of breast-feeding on the intestinal microflora. Owing to their synergistic effect, the new synbiotics are expected to be more helpful than using probiotics and prebiotics individually. Maintenance of the viability of the probiotics during food processing and the passage through the gastrointestinal tract should be the most important consideration, since a sufficient number of bacteria (108 cfu/g) should reach the intended location to have a positive effect on the host. Storage conditions and the processing technology used for the manufacture of products such as infant formula adversely affect the viability of the probiotics. When an appropriate and cost-effective microencapsulation methodology using the generally recognized as safe (GRAS) status and substances with high biological value are developed, the quality of infant formulas would improve. The effect of probiotics may be called a double-effect, where one is an immunomodulatory effect, induced by live probiotics that advantageously alter the gastrointestinal microflora, and the other comprises anti-inflammatory responses elicited by dead cells. At present, a new terminology is required to define the dead microorganisms or crude microbial fractions that positively affect health. The term “paraprobiotics” (or ghost probiotics) has been proposed to define dead microbial cells (not damaged or broken) or crude cell extracts (i.e., cell extracts with complex chemical composition) that are beneficial to humans and animals when a sufficient amount is orally or topically administered. The fecal microflora of bottle-fed infants is altered when the milk-based infant formula is supplemented with probiotics or prebiotics. Thus, by increasing the proportion of beneficial bacteria such as bifidobacteria and lactobacilli, prebiotics modify the fecal microbial composition and accordingly regulate the activity of the immune system. Therefore, considerable attention has been focused on the improvement of infant formula quality such that its beneficial effects are comparable to those of human milk, using prebiotics such as inulin and oligosaccharides and potential specific probiotics such as bifidobacteria, which selectively stimulate the proliferation of beneficial bacteria in the microflora and the indigenous intestinal metabolic activity of the microflora.

Multifunctional chitosan-coated poly(lactic-co-glycolic acid) nanoparticles for spatiotemporally controlled codelivery of ceramide and C-phycocyanin to treat atopic dermatitis

Min, Seul Ki,Lee, Hoo Cheol,Song, Hyeongi,Shin, Hwa Sung SAGE Publications 2019 Journal of bioactive and compatible polymers Vol.34 No.2

Purification, crystallization and X-ray crystallographic analysis of methylmalonyl-CoA epimerase from Metallosphaera sedula

Seongjoon Joo,Seul Hoo Lee,Donghoon Lee,Kyung-Jin Kim 한국구조생물학회 2021 Biodesign Vol.9 No.2

Methylmalonyl-CoA epimerase (MMCE) is an enzyme involved in the carbon capturing 3-HP/4-HB cycle, by catalyzing the reaction of converting (S)-methylmalonyl-CoA to (R)-methylmalonyl-CoA. In this study, we overexpressed MMCE from Metallosphaera sedula (MsMMCE) and purified the protein to homogeneity by Ni-NTA affinity and size-exclusion chromatography. The MsMMCE protein was crystallized using the hanging-drop vapor-diffusion method in the presence of 20% (w/v) polyethylene glycol 3350, and 0.2 M ammonium nitrate at 293 K. X-ray diffraction data were collected to a maximum resolution of 2.1 Å. The MsMMCE crystals belong to the space group P21 with unit cell parameters a = 51.87 Å, b = 79.00 Å, c = 106.09, α = γ = 90.0°, β = 95.80°. With six molecules of MsMMCE per an asymmetric unit, the crystal volume per unit of protein mass is 2.33 Å3 Da–1, which corresponds to a solvent content of approximately 47.13%.