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Park JG, Jeon H, Hwang KY, Cha SS, Han RT, Cho H, Lee IG. Cargo specificity, regulation, and therapeutic potential of cytoplasmic dynein. Exp Mol Med 2024; 56:827-835. [PMID: 38556551 PMCID: PMC11059388 DOI: 10.1038/s12276-024-01200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 04/02/2024] Open
Abstract
Intracellular retrograde transport in eukaryotic cells relies exclusively on the molecular motor cytoplasmic dynein 1. Unlike its counterpart, kinesin, dynein has a single isoform, which raises questions about its cargo specificity and regulatory mechanisms. The precision of dynein-mediated cargo transport is governed by a multitude of factors, including temperature, phosphorylation, the microtubule track, and interactions with a family of activating adaptor proteins. Activating adaptors are of particular importance because they not only activate the unidirectional motility of the motor but also connect a diverse array of cargoes with the dynein motor. Therefore, it is unsurprising that dysregulation of the dynein-activating adaptor transport machinery can lead to diseases such as spinal muscular atrophy, lower extremity, and dominant. Here, we discuss dynein motor motility within cells and in in vitro, and we present several methodologies employed to track the motion of the motor. We highlight several newly identified activating adaptors and their roles in regulating dynein. Finally, we explore the potential therapeutic applications of manipulating dynein transport to address diseases linked to dynein malfunction.
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Affiliation(s)
- Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, South Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, 03760, South Korea
| | - Rafael T Han
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - Hyesung Cho
- Extreme Materials Research Center, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, 02792, South Korea.
- Department of Biological Chemistry, University of Science and Technology, Daejeon, 34113, South Korea.
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Jeon H, Han AR, Oh S, Park JG, Namkoong M, Bang KM, Kim HM, Kim NK, Hwang KY, Hur K, Lee BJ, Heo J, Kim S, Song HK, Cho H, Lee IG. Polymorphic Self-Assembly with Procedural Flexibility for Monodisperse Quaternary Protein Structures of DegQ Enzymes. Adv Mater 2024:e2308837. [PMID: 38351715 DOI: 10.1002/adma.202308837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/08/2024] [Indexed: 02/29/2024]
Abstract
As large molecular tertiary structures, some proteins can act as small robots that find, bind, and chaperone target protein clients, showing the potential to serve as smart building blocks in self-assembly fields. Instead of using such intrinsic functions, most self-assembly methodologies for proteins aim for de novo-designed structures with accurate geometric assemblies, which can limit procedural flexibility. Here, a strategy enabling polymorphic clustering of quaternary proteins, exhibiting simplicity and flexibility of self-assembling paths for proteins in forming monodisperse quaternary cage particles is presented. It is proposed that the enzyme protomer DegQ, previously solved at low resolution, may potentially be usable as a threefold symmetric building block, which can form polyhedral cages incorporated by the chaperone action of DegQ in the presence of protein clients. To obtain highly monodisperse cage particles, soft, and hence, less resistive client proteins, which can program the inherent chaperone activity of DegQ to efficient formations of polymorphic cages, depending on the size of clients are utilized. By reconstructing the atomic resolution cryogenic electron microscopy DegQ structures using obtained 12- and 24-meric clusters, the polymorphic clustering of DegQ enzymes is validated in terms of soft and rigid domains, which will provide effective routes for protein self-assemblies with procedural flexibility.
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Affiliation(s)
- Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ah-Reum Han
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
| | - Sangmin Oh
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Myeong Namkoong
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kyeong-Mi Bang
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291, Daehak-ro, Daejeon, 34126, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Kahyun Hur
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Science, Seoul National University, 599, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- College of Pharmacy, Ajou University, 206, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Jeongyun Heo
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Sehoon Kim
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyun Kyu Song
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyesung Cho
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
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Lee S, Tri Le Q, Yang S, Hwang KY, Lee H. Arabidopsis ecotype Ct-1, with its altered nitrate sensing ability, exhibits enhanced growth under low nitrate conditions in comparison to Col-0. Plant Sci 2023; 336:111827. [PMID: 37586419 DOI: 10.1016/j.plantsci.2023.111827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
To address the urgent need for sustainable solutions to the increased use of nitrogen fertilizers in agriculture, it is imperative to acquire an in-depth comprehension of the intricate interplay between plants and nitrogen. In this context, our research aimed to elucidate the molecular mechanism behind NO3- sensing/signaling in plants, which can enhance nitrogen utilization efficiency. Previous reports have revealed that the density and quantity of root hairs exhibit responsive behavior to varying levels of NO3-, while the precise molecular mechanisms governing these changes remain elusive. To further investigate this phenomenon, we specifically selected the Ct-1 ecotype, which manifested a greater abundance of root hairs compared to the Col-0 ecotype under conditions of low NO3-. Our investigations unveiled that the dissimilarities in the amino acid sequence of NRT1.1, a transceptor responsible for regulating nitrate signaling and transport, accounted for the observed variation in root hair numbers. These results suggest that NRT1.1 represents a promising target for gene editing technology, offering potential applications in enhancing the efficiency of nitrogen utilization in agricultural crops.
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Affiliation(s)
- Seokjin Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Quang Tri Le
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Seonyoung Yang
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea
| | - Hojoung Lee
- Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-713, the Republic of Korea.
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Ki H, Baek JS, Hawkes HJK, Kim YS, Hwang KY. Fermented Kamut Sprout Extract Decreases Cell Cytotoxicity and Increases the Anti-Oxidant and Anti-Inflammation Effect. Foods 2023; 12:foods12112107. [PMID: 37297352 DOI: 10.3390/foods12112107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Kamut sprouts (KaS) contain several biologically active compounds. In this study, solid-state fermentation using Saccharomyces cerevisiae and Latilactobacillus sakei was used to ferment KaS (fKaS-ex) for 6 days. The fKaS-ex showed a 26.3 mg/g dried weight (dw) and 46.88 mg/g dw of polyphenol and the β-glucan contents, respectively. In the Raw264.7 and HaCaT cell lines, the non-fermented KaS (nfKaS-ex) decreased cell viability from 85.3% to 62.1% at concentrations of 0.63 and 2.5 mg/mL, respectively. Similarly, the fKaS-ex decreased cell viability, but showed more than 100% even at 1.25 and 5.0 mg/mL concentrations, respectively. The anti-inflammatory effect of fKaS-ex also increased. At 600 µg/mL, the fKaS-ex exhibited a significantly higher ability to reduce cytotoxicity by suppressing COX-2 and IL-6 mRNA expressions as well as that for IL-1β mRNA. In summary, fKaS-ex exhibited significantly lower cytotoxicity and increased anti-oxidant and anti-inflammatory properties, indicating that fKaS-ex is beneficial for use in food and other industries.
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Affiliation(s)
- Hosam Ki
- Materials Science Research Institute, LABIO Co., Ltd., Seoul 08501, Republic of Korea
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Seok Baek
- Materials Science Research Institute, LABIO Co., Ltd., Seoul 08501, Republic of Korea
| | - Hye-Jin Kim Hawkes
- Center for Creative Convergence Education, Hanyang University, Seoul 04763, Republic of Korea
| | - Young Soo Kim
- Materials Science Research Institute, LABIO Co., Ltd., Seoul 08501, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
- Korea BioDefense Research Institute, Korea University, Seoul 02841, Republic of Korea
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5
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Yoon I, Kim S, Cho M, You KA, Son J, Lee C, Suh JH, Bae DJ, Kim JM, Oh S, Park S, Kim S, Cho SH, Park S, Bang K, Seo M, Kim JH, Lee B, Park JS, Hwang KY, Kim S. Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1. EMBO Mol Med 2023:e16940. [PMID: 37212275 DOI: 10.15252/emmm.202216940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
Prolyl-tRNA synthetase 1 (PARS1) has attracted much interest in controlling pathologic accumulation of collagen containing high amounts of proline in fibrotic diseases. However, there are concerns about its catalytic inhibition for potential adverse effects on global protein synthesis. We developed a novel compound, DWN12088, whose safety was validated by clinical phase 1 studies, and therapeutic efficacy was shown in idiopathic pulmonary fibrosis model. Structural and kinetic analyses revealed that DWN12088 binds to catalytic site of each protomer of PARS1 dimer in an asymmetric mode with different affinity, resulting in decreased responsiveness at higher doses, thereby expanding safety window. The mutations disrupting PARS1 homodimerization restored the sensitivity to DWN12088, validating negative communication between PARS1 promoters for the DWN12088 binding. Thus, this work suggests that DWN12088, an asymmetric catalytic inhibitor of PARS1 as a novel therapeutic agent against fibrosis with enhanced safety.
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Affiliation(s)
- Ina Yoon
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, Korea
| | - Sulhee Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Minjae Cho
- Drug Discovery Center, Daewoong Pharmaceutical Co., Ltd, Yongin, Korea
| | - Kyung Ah You
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
| | - Jonghyeon Son
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Caroline Lee
- Drug Discovery Center, Daewoong Pharmaceutical Co., Ltd, Yongin, Korea
| | - Ji Hun Suh
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, Korea
| | - Da-Jeong Bae
- Drug Discovery Center, Daewoong Pharmaceutical Co., Ltd, Yongin, Korea
| | - Jong Min Kim
- Drug Discovery Center, Daewoong Pharmaceutical Co., Ltd, Yongin, Korea
| | - Sinae Oh
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
| | - Songhwa Park
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
| | - Sanga Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
| | - Seong Hyeok Cho
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
| | - Seonha Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Kyuhyeon Bang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Minjeong Seo
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Jong Hyun Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
- Department of Biochemistry, School of Medicine, Catholic University of Daegu, Daegu, Korea
| | - Bongyong Lee
- Drug Discovery Center, Daewoong Pharmaceutical Co., Ltd, Yongin, Korea
| | - Joon Seok Park
- Drug Discovery Center, Daewoong Pharmaceutical Co., Ltd, Yongin, Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Sunghoon Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, Korea
- College of Medicine, Gangnam Severance Hospital, Yonsei University, Seoul, Korea
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Yoon I, Song JA, Suh JH, Kim S, Son J, Kim JH, Jang SY, Hwang KY, Kim MH, Kim S. EPRS1 Controls the TGF- β Signaling Pathway via Interaction with TβRI in Hepatic Stellate Cell. Mol Cell Biol 2023; 43:223-240. [PMID: 37154023 PMCID: PMC10184599 DOI: 10.1080/10985549.2023.2205344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is known to associated with fibrosis through its catalytic activity to produce prolyl-tRNA. Although its catalytic inhibitor halofuginone (HF) has been known to inhibit the TGF-β pathway as well as to reduce prolyl-tRNA production for the control of fibrosis, the underlying mechanism how EPRS1 regulates the TGF-β pathway was not fully understood. Here, we show a noncatalytic function of EPRS1 in controlling the TGF-β pathway and hepatic stellate cell activation via its interaction with TGF-β receptor I (TβRI). Upon stimulation with TGF-β, EPRS1 is phosphorylated by TGF-β-activated kinase 1 (TAK1), leading to its dissociation from the multi-tRNA synthetase complex and subsequent binding with TβRI. This interaction increases the association of TβRI with SMAD2/3 while decreases that of TβRI with SMAD7. Accordingly, EPRS1 stabilizes TβRI by preventing the ubiquitin-mediated degradation of TβRI. HF disrupts the interaction between EPRS1 and TβRI, and reduces TβRI protein levels, leading to inhibition of the TGF-β pathway. In conclusion, this work suggests the novel function of EPRS1 involved in the development of fibrosis by regulating the TGF-β pathway and the antifibrotic effects of HF by controlling both of EPRS1 functions.
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Affiliation(s)
- Ina Yoon
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Republic of Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, Republic of Korea
| | - Ji Ae Song
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Republic of Korea
| | - Ji Hun Suh
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Republic of Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, Republic of Korea
| | - Sulhee Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jonghyeon Son
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Jong Hyun Kim
- Department of Biochemistry, School of Medicine, Catholic University of Daegu, Daegu, Republic of Korea
| | - Song Yee Jang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea Research Republic of Korea
- Core Research Facility & Analysis Center, KRIBB, Daejeon, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea Research Republic of Korea
| | - Sunghoon Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, Yonsei University, Incheon, Republic of Korea
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon, Republic of Korea
- College of Medicine, Gangnam Severance Hospital, Yonsei University, Seoul, Republic of Korea
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Park JG, Jeon H, Shin S, Song C, Lee H, Kim NK, Kim EE, Hwang KY, Lee BJ, Lee IG. Structural basis for CEP192-mediated regulation of centrosomal AURKA. Sci Adv 2023; 9:eadf8582. [PMID: 37083534 PMCID: PMC10121170 DOI: 10.1126/sciadv.adf8582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aurora kinase A (AURKA) performs critical functions in mitosis. Thus, the activity and subcellular localization of AURKA are tightly regulated and depend on diverse factors including interactions with the multiple binding cofactors. How these different cofactors regulate AURKA to elicit different levels of activity at distinct subcellular locations and times is poorly understood. Here, we identified a conserved region of CEP192, the major cofactor of AURKA, that mediates the interaction with AURKA. Quantitative binding studies were performed to map the interactions of a conserved helix (Helix-1) within CEP192. The crystal structure of Helix-1 bound to AURKA revealed a distinct binding site that is different from other cofactor proteins such as TPX2. Inhibiting the interaction between Helix-1 and AURKA in cells led to the mitotic defects, demonstrating the importance of the interaction. Collectively, we revealed a structural basis for the CEP192-mediated AURKA regulation at the centrosome, which is distinct from TPX2-mediated regulation on the spindle microtubule.
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Affiliation(s)
- Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Sangchul Shin
- Technology Support Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Chiman Song
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
- Department of Biological Chemistry, University of Science and Technology, Daejeon 34113, South Korea
| | - Hyomin Lee
- Department of Biological Chemistry, University of Science and Technology, Daejeon 34113, South Korea
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Eunice EunKyeong Kim
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul 02792, South Korea
- Department of Biological Chemistry, University of Science and Technology, Daejeon 34113, South Korea
- Corresponding author.
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8
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Kim S, Koo M, Tak Y, Jang S, Park J, Hwang KY, Park S. Development of carbon nanoparticles-based soluble solid-phase immune sensor for the quantitative diagnosis of inflammation. Biosens Bioelectron 2023; 222:114975. [PMID: 36473421 DOI: 10.1016/j.bios.2022.114975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/29/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Quantitative immunodiagnosis is one of the most commonly used methods for in vitro diagnostics. Various bioanalytical methods have been developed to quantitatively diagnose immune analytes; however, they require blood dilution pretreatment, reaction mixing, complicated experimental steps, and can cause diagnostic errors due to the hook effect. To address this issue, we introduced a simple immunoassay based on carbon nanoparticles (CNPs). The assay was designed to have high flexibility for use in various in vitro diagnostic devices by constructing a soluble solid-phase immune sensor with high solubility using antibody-conjugated CNPs and polymer materials. Excellent performance was achieved using a free-antibody system with dual calibration. To verify the performance of this method with high reliability, canine C-reactive protein was selected as the immune analyte. Interestingly, our method efficiently mitigated the hook effect with outstanding performance in a one-step reaction without blood dilution or reaction mixing. The detection range of the target can be effectively controlled using free antibodies. Therefore, our CNP-based immunodiagnosis method may advance the commercialization of point-of-care immune biosensors.
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Affiliation(s)
- Sulhee Kim
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Miyoung Koo
- Development Center, Samsung Bioepis Co., Ltd., 76, Songdogyoyuk-ro, Yeonsu-gu, Incheon, 21987, Republic of Korea
| | - Yukyung Tak
- Health and Medical Equipment Division, Samsung Electronics Co., Ltd., 129, Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16677, Republic of Korea
| | - Seonhye Jang
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jongmyeon Park
- Research Institute, Precision Biosensor, Inc., 306, Techno 2-ro, Yuseong-gu, Daejeon, 34036, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
| | - Sungha Park
- Department of Bioengineering, Incheon JEI University, 15, Songdogyoyuk-ro 111beon-gil, Yeonsu-gu, Incheon, 21987, Republic of Korea.
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Yoon E, Kim D, Jeon H, Kwon Y, Jang Y, Kim S, Yeon Hwang K. Severe Acute Respiratory Syndrome Coronavirus 2 Variants—Possibility of Universal Vaccine Design: A Review. Comput Struct Biotechnol J 2022; 20:3533-3544. [PMID: 35765543 PMCID: PMC9221512 DOI: 10.1016/j.csbj.2022.06.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/18/2022] [Indexed: 11/28/2022] Open
Abstract
Both novel and conventional vaccination strategies have been implemented worldwide since the onset of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite various medical advances in the treatment and prevention of the spread of this contagious disease, it remains a major public health threat with a high mortality rate. As several lethal SARS-CoV-2 variants continue to emerge, the development of several vaccines and medicines, each with certain advantages and disadvantages, is underway. Additionally, many modalities are at various stages of research and development or clinical trials. Here, we summarize emerging SARS-CoV-2 variants, including delta, omicron, and “stealth omicron,” as well as available oral drugs for COVID-19. We also discuss possible antigen candidates other than the receptor-binding domain protein for the development of a universal COVID-19 vaccine. The present review will serve as a helpful resource for future vaccine and drug development to combat COVID-19.
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Shim MK, Song SK, Jeon SI, Hwang KY, Kim K. Nano-sized drug delivery systems to potentiate the immune checkpoint blockade therapy. Expert Opin Drug Deliv 2022; 19:641-652. [DOI: 10.1080/17425247.2022.2081683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Man Kyu Shim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Su Kyung Song
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Department of Biosystems & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Seong Ik Jeon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biosystems & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Kwangmeyung Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
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Han G, Cho H, Kim H, Jang Y, Jang H, Kim DE, Kim ES, Kim EH, Hwang KY, Kim K, Yang Y, Kim SH. Bovine colostrum derived-exosomes prevent dextran sulfate sodium-induced intestinal colitis via suppression of inflammation and oxidative stress. Biomater Sci 2022; 10:2076-2087. [PMID: 35315847 DOI: 10.1039/d1bm01797g] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite the rise in the global burden of inflammatory bowel disease, there is a lack of safe and effective therapies that can meet the needs of clinical patients. In this study, we investigated the beneficial effects of bovine milk, especially colostrum-derived exosomes (Col-exo) in a murine model of ulcerative colitis induced by dextran sodium sulfate (DSS). Col-exo activated the proliferation of colonic epithelial cells and macrophages, and created an environment to relieve inflammation by effectively removing reactive oxygen species and regulating the expression of immune cytokines. Besides, Col-exo could pass through the gastrointestinal tract intact and efficiently deliver bioactive cargoes to the stomach, small intestine, and colon. Our results showed that oral gavage of Col-exo can alleviate colitis symptoms including weight loss, gastrointestinal bleeding, and chronic diarrhea by modulating intestinal inflammatory immune responses. Overall, bovine colostrum-derived exosomes with excellent structural and functional stability may offer great potential as natural therapeutics for the recovery of colitis.
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Affiliation(s)
- Geonhee Han
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea. .,Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.
| | - Haeun Cho
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea. .,Department of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 02841, Korea.
| | - Hyosuk Kim
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.
| | - Yeongji Jang
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea. .,Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hochung Jang
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea. .,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Da Eun Kim
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea. .,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Eun Sun Kim
- Korea University College of Medicine, Department of Gastroenterology, Korea.
| | - Eun Hye Kim
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea. .,Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 02841, Korea.
| | - Kwangmeyung Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea. .,Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.
| | - Yoosoo Yang
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea. .,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Sun Hwa Kim
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.
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Kim H, Jang H, Cho H, Choi J, Hwang KY, Choi Y, Kim SH, Yang Y. Recent Advances in Exosome-Based Drug Delivery for Cancer Therapy. Cancers (Basel) 2021; 13:cancers13174435. [PMID: 34503245 PMCID: PMC8430743 DOI: 10.3390/cancers13174435] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Exosomes derived from various sources can deliver therapeutic agents such as small molecule drugs, nucleic acids, and proteins to cancer cells by passive or active targeting. These exosomes can encapsulate drugs inside the exosomes, extending drug half-life and increasing drug release stability. In addition, exosomes are highly biocompatible due to their endogenous origin and can be used as nanocarriers for tissue-specific targeted delivery. This review discusses recent advances in exosome-based drug delivery for cancer therapy. Abstract Exosomes are a class of extracellular vesicles, with a size of about 100 nm, secreted by most cells and carrying various bioactive molecules such as nucleic acids, proteins, and lipids, and reflect the biological status of parent cells. Exosomes have natural advantages such as high biocompatibility and low immunogenicity for efficient delivery of therapeutic agents such as chemotherapeutic drugs, nucleic acids, and proteins. In this review, we introduce the latest explorations of exosome-based drug delivery systems for cancer therapy, with particular focus on the targeted delivery of various types of cargoes.
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Affiliation(s)
- Hyosuk Kim
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (H.J.); (H.C.); (J.C.)
| | - Hochung Jang
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (H.J.); (H.C.); (J.C.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Haeun Cho
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (H.J.); (H.C.); (J.C.)
- Department of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 02841, Korea;
| | - Jiwon Choi
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (H.J.); (H.C.); (J.C.)
- Department of Bioengineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea;
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 02841, Korea;
| | - Yeonho Choi
- Department of Bioengineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea;
| | - Sun Hwa Kim
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (H.J.); (H.C.); (J.C.)
- Correspondence: (S.H.K.); (Y.Y.); Tel.: +82-02-958-6639 (S.H.K.); +82-02-958-6655 (Y.Y.)
| | - Yoosoo Yang
- Center for Theragnosis, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (H.K.); (H.J.); (H.C.); (J.C.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
- Correspondence: (S.H.K.); (Y.Y.); Tel.: +82-02-958-6639 (S.H.K.); +82-02-958-6655 (Y.Y.)
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Kim S, Yoon I, Kim S, Hwang KY. Protocol for improving diffraction quality of leucyl-tRNA synthetase 1 with methylation and post-crystallization soaking and cooling in cryoprotectants. STAR Protoc 2021; 2:100642. [PMID: 34258600 PMCID: PMC8260868 DOI: 10.1016/j.xpro.2021.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Leucyl-tRNA synthetase 1 (LARS1) synthesizes Leu-tRNALeu for protein synthesis and plays an important role in mTORC1 activation by sensing intracellular leucine concentrations. Here, we describe a protocol for the purification, reductive methylation, binding affinity measurement by microscale thermophoresis, T i value measurement by Tycho, and post-crystallization soaking and cooling in cryoprotectants to improve crystallization of LARS1. Collectively, this allowed us to build the RagD binding domain, which was shown to be a dynamic region of LARS1 refractory to crystallization. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021).
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Affiliation(s)
- Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea,Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea,Corresponding author
| | - Ina Yoon
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea,Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea,Corresponding author
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Kim S, Yoon I, Son J, Park J, Kim K, Lee JH, Park SY, Kang BS, Han JM, Hwang KY, Kim S. Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation. Cell Rep 2021; 35:109031. [PMID: 33910001 DOI: 10.1016/j.celrep.2021.109031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 12/18/2020] [Accepted: 04/02/2021] [Indexed: 01/07/2023] Open
Abstract
Leucyl-tRNA synthetase 1 (LARS1) mediates activation of leucine-dependent mechanistic target of rapamycin complex 1 (mTORC1) as well as ligation of leucine to its cognate tRNAs, yet its mechanism of leucine sensing is poorly understood. Here we describe leucine binding-induced conformational changes of LARS1. We determine different crystal structures of LARS1 complexed with leucine, ATP, and a reaction intermediate analog, leucyl-sulfamoyl-adenylate (Leu-AMS), and find two distinct functional states of LARS1 for mTORC1 activation. Upon leucine binding to the synthetic site, H251 and R517 in the connective polypeptide and 50FPYPY54 in the catalytic domain change the hydrogen bond network, leading to conformational change in the C-terminal domain, correlating with RagD association. Leucine binding to LARS1 is increased in the presence of ATP, further augmenting leucine-dependent interaction of LARS1 and RagD. Thus, this work unveils the structural basis for leucine-dependent long-range communication between the catalytic and RagD-binding domains of LARS1 for mTORC1 activation.
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Affiliation(s)
- Sulhee Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ina Yoon
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Jonghyeon Son
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Junga Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Kibum Kim
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea; Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji-Ho Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Beom Sik Kang
- School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung Min Han
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea; Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea.
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Kim S, Lee K, Park SH, Kwak GH, Kim MS, Kim HY, Hwang KY. Structural Insights into a Bifunctional Peptide Methionine Sulfoxide Reductase MsrA/B Fusion Protein from Helicobacter pylori. Antioxidants (Basel) 2021; 10:antiox10030389. [PMID: 33807684 PMCID: PMC8000184 DOI: 10.3390/antiox10030389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
Methionine sulfoxide reductase (Msr) is a family of enzymes that reduces oxidized methionine and plays an important role in the survival of bacteria under oxidative stress conditions. MsrA and MsrB exist in a fusion protein form (MsrAB) in some pathogenic bacteria, such as Helicobacter pylori (Hp), Streptococcus pneumoniae, and Treponema denticola. To understand the fused form instead of the separated enzyme at the molecular level, we determined the crystal structure of HpMsrABC44S/C318S at 2.2 Å, which showed that a linker region (Hpiloop, 193–205) between two domains interacted with each HpMsrA or HpMsrB domain via three salt bridges (E193-K107, D197-R103, and K200-D339). Two acetate molecules in the active site pocket showed an sp2 planar electron density map in the crystal structure, which interacted with the conserved residues in fusion MsrABs from the pathogen. Biochemical and kinetic analyses revealed that Hpiloop is required to increase the catalytic efficiency of HpMsrAB. Two salt bridge mutants (D193A and E199A) were located at the entrance or tailgate of Hpiloop. Therefore, the linker region of the MsrAB fusion enzyme plays a key role in the structural stability and catalytic efficiency and provides a better understanding of why MsrAB exists in a fused form.
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Affiliation(s)
- Sulhee Kim
- Department of Biotechnology, Korea University, Seoul 02841, Korea; (S.K.); (K.L.); (S.-H.P.); (M.S.K.)
| | - Kitaik Lee
- Department of Biotechnology, Korea University, Seoul 02841, Korea; (S.K.); (K.L.); (S.-H.P.); (M.S.K.)
| | - Sun-Ha Park
- Department of Biotechnology, Korea University, Seoul 02841, Korea; (S.K.); (K.L.); (S.-H.P.); (M.S.K.)
| | - Geun-Hee Kwak
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 42415, Korea;
| | - Min Seok Kim
- Department of Biotechnology, Korea University, Seoul 02841, Korea; (S.K.); (K.L.); (S.-H.P.); (M.S.K.)
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 42415, Korea;
- Correspondence: (H.-Y.K.); (K.Y.H.)
| | - Kwang Yeon Hwang
- Department of Biotechnology, Korea University, Seoul 02841, Korea; (S.K.); (K.L.); (S.-H.P.); (M.S.K.)
- Correspondence: (H.-Y.K.); (K.Y.H.)
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Jeon BJ, Kim S, Kim MS, Lee JH, Kim BS, Hwang KY. Insights into the structure of mature streptavidin C1 from Streptomyces cinnamonensis reveal the self-binding of the extension C-terminal peptide to biotin-binding sites. IUCrJ 2021; 8:168-177. [PMID: 33708394 PMCID: PMC7924230 DOI: 10.1107/s2052252520015675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
The members of the avidin protein family are well known for their high affinity towards d-biotin and their structural stability. These properties make avidins a valuable tool for various biotechnological applications. In the present study, two avidin-like biotin-binding proteins (named streptavidin C1 and C2) from Streptomyces cinnamonensis were newly identified while exploring antifungal proteins against Fusarium oxysporum f. sp. cucumerinum. Streptavidin C1 reveals a low correlation (a sequence identity of approximately 64%) with all known streptavidins, whereas streptavidin C2 shares a sequence identity of approximately 94% with other streptavidins. Here, the crystal structures of streptavidin C1 in the mature form and in complex with biotin at 2.1 and 2.5 Å resolution, respectively, were assessed. The overall structures present similar tetrameric features with D 2 symmetry to other (strept)avidin structures. Interestingly, the long C-terminal region comprises a short α-helix (C-Lid; residues 169-179) and an extension C-terminal peptide (ECP; residues 180-191) which stretches into the biotin-binding sites of the same monomer. This ECP sequence (-180VTSANPPAS188-) is a newly defined biotin-binding site, which reduces the ability to bind to (strept)avidin family proteins. The novel streptavidin C1 could help in the development of an engineered tetrameric streptavidin with reduced biotin-binding capacity as well as other biomaterial tools.
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Affiliation(s)
- Byeong Jun Jeon
- Department of Plant Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Sulhee Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Min-Seok Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Ji-Ho Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Beom Seok Kim
- Department of Plant Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
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Lee K, Yeo KJ, Choi SH, Lee EH, Kim BK, Kim S, Cheong HK, Lee WK, Kim HY, Hwang E, Woo JR, Lee SJ, Hwang KY. Monothiol and dithiol glutaredoxin-1 from Clostridium oremlandii: identification of domain-swapped structures by NMR, X-ray crystallography and HDX mass spectrometry. IUCrJ 2020; 7:1019-1027. [PMID: 33209316 PMCID: PMC7642778 DOI: 10.1107/s2052252520011598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Protein dimerization or oligomerization resulting from swapping part of the protein between neighboring polypeptide chains is known to play a key role in the regulation of protein function and in the formation of protein aggregates. Glutaredoxin-1 from Clostridium oremlandii (cGrx1) was used as a model to explore the formation of multiple domain-swapped conformations, which were made possible by modulating several hinge-loop residues that can form a pivot for domain swapping. Specifically, two alternative domain-swapped structures were generated and analyzed using nuclear magnetic resonance (NMR), X-ray crystallography, circular-dichroism spectroscopy and hydrogen/deuterium-exchange (HDX) mass spectrometry. The first domain-swapped structure (β3-swap) was formed by the hexameric cGrx1-cMsrA complex. The second domain-swapped structure (β1-swap) was formed by monothiol cGrx1 (C16S) alone. In summary, the first domain-swapped structure of an oxidoreductase in a hetero-oligomeric complex is presented. In particular, a single point mutation of a key cysteine residue to serine led to the formation of an intramolecular disulfide bond, as opposed to an intermolecular disulfide bond, and resulted in modulation of the underlying free-energy landscape of protein oligomerization.
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Affiliation(s)
- Kitaik Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Kwon Joo Yeo
- Division of Magnetic Resonance, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang, Chungbuk 28119, Republic of Korea
| | - Sae Hae Choi
- New Drug Development Center, Osong Medical Innovation Foundation, Osong, Cheongju, Chungbuk 28160, Republic of Korea
| | - Eun Hye Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Bo Keun Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sulhee Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang, Chungbuk 28119, Republic of Korea
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation, Osong, Cheongju, Chungbuk 28160, Republic of Korea
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 38541, Republic of Korea
| | - Eunha Hwang
- Division of Magnetic Resonance, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang, Chungbuk 28119, Republic of Korea
| | - Ju Rang Woo
- New Drug Development Center, Osong Medical Innovation Foundation, Osong, Cheongju, Chungbuk 28160, Republic of Korea
| | - Sung-Joon Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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Ke YH, Hwang KY, Thin TN, Sim YE, Abdullah HR. The usefulness of non-invasive co-oximetry haemoglobin measurement for screening pre-operative anaemia. Anaesthesia 2020; 76:54-60. [PMID: 32592515 DOI: 10.1111/anae.15171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 01/02/2023]
Abstract
Pre-operative anaemia (haemoglobin < 13.0 g.dl-1 ) is a modifiable peri-operative risk-factor. This is screened for using formal laboratory testing. A non-invasive finger-probe sensor that can accurately measure haemoglobin is a possible alternative. This study considers the accuracy of non-invasive haemoglobin measurement using the Rad-67™ Rainbow (Masimo Corp., Irvine, CA, USA) compared with formal laboratory testing and its usefulness in detecting pre-operative anaemia. A total of 392 patients had measurements taken for non-invasive haemoglobin and perfusion index values using the Rad-67 Rainbow, alongside further peri-operative parameters and a formal laboratory haemoglobin test. Bland-Altman and sensitivity analysis showed that the limits of agreement between non-invasive and formal laboratory haemoglobin testing were between -1.95 g.dl-1 and 2.23 g.dl-1 (p < 0.001). The overall performance of non-invasive haemoglobin measurement was better in men than women (ROC 91.1% vs. 78.2%) and less biased in men, mean -0.08 (SD 1.09, 95%Cl -0.23-0.07) compared with women (mean 0.38 (SD 0.99, 95%CI 0.24-0.52)). Pre-operative anaemia was more prevalent in women than men (50.3% vs. 14.4%). The sensitivity of non-invasive anaemia detection (haemoglobin < 13 g.dl-1 ) was 66% for women and 52% for men. A non-invasive haemoglobin value of 14.0 g.dl-1 had an overall 91% sensitivity for detecting pre-operative anaemia (82% in men and 93% in women). The Rad-67 Rainbow is inadequate for the estimation of formal laboratory haemoglobin and lacks sensitivity for detecting pre-operative anaemia, especially in women. Further advancement in technology and accuracy is needed before it can be recommended as a routine pre-operative screening test.
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Affiliation(s)
- Y H Ke
- Division of Anaesthesiology and Peri-operative Medicine, Singapore General Hospital, Singapore
| | - K Y Hwang
- Department of Anaesthesia, National University Hospital, Singapore
| | - T N Thin
- Division of Anaesthesiology and Peri-operative Medicine, Singapore General Hospital, Singapore
| | - Y E Sim
- Division of Anaesthesiology and Peri-operative Medicine, Singapore General Hospital, Singapore
| | - H R Abdullah
- Division of Anaesthesiology and Peri-operative Medicine, Singapore General Hospital, Singapore.,Duke NUS Medical School, Singapore
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Song S, Shim MK, Lim S, Moon Y, Yang S, Kim J, Hong Y, Yoon HY, Kim IS, Hwang KY, Kim K. In Situ One-Step Fluorescence Labeling Strategy of Exosomes via Bioorthogonal Click Chemistry for Real-Time Exosome Tracking In Vitro and In Vivo. Bioconjug Chem 2020; 31:1562-1574. [PMID: 32369345 DOI: 10.1021/acs.bioconjchem.0c00216] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Exosomes are cellular components with promising uses in cancer diagnostics and therapeutics, and their imaging and tracking are essential to study their biological properties. Herein, we report on an in situ one-step fluorescence labeling strategy for exosomes via bioorthogonal click chemistry. First, exosome donor cancer cells were treated with tetraacetylated N-azidoacetyl-d-mannosamine (Ac4ManNAz) to generate unnatural azide groups (-N3) on their surface via metabolic glycoengineering. Then, the azide groups were labeled with near-infrared fluorescent dye-conjugated dibenzylcyclooctyne (DBCO-Cy5) via bioorthogonal click chemistry. After 2 days of incubation, the DBCO-Cy5-labeled exosomes (Cy5-Exo) were successfully secreted from the donor cancer cells and were isolated via classical ultracentrifugation, providing a high-yield of fluorescent dye-labeled exosomes. This in situ one-step bioorthogonal click chemistry offers improved labeling efficiency, biocompatibility, and imaging sensitivy compared to standard exosomes (ST-Exo), purified with classical ultracentrifugation or carbocyanine lipophilic dye (DiD)-labeled exosomes (DiD-Exo) in vitro. In particular, the Cy5-Exo were successfully taken up by A549 cells in a time-dependent manner, and they could escape from lysosome confinement, showing their possible use as a delivery carrier of therapeutic drugs or imaging agents. Finally, intraveneously injected Cy5-Exo were noninvasively tracked and imaged via near-infrared fluorescence (NIRF) imaging in tumor-bearing mice. This new fluorescence labeling strategy for natural exosomes may be useful to provide better understanding of their theranostic effects in many biomedical applications.
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Affiliation(s)
- Sukyung Song
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Department of Biosystems & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Man Kyu Shim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seungho Lim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Yujeong Moon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Department of Bioengineering, Korea University, Seoul 02841, Republic of Korea
| | - Suah Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Jinseong Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Yeonsun Hong
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Hong Yeol Yoon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - In-San Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biosystems & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Kwangmeyung Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
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20
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Chung S, Kim S, Ryu SH, Hwang KY, Cho Y. Structural Basis for the Antibiotic Resistance of Eukaryotic Isoleucyl-tRNA Synthetase. Mol Cells 2020; 43:350-359. [PMID: 32088946 PMCID: PMC7191050 DOI: 10.14348/molcells.2020.2287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/13/2019] [Accepted: 12/14/2019] [Indexed: 12/02/2022] Open
Abstract
Pathogenic aminoacyl-tRNA synthetases (ARSs) are attractive targets for anti-infective agents because their catalytic active sites are different from those of human ARSs. Mupirocin is a topical antibiotic that specifically inhibits bacterial isoleucy-ltRNA synthetase (IleRS), resulting in a block to protein synthesis. Previous studies on Thermus thermophilus IleRS indicated that mupirocin-resistance of eukaryotic IleRS is primarily due to differences in two amino acids, His581 and Leu583, in the active site. However, without a eukaryotic IleRS structure, the structural basis for mupirocin-resistance of eukaryotic IleRS remains elusive. Herein, we determined the crystal structure of Candida albicans IleRS complexed with Ile-AMP at 2.9 Å resolution. The largest difference between eukaryotic and prokaryotic IleRS enzymes is closure of the active site pocket by Phe55 in the HIGH loop; Arg410 in the CP core loop; and the second Lys in the KMSKR loop. The Ile-AMP product is lodged in a closed active site, which may restrict its release and thereby enhance catalytic efficiency. The compact active site also prevents the optimal positioning of the 9-hydroxynonanoic acid of mupirocin and plays a critical role in resistance of eukaryotic IleRS to anti-infective agents.
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Affiliation(s)
- Scisung Chung
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang 37673, Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and
Biotechnology, Korea University, Seoul 0841, Korea
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang 37673, Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and
Biotechnology, Korea University, Seoul 0841, Korea
| | - Yunje Cho
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang 37673, Korea
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21
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Thach TT, Wu C, Hwang KY, Lee SJ. Azelaic Acid Induces Mitochondrial Biogenesis in Skeletal Muscle by Activation of Olfactory Receptor 544. Front Physiol 2020; 11:329. [PMID: 32411005 PMCID: PMC7199515 DOI: 10.3389/fphys.2020.00329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/20/2020] [Indexed: 12/31/2022] Open
Abstract
Mouse olfactory receptor 544 (Olfr544) is ectopically expressed in varied extra-nasal organs with tissue specific functions. Here, we investigated the functionality of Olfr544 in skeletal muscle cells and tissue. The expression of Olfr544 is confirmed by RT-PCR and qPCR in skeletal muscle cells and mouse skeletal muscle assessed by RT-PCR and qPCR. Olfr544 activation by its ligand, azelaic acid (AzA, 50 μM), induced mitochondrial biogenesis and autophagy in cultured skeletal myotubes by induction of cyclic adenosine monophosphate-response element binding protein (CREB)-peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α)-extracellular signal-regulated kinase-1/2 (ERK1/2) signaling axis. The silencing Olfr544 gene expression abrogated these effects of AzA in cultured myotubes. Similarly, in mice, the acute subcutaneous injection of AzA induced the CREB-PGC-1α-ERK1/2 pathways in mouse skeletal muscle, but these activations were negated in those of Olfr544 knockout mice. These demonstrate that the induction of mitochondrial biogenesis in skeletal muscle by AzA is Olfr544-dependent. Oral administration of AzA to high-fat-diet fed obese mice for 6 weeks increased mitochondrial DNA content in the skeletal muscle as well. Collectively, these findings demonstrate that Olfr544 activation by AzA regulates mitochondrial biogenesis in skeletal muscle. Intake of AzA or food containing AzA may help to improve skeletal muscle function.
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Affiliation(s)
- Trung Thanh Thach
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21-PLUS, Korea University, Seoul, South Korea.,Department of Food Bioscience and Technology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Chunyan Wu
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21-PLUS, Korea University, Seoul, South Korea.,Department of Food Bioscience and Technology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Sung-Joon Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21-PLUS, Korea University, Seoul, South Korea.,Department of Food Bioscience and Technology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
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22
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Kim J, Lee H, Roh YJ, Kim HU, Shin D, Kim S, Son J, Lee A, Kim M, Park J, Hwang SY, Kim K, Lee YK, Jung HS, Hwang KY, Lee BC. Structural and kinetic insights into flavin-containing monooxygenase and calponin-homology domains in human MICAL3. IUCrJ 2020; 7:90-99. [PMID: 31949908 PMCID: PMC6949599 DOI: 10.1107/s2052252519015409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
MICAL is an oxidoreductase that participates in cytoskeleton reorganization via actin disassembly in the presence of NADPH. Although three MICALs (MICAL1, MICAL2 and MICAL3) have been identified in mammals, only the structure of mouse MICAL1 has been reported. Here, the first crystal structure of human MICAL3, which contains the flavin-containing monooxygenase (FMO) and calponin-homology (CH) domains, is reported. MICAL3 has an FAD/NADP-binding Rossmann-fold domain for mono-oxygenase activity like MICAL1. The FMO and CH domains of both MICAL3 and MICAL1 are highly similar in structure, but superimposition of the two structures shows a different relative position of the CH domain in the asymmetric unit. Based on kinetic analyses, the catalytic efficiency of MICAL3 dramatically increased on adding F-actin only when the CH domain was available. However, this did not occur when two residues, Glu213 and Arg530, were mutated in the FMO and CH domains, respectively. Overall, MICAL3 is structurally highly similar to MICAL1, which suggests that they may adopt the same catalytic mechanism, but the difference in the relative position of the CH domain produces a difference in F-actin substrate specificity.
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Affiliation(s)
- Junsoo Kim
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Haemin Lee
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Yeon Jin Roh
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Han-ul Kim
- Biochemistry Laboratory, Department of Biosystems and Biotechnology, Kangwon National University, 1 Kangwondaekak-gil, Chuncheon-si, Gangwon-do 24341, Republic of Korea
| | - Donghyuk Shin
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sorah Kim
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jonghyeon Son
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Aro Lee
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Minseo Kim
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Junga Park
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Seong Yun Hwang
- Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Kyunghwan Kim
- Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Yong Kwon Lee
- Department of Culinary Art and Food Service Management, Yuhan University, 590 Gyeongin-ro, Bucheon-si, Gyeonggi-do 14780, Republic of Korea
| | - Hyun Suk Jung
- Biochemistry Laboratory, Department of Biosystems and Biotechnology, Kangwon National University, 1 Kangwondaekak-gil, Chuncheon-si, Gangwon-do 24341, Republic of Korea
| | - Kwang Yeon Hwang
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Byung Cheon Lee
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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23
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Yoon I, Nam M, Kim HK, Moon HS, Kim S, Jang J, Song JA, Jeong SJ, Kim SB, Cho S, Kim Y, Lee J, Yang WS, Yoo HC, Kim K, Kim MS, Yang A, Cho K, Park HS, Hwang GS, Hwang KY, Han JM, Kim JH, Kim S. Glucose-dependent control of leucine metabolism by leucyl-tRNA synthetase 1. Science 2019; 367:205-210. [PMID: 31780625 DOI: 10.1126/science.aau2753] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 03/20/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022]
Abstract
Despite the importance of glucose and amino acids for energy metabolism, interactions between the two nutrients are not well understood. We provide evidence for a role of leucyl-tRNA synthetase 1 (LARS1) in glucose-dependent control of leucine usage. Upon glucose starvation, LARS1 was phosphorylated by Unc-51 like autophagy activating kinase 1 (ULK1) at the residues crucial for leucine binding. The phosphorylated LARS1 showed decreased leucine binding, which may inhibit protein synthesis and help save energy. Leucine that is not used for anabolic processes may be available for catabolic pathway energy generation. The LARS1-mediated changes in leucine utilization might help support cell survival under glucose deprivation. Thus, depending on glucose availability, LARS1 may help regulate whether leucine is used for protein synthesis or energy production.
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Affiliation(s)
- Ina Yoon
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Miso Nam
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea
| | - Hoi Kyoung Kim
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hee-Sun Moon
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sungmin Kim
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jayun Jang
- Department of Molecular Medicine and Biopharmaceutical Sciences and Graduate School for Convergence Technologies, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Ae Song
- Department of Molecular Medicine and Biopharmaceutical Sciences and Graduate School for Convergence Technologies, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Jae Jeong
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Bum Kim
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Seongmin Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences and Graduate School for Convergence Technologies, Seoul National University, Seoul 08826, Republic of Korea
| | - YounHa Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences and Graduate School for Convergence Technologies, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihye Lee
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Suk Yang
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hee Chan Yoo
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Kibum Kim
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Min-Sun Kim
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea
| | - Aerin Yang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyukwang Cho
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Geum-Sook Hwang
- Integrated Metabolomics Research Group, Western Seoul Center, Korea Basic Science Institute, Seoul 03759, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jung Min Han
- Yonsei Institute of Pharmaceutical Sciences, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Jong Hyun Kim
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center and College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea. .,Department of Molecular Medicine and Biopharmaceutical Sciences and Graduate School for Convergence Technologies, Seoul National University, Seoul 08826, Republic of Korea
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24
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Kim SE, Hwang KY, Nam KH. Spectral and structural analysis of a red fluorescent protein from Acropora digitifera. Protein Sci 2019; 28:375-381. [PMID: 30368951 PMCID: PMC6319757 DOI: 10.1002/pro.3540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
Fluorescent proteins (FPs) possess a wide variety of spectral properties that make them of widespread interest as optical markers. These proteins can be applied as pH indicators or metal biosensors. The discovery and characterization of new fluorescent proteins is expected to further extend their application. Here, we report the spectral and structural analysis of a red fluorescent protein from Acropora digitifera (designated AdRed). This protein shows a tetrameric state and is red emitting, with excitation and emission maxima at 567 and 612 nm, respectively. Its crystal structure shows the tetrameric interface stabilized by hydrogen bonding and salt bridges. The electron density map of the chromophore, consisting of Asp66-Tyr67-Gly68, shows the decarboxylated side chain of Asp66. Ser223, located near the chromophore, has the role of bridging His202 and Glu221, and is part of the hydrogen bond network. Mutated AdRed with Cys148Ser reveals a blue shift in fluorescence excitation and emission. Our results provide insights into understanding the molecular function of AdRed and other FPs.
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Affiliation(s)
- So Eun Kim
- Division of Biotechnology, College of Life Sciences and BiotechnologyKorea UniversitySeoul02841Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and BiotechnologyKorea UniversitySeoul02841Republic of Korea
| | - Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and BiotechnologyKorea UniversitySeoul02841Republic of Korea
- Institute of Life Science and Natural ResourcesKorea UniversitySeoul02841Republic of Korea
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25
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Chung WC, Kim J, Kim BC, Kang HR, Son J, Ki H, Hwang KY, Song MJ. Structure-based mechanism of action of a viral poly(ADP-ribose) polymerase 1-interacting protein facilitating virus replication. IUCrJ 2018; 5:866-879. [PMID: 30443370 PMCID: PMC6211522 DOI: 10.1107/s2052252518013854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/01/2018] [Indexed: 06/09/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA. Here, the structure of MHV-68 vPIP was determined at 2.2 Å resolution. The structure consists of 12 α-helices with characteristic N-terminal β-strands (Nβ) and forms a V-shaped-twist dimer in the asymmetric unit. Structure-based mutagenesis revealed that Nβ and the α1 helix (residues 2-26) are essential for the nuclear localization and function of vPIP; three residues were then identified (Phe5, Ser12 and Thr16) that were critical for the function of vPIP and its interaction with PARP-1. A recombinant MHV-68 harboring mutations of these three residues showed severely attenuated viral replication both in vitro and in vivo. Moreover, ORF49 of Kaposi's sarcoma-associated herpesvirus also directly interacted with PARP-1, indicating a conserved mechanism of action of vPIPs. The results elucidate the novel molecular mechanisms by which oncogenic gammaherpesviruses overcome repression by PARP-1 using vPIPs.
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Affiliation(s)
- Woo-Chang Chung
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Junsoo Kim
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Byung Chul Kim
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hye-Ri Kang
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - JongHyeon Son
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hosam Ki
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Kwang Yeon Hwang
- Structural Proteomics Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Moon Jung Song
- Virus–Host Interactions Laboratory, Department of Biosystems and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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26
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Son J, Kim S, Kim SE, Lee H, Lee MR, Hwang KY. Structural Analysis of an Epitope Candidate of Triosephosphate Isomerase in Opisthorchis viverrini. Sci Rep 2018; 8:15075. [PMID: 30305716 PMCID: PMC6180082 DOI: 10.1038/s41598-018-33479-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/19/2018] [Indexed: 01/07/2023] Open
Abstract
Opisthorchis viverrini, a parasitic trematode, was recategorized as a group 1 biological carcinogen because it causes opisthorchiasis, which may result in cholangiocarcinoma. A new strategy for controlling opisthorchiasis is needed because of issues such as drug resistance and reinfection. Triosephosphate isomerase (TIM), a key enzyme in energy metabolism, is regarded as a potential drug target and vaccine candidate against various pathogens. Here, we determined the crystal structures of wild-type and 3 variants of TIMs from O. viverrini (OvTIM) at high resolution. The unique tripeptide of parasite trematodes, the SAD motif, was located on the surface of OvTIM and contributed to forming a 310-helix of the following loop in a sequence-independent manner. Through thermal stability and structural analyses of OvTIM variants, we found that the SAD motif induced local structural alterations of the surface and was involved in the overall stability of OvTIM in a complementary manner with another parasite-specific residue, N115. Comparison of the surface characteristics between OvTIM and Homo sapiens TIM (HsTIM) and structure-based epitope prediction suggested that the SAD motif functions as an epitope.
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Affiliation(s)
- Jonghyeon Son
- 0000 0001 0840 2678grid.222754.4Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, 136-701 South Korea
| | - Sulhee Kim
- 0000 0001 0840 2678grid.222754.4Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, 136-701 South Korea
| | - So Eun Kim
- 0000 0001 0840 2678grid.222754.4Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, 136-701 South Korea
| | - Haemin Lee
- 0000 0001 0840 2678grid.222754.4Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, 136-701 South Korea
| | - Myoung-Ro Lee
- 0000 0004 0647 4899grid.415482.eDivision of Malaria & Parasitic Disease, Korea National Institute of Health, Osong, 28159 Republic of Korea
| | - Kwang Yeon Hwang
- 0000 0001 0840 2678grid.222754.4Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, 136-701 South Korea
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27
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Kim N, Kang JH, Lee WK, Kim SG, Lee JS, Lee SH, Park JB, Kim KH, Gong YD, Hwang KY, Kim SY. Allosteric inhibition site of transglutaminase 2 is unveiled in the N terminus. Amino Acids 2018; 50:1583-1594. [PMID: 30105541 DOI: 10.1007/s00726-018-2635-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/09/2018] [Indexed: 12/22/2022]
Abstract
Previously we have demonstrated transglutaminase 2 (TGase 2) inhibition abrogated renal cell carcinoma (RCC) using GK921 (3-(phenylethynyl)-2-(2-(pyridin-2-yl)ethoxy)pyrido[3,2-b]pyrazine), although the mechanism of TGase 2 inhibition remains unsolved. Recently, we found that the increase of TGase 2 expression is required for p53 depletion in RCC by transporting the TGase 2 (1-139 a.a)-p53 complex to the autophagosome, through TGase 2 (472-687 a.a) binding p62. In this study, mass analysis revealed that GK921 bound to the N terminus of TGase 2 (81-116 a.a), which stabilized p53 by blocking TGase 2 binding. This suggests that RCC survival can be stopped by p53-induced cell death through blocking the p53-TGase 2 complex formation using GK921. Although GK921 does not bind to the active site of TGase 2, GK921 binding to the N terminus of TGase 2 also inactivated TGase 2 activity through acceleration of non-covalent self-polymerization of TGase 2 via conformational change. This suggests that TGase 2 has an allosteric binding site (81-116 a.a) which changes the conformation of TGase 2 enough to accelerate inactivation through self-polymer formation.
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Affiliation(s)
- Nayeon Kim
- Tumor Microenvironment Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Joon Hee Kang
- Tumor Microenvironment Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk, 28160, Republic of Korea
| | - Seul-Gi Kim
- Tumor Microenvironment Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Jae-Seon Lee
- Tumor Microenvironment Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Seon-Hyeong Lee
- Tumor Microenvironment Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Jong Bae Park
- Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Kyung-Hee Kim
- Omics Core Lab, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Young-Dae Gong
- Department of Chemistry, College of Science, Dongguk University, Seoul, 04620, Republic of Korea
| | - Kwang Yeon Hwang
- Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea
| | - Soo-Youl Kim
- Tumor Microenvironment Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea.
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Jeong CY, Lee WJ, Truong HA, Trịnh CS, Jin JY, Kim S, Hwang KY, Kang CS, Moon JK, Hong SW, Lee H. Dual role of SND1 facilitates efficient communication between abiotic stress signalling and normal growth in Arabidopsis. Sci Rep 2018; 8:10114. [PMID: 29973639 PMCID: PMC6031621 DOI: 10.1038/s41598-018-28413-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/22/2018] [Indexed: 01/21/2023] Open
Abstract
Certain plant cells synthesize secondary cell walls besides primary cell walls. This biosynthesis is strictly controlled by an array of transcription factors. Here, we show that SND1, a regulator of cell-wall biosynthesis, regulates abscisic acid (ABA) biosynthesis to ensure optimal plant growth. In Arabidopsis, the lack of SND1 and its homolog NST1 leads to the deficiency of secondary cell walls, preventing snd1nst1 double mutant seedlings from growing upright. Compared to wild type seedlings, the snd1 knockout mutant seedlings accumulated less anthocyanin and exhibited low tolerance to salt stress. Compared to wild type seedlings, the snd1 knockout seedlings were more sensitive to salt stress. Although SND1 can bind to the promoter of Myb46, we observed that SND1 binds directly to the promoter of the ABI4 gene, thereby reducing ABA levels under normal growth conditions. Thus, plants adjust secondary cell wall thickening and growth via SND1. SND1 has a dual function: it activates the Myb46 pathway, fostering lignin biosynthesis to produce sufficient cell wall components for growth, while maintaining a low ABA concentration, as it inhibits growth. This dual function of SND1 may help plants modulate their growth efficiently.
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Affiliation(s)
- Chan Young Jeong
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea.,Institute of Life Science and Natural Resources, Korea University, Seoul, 136-713, Republic of Korea
| | - Won Je Lee
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Hai An Truong
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Cao Sơn Trịnh
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Joo Yeon Jin
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Sulhee Kim
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea
| | - Chon-Sik Kang
- Crop Breeding Division, National Institute of Crop Science, RDA, 181 Hyeoksin-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 54955, Republic of Korea
| | - Joon-Kwan Moon
- Department of Plant Life and Environmental Sciences, Hankyong National University, 327 Jungangro, Anseong, 17579, Republic of Korea
| | - Suk-Whan Hong
- Department of Molecular Biotechnology, College of Agriculture and Life Sciences, Bioenergy Research Center, Chonnam National University, Gwangju, Republic of Korea.
| | - Hojoung Lee
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul, 136-713, Republic of Korea. .,Institute of Life Science and Natural Resources, Korea University, Seoul, 136-713, Republic of Korea.
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Bae JE, Hwang KY, Nam KH. Structural analysis of substrate recognition by glucose isomerase in Mn 2+ binding mode at M2 site in S. rubiginosus. Biochem Biophys Res Commun 2018; 503:770-775. [PMID: 29909012 DOI: 10.1016/j.bbrc.2018.06.074] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/14/2018] [Indexed: 11/29/2022]
Abstract
Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn2+, but not in the presence of Mg2+. Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn2+ at the M2 site. Glucose and Mn2+ at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55-110°, whereas the M1 site has a relatively stable octahedral coordination with an angle of 85-95°. We suggest a two-step sequential process for SruGI substrate recognition, in Mn2+ binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition.
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Affiliation(s)
- Ji-Eun Bae
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea.
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Kim HT, Na BK, Chung J, Kim S, Kwon SK, Cha H, Son J, Cho JM, Hwang KY. Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase. Cell Chem Biol 2018; 25:426-438.e4. [PMID: 29429898 DOI: 10.1016/j.chembiol.2018.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/17/2017] [Accepted: 01/08/2018] [Indexed: 11/18/2022]
Abstract
Kynurenine 3-monooxygenase (KMO) inhibitors have been developed for the treatment of neurodegenerative disorders. The mechanisms of flavin reduction and hydrogen peroxide production by KMO inhibitors are unknown. Herein, we report the structure of human KMO and crystal structures of Saccharomyces cerevisiae (sc) and Pseudomonas fluorescens (pf) KMO with Ro 61-8048. Proton transfer in the hydrogen bond network triggers flavin reduction in p-hydroxybenzoate hydroxylase, but the mechanism triggering flavin reduction in KMO is different. Conformational changes via π-π interactions between the loop above the flavin and substrate or non-substrate effectors lead to disorder of the C-terminal α helix in scKMO and shifts of domain III in pfKMO, stimulating flavin reduction. Interestingly, Ro 61-8048 has two different binding modes. It acts as a competitive inhibitor in scKMO and as a non-substrate effector in pfKMO. These findings provide understanding of the catalytic cycle of KMO and insight for structure-based drug design of KMO inhibitors.
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Affiliation(s)
- Hyun Tae Kim
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Byeong Kwan Na
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jiwoung Chung
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Sool Ki Kwon
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Hyunju Cha
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea
| | - Jonghyeon Son
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Joong Myung Cho
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, Korea.
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
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Kim HT, Kim S, Na BK, Chung J, Hwang E, Hwang KY. Structural insights into the dimer-tetramer transition of FabI from Bacillus anthracis. Biochem Biophys Res Commun 2017; 493:28-33. [PMID: 28935372 DOI: 10.1016/j.bbrc.2017.09.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 11/30/2022]
Abstract
Enoyl-ACP reductase (ENR, also known as FabI) has received considerable interest as an anti-bacterial target due to its essentiality in fatty acid synthesis. All the FabI structures reported to date, regardless of the organism, are composed of homo-tetramers, except for two structures: Bacillus cereus and Staphylococcus aureus FabI (bcFabI and saFabI, respectively), which have been reported as dimers. However, the reason for the existence of the dimeric form in these organisms and the biological meaning of dimeric and tetrameric forms of FabI are ambiguous. Herein, we report the high-resolution crystal structure of a dimeric form of Bacillus anthracis FabI (baFabI) and the crystal structures of tetrameric forms of baFabI in the apo state and in complex with NAD+ and with NAD+-triclosan, at 1.7 Å, 1.85 Å, 1.96 Å, and 1.95 Å, respectively. Interestingly, we found that baFabI with a His6-tag at its C-terminus exists as a dimer, whereas untagged-baFabI exists as a tetramer. The His6-tag may block the dimer-tetramer transition, since baFabI has relatively short-length amino acids (255LG256) after the 310-helix η7 compared to those of FabI of other organisms. The dimeric form of baFabI is catalytically inactive, because the α-helix α5 occupies the NADH-binding site. During the process of dimer-tetramer transition, this α5 helix rotates about 55° toward the tetramer interface and the active site is established. Therefore, tetramerization of baFabI is required for cofactor binding and catalytic activity.
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Affiliation(s)
- Hyun Tae Kim
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Byeong Kwan Na
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea
| | - Jiwoung Chung
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea
| | - Eunha Hwang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.
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Abstract
tRNA maturation involves several steps, including processing, splicing, CCA addition, and posttranscriptional modifications. tRNAHis guanylyltransferase (Thg1) is the only enzyme known to catalyze templated nucleotide addition in the 3'-5' direction, unlike other DNA and RNA polymerases. For a better understanding of its unique catalytic mechanism at the molecular level, we determined the crystal structure of GTP-bound Thg1 from Saccharomyces cerevisiae at the maximum resolution of 3.0 Å. The structure revealed the enzyme to have a tetrameric conformation that is well conserved among different species, and the GTP molecule was clearly bound at the active site, coordinating with two magnesium ions. In addition, two flexible protomers at the potential binding site (PBS) for tRNAHis were observed. We suggest that the PBS of the tetramer could also be one of the sites for interaction with partner proteins.
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Affiliation(s)
- Kitaik Lee
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea
| | - Eun Hye Lee
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea
| | - Jonghyeon Son
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-791, Republic of Korea.
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Kwon DH, Kim S, Jung YO, Roh KH, Kim L, Kim BW, Hong SB, Lee IY, Song JH, Lee WC, Choi EJ, Hwang KY, Song HK. The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane. Autophagy 2016; 13:70-81. [PMID: 27791457 DOI: 10.1080/15548627.2016.1243199] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Hosts utilize macroautophagy/autophagy to clear invading bacteria; however, bacteria have also developed a specific mechanism to survive by manipulating the host cell autophagy mechanism. One pathogen, Legionella pneumophila, can hinder host cell autophagy by using the specific effector protein RavZ that cleaves phosphatidylethanolamine-conjugated LC3 on the phagophore membrane. However, the detailed molecular mechanisms associated with the function of RavZ have hitherto remained unclear. Here, we report on the biochemical characteristics of the RavZ-LC3 interaction, the solution structure of the 1:2 complex between RavZ and LC3, and crystal structures of RavZ showing different conformations of the active site loop without LC3. Based on our biochemical, structural, and cell-based analyses of RavZ and LC3, both distant flexible N- and C-terminal regions containing LC3-interacting region (LIR) motifs are important for substrate recognition. These results suggest a novel mechanism of RavZ action on the phagophore membrane and lay the groundwork for understanding how bacterial pathogens can survive autophagy.
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Affiliation(s)
- Do Hoon Kwon
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Sulhee Kim
- b Division of Biotechnology, Korea University , Seongbuk-gu, Seoul , Korea
| | - Yang Ouk Jung
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Kyung-Hye Roh
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Leehyeon Kim
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Byeong-Won Kim
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Seung Beom Hong
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - In Young Lee
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Ju Han Song
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Woo Cheol Lee
- b Division of Biotechnology, Korea University , Seongbuk-gu, Seoul , Korea
| | - Eui-Ju Choi
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Kwang Yeon Hwang
- b Division of Biotechnology, Korea University , Seongbuk-gu, Seoul , Korea
| | - Hyun Kyu Song
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
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Yeo KJ, Park JW, Kim EH, Jeon YH, Hwang KY, Cheong HK. Characterization of the sensor domain of QseE histidine kinase from Escherichia coli. Protein Expr Purif 2016; 126:122-126. [DOI: 10.1016/j.pep.2016.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/05/2023]
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Han AR, Kang HR, Son J, Kwon DH, Kim S, Lee WC, Song HK, Song MJ, Hwang KY. The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism. Nucleic Acids Res 2016; 44:9483-9493. [PMID: 27596595 PMCID: PMC5100569 DOI: 10.1093/nar/gkw775] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022] Open
Abstract
GTP and branched-chain amino acids (BCAAs) are metabolic sensors that are indispensable for the determination of the metabolic status of cells. However, their molecular sensing mechanism remains unclear. CodY is a unique global transcription regulator that recognizes GTP and BCAAs as specific signals and affects expression of more than 100 genes associated with metabolism. Herein, we report the first crystal structures of the full-length CodY complex with sensing molecules and describe their functional states. We observed two different oligomeric states of CodY: a dimeric complex of CodY from Staphylococcus aureus with the two metabolites GTP and isoleucine, and a tetrameric form (apo) of CodY from Bacillus cereus. Notably, the tetrameric state shows in an auto-inhibitory manner by blocking the GTP-binding site, whereas the binding sites of GTP and isoleucine are clearly visible in the dimeric state. The GTP is located at a hinge site between the long helical region and the metabolite-binding site. Together, data from structural and electrophoretic mobility shift assay analyses improve understanding of how CodY senses GTP and operates as a DNA-binding protein and a pleiotropic transcription regulator.
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Affiliation(s)
- Ah-Reum Han
- Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Hye-Ri Kang
- Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Jonghyeon Son
- Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Do Hoon Kwon
- Department of Life Sciences, College of Life Sciences & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Sulhee Kim
- Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Woo Cheol Lee
- Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, College of Life Sciences & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Moon Jung Song
- Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
| | - Kwang Yeon Hwang
- Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea
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Han AR, Kim MJ, Kwak GH, Son J, Hwang KY, Kim HY. Essential Role of the Linker Region in the Higher Catalytic Efficiency of a Bifunctional MsrA-MsrB Fusion Protein. Biochemistry 2016; 55:5117-27. [PMID: 27551953 DOI: 10.1021/acs.biochem.6b00544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many bacteria, particularly pathogens, possess methionine sulfoxide reductase A (MsrA) and B (MsrB) as a fusion form (MsrAB). However, it is not clear why they possess a fusion MsrAB form rather than the separate enzymes that exist in most organisms. In this study, we performed biochemical and kinetic analyses of MsrAB from Treponema denticola (TdMsrAB), single-domain forms (TdMsrA and TdMsrB), and catalytic Cys mutants (TdMsrAB(C11S) and TdMsrAB(C285S)). We found that the catalytic efficiency of both MsrA and MsrB increased after fusion of the domains and that the linker region (iloop) that connects TdMsrA and TdMsrB is required for the higher catalytic efficiency of TdMsrAB. We also determined the crystal structure of TdMsrAB at 2.3 Å, showing that the iloop mainly interacts with TdMsrB via hydrogen bonds. Further kinetic analysis using the iloop mutants revealed that the iloop-TdMsrB interactions are critical to MsrB and MsrA activities. We also report the structure in which an oxidized form of dithiothreitol, an in vitro reductant for MsrA and MsrB, is present in the active site of TdMsrA. Collectively, the results of this study reveal an essential role of the iloop in maintaining the higher catalytic efficiency of the MsrAB fusion enzyme and provide a better understanding of why the MsrAB enzyme exists as a fused form.
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Affiliation(s)
- Ah-Reum Han
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University , Seoul 02841, Republic of Korea
| | - Moon-Jung Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine , Daegu 42415, Republic of Korea
| | - Geun-Hee Kwak
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine , Daegu 42415, Republic of Korea
| | - Jonghyeon Son
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University , Seoul 02841, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University , Seoul 02841, Republic of Korea
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine , Daegu 42415, Republic of Korea
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Kim J, Sambalkhundev GO, Kim S, Son J, Han AR, Ko SM, Hwang KY, Lee WC. Processing of A-form ssDNA by cryptic RNase H fold exonuclease PF2046. Arch Biochem Biophys 2016; 606:143-50. [PMID: 27495739 DOI: 10.1016/j.abb.2016.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 11/18/2022]
Abstract
RNase H fold protein PF2046 of Pyrococcus furiosus is a 3'-5' ssDNA exonuclease that cleaves after the second nucleotide from the 3' end of ssDNA and prefers poly-dT over poly-dA as a substrate. In our crystal structure of PF2046 complexed with an oligonucleotide of four thymidine nucleotides (dT4), PF2046 accommodates dT4 tightly in a groove and imposes steric hindrance on dT4 mainly by Phe220 such that dT4 assumes the A-form. As poly-dA prefer B-form due to the stereochemical restrictions, the A-form ssDNA binding by PF2046 should disfavor the processing of poly-dA. Phe220 variants display reduced activity toward poly-dA and the A-form appears to be a prerequisite for the processing by PF2046.
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Affiliation(s)
- Junsoo Kim
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea; Institute for Life Sciences and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - Gerelt-Od Sambalkhundev
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea; Institute for Life Sciences and Natural Resources, Korea University, Seoul 136-713, Republic of Korea
| | - Sulhee Kim
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Jonghyeon Son
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Ah-Reum Han
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Sul-Min Ko
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea.
| | - Woo Cheol Lee
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-gu, Seoul 136-713, Republic of Korea; Institute for Life Sciences and Natural Resources, Korea University, Seoul 136-713, Republic of Korea.
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Kim IJ, Kim S, Park J, Eom I, Kim S, Kim JH, Ha SC, Kim YG, Hwang KY, Nam KH. Crystal structures of Dronpa complexed with quenchable metal ions provide insight into metal biosensor development. FEBS Lett 2016; 590:2982-90. [DOI: 10.1002/1873-3468.12316] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/27/2016] [Accepted: 07/11/2016] [Indexed: 11/12/2022]
Affiliation(s)
- In Jung Kim
- Division of Biotechnology; College of Life Sciences & Biotechnology; Korea University; Seoul Korea
| | - Sangsoo Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Jeahyun Park
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Intae Eom
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Sunam Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Jin-Hong Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Yeon Gil Kim
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology; College of Life Sciences & Biotechnology; Korea University; Seoul Korea
| | - Ki Hyun Nam
- Pohang Accelerator Laboratory; Pohang University of Science and Technology; Korea
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Jo CH, Kim J, Han AR, Park SY, Hwang KY, Nam KH. Crystal structure of Thermoplasma acidophilum XerA recombinase shows large C-shape clamp conformation and cis-cleavage mode for nucleophilic tyrosine. FEBS Lett 2016; 590:848-56. [PMID: 26919387 DOI: 10.1002/1873-3468.12109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 02/15/2016] [Accepted: 02/18/2016] [Indexed: 11/08/2022]
Abstract
Site-specific Xer recombination plays a pivotal role in reshuffling genetic information. Here, we report the 2.5 Å crystal structure of XerA from the archaean Thermoplasma acidophilum. Crystallographic data reveal a uniquely open conformational state, resulting in a C-shaped clamp with an angle of ~ 48° and a distance of 57 Å between the core-binding and the catalytic domains. The catalytic nucleophile, Tyr264, is positioned in cis-cleavage mode by XerA's C-term tail that interacts with the CAT domain of a neighboring monomer without DNA substrate. Structural comparisons of tyrosine recombinases elucidate the dynamics of Xer recombinase.
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Affiliation(s)
- Chang Hwa Jo
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Junsoo Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Ah-reum Han
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Sam Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Ki Hyun Nam
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Kyungbuk, Korea
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40
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Abstract
The crystallinity of polyethylene, which significantly affects the properties of the polymer, is quite sensitive to the concentration of its branches. Thus, it is necessary to estimate branch concentration with reasonable accuracy. Currently, (13)C NMR and gel permeation chromatography-Fourier transform infrared spectroscopy are widely-used analysis methods for the analysis of branch concentration. Despite several advantages, these methods sometimes have limitations. For instance, the preparation of samples for (13)C- NMR is tedious because high-concentration samples are required and the time for analysis is greater than 12 h. To more efficiently estimate the branch concentration of polyethylene, we developed a new high-field (1)H NMR method with an improved peak resolution by employing (1) homonuclear decoupling and (2) 2D heteronuclear correlation. The new method was observed to significantly reduce the experimental time to ∼ 30 min; furthermore, sample preparation was relatively simple because the method did not require high-concentration samples.
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Affiliation(s)
- Minhwan Jung
- Corporate R&D, LG Chem Research Park , 104-1, Moonji-dong, Yuseung-gu, Daejeon, 305-380, Republic of Korea.,Department of Biosystems & Biotechnology, Division of Biotechnology, Korea University , Seoul, 136-713, Republic of Korea
| | - Yura Lee
- Corporate R&D, LG Chem Research Park , 104-1, Moonji-dong, Yuseung-gu, Daejeon, 305-380, Republic of Korea
| | - Sooyoung Kwak
- Corporate R&D, LG Chem Research Park , 104-1, Moonji-dong, Yuseung-gu, Daejeon, 305-380, Republic of Korea
| | - Heeyong Park
- Corporate R&D, LG Chem Research Park , 104-1, Moonji-dong, Yuseung-gu, Daejeon, 305-380, Republic of Korea
| | - Byoungsoo Kim
- Corporate R&D, LG Chem Research Park , 104-1, Moonji-dong, Yuseung-gu, Daejeon, 305-380, Republic of Korea
| | - Sulhee Kim
- Department of Biosystems & Biotechnology, Division of Biotechnology, Korea University , Seoul, 136-713, Republic of Korea
| | - Kwang Hwan Lee
- Bruker Korea , 4F. KT Net Building, Pangyoro 338, Bundang-Gu, Seongnam-si, Gyeonggi-do 463-847, Republic of Korea
| | - Hye Sung Cho
- Corporate R&D, LG Chem Research Park , 104-1, Moonji-dong, Yuseung-gu, Daejeon, 305-380, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biosystems & Biotechnology, Division of Biotechnology, Korea University , Seoul, 136-713, Republic of Korea
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Son J, Jo CH, Murugan RN, Bang JK, Hwang KY, Lee WC. Crystal structure of Legionella pneumophila type IV secretion system effector LegAS4. Biochem Biophys Res Commun 2015; 465:817-24. [PMID: 26315269 DOI: 10.1016/j.bbrc.2015.08.094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 08/21/2015] [Indexed: 12/15/2022]
Abstract
The SET domain of LegAS4, a type IV secretion system effector of Legionella pneumophila, is a eukaryotic protein motif involved in histone methylation and epigenetic modulation. The SET domain of LegAS4 is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. Moreover, LegAS4 contains an ankyrin repeat domain of unknown function at its C-terminal region. Here, we report the crystal structure of LegAS4 in complex with S-adenosyl-l-methionine (SAM). Our data indicate that the ankyrin repeats interact extensively with the SET domain, especially with the SAM-binding amino acids, through conserved residues. Conserved surface analysis marks Glu159, Glu203, and Glu206 on the SET domain serve as candidate residues involved in interaction with the positively charged histone tail. Conserved surface residues on the ankyrin repeat domain surround a small pocket, which is suspected to serve as a binding site for an unknown ligand.
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Affiliation(s)
- Jonghyeon Son
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, Republic of Korea
| | - Chang Hwa Jo
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, Republic of Korea
| | - Ravichandran N Murugan
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk 363-883, Republic of Korea
| | - Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk 363-883, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, Republic of Korea.
| | - Woo Cheol Lee
- Division of Biotechnology, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Republic of Korea.
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Yeo KJ, Hwang E, Min KM, Jee JG, Lee CK, Hwang KY, Jeon YH, Chang SI, Cheong HK. The dual binding site of angiogenin and its inhibition mechanism: the crystal structure of the rat angiogenin-heparin complex. Chem Commun (Camb) 2015; 50:12966-9. [PMID: 25219815 DOI: 10.1039/c4cc05175k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The heparin complex of rat angiogenin revealed that a heparin strand is fitted into a positively charged groove formed by the dual binding site of rat angiogenin, suggesting that cell adhesion to angiogenin is facilitated by its interaction with substrates on the cell surface and can be inhibited by heparin.
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Affiliation(s)
- Kwon Joo Yeo
- Division of Magnetic Resonance, Korea Basic Science Institute (KBSI), 162 Yeongudanji-ro, Ochang, Chungbuk 363-883, Republic of Korea.
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Kim MJ, Lee BC, Hwang KY, Gladyshev VN, Kim HY. Selenium utilization in thioredoxin and catalytic advantage provided by selenocysteine. Biochem Biophys Res Commun 2015; 461:648-52. [PMID: 25912135 DOI: 10.1016/j.bbrc.2015.04.082] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 04/16/2015] [Indexed: 12/13/2022]
Abstract
Thioredoxin (Trx) is a major thiol-disulfide reductase that plays a role in many biological processes, including DNA replication and redox signaling. Although selenocysteine (Sec)-containing Trxs have been identified in certain bacteria, their enzymatic properties have not been characterized. In this study, we expressed a selenoprotein Trx from Treponema denticola, an oral spirochete, in Escherichia coli and characterized this selenoenzyme and its natural cysteine (Cys) homologue using E. coli Trx1 as a positive control. (75)Se metabolic labeling and mutation analyses showed that the SECIS (Sec insertion sequence) of T. denticola selenoprotein Trx is functional in the E. coli Sec insertion system with specific selenium incorporation into the Sec residue. The selenoprotein Trx exhibited approximately 10-fold higher catalytic activity than the Sec-to-Cys version and natural Cys homologue and E. coli Trx1, suggesting that Sec confers higher catalytic activity on this thiol-disulfide reductase. Kinetic analysis also showed that the selenoprotein Trx had a 30-fold higher Km than Cys-containing homologues, suggesting that this selenoenzyme is adapted to work efficiently with high concentrations of substrate. Collectively, the results of this study support the hypothesis that selenium utilization in oxidoreductase systems is primarily due to the catalytic advantage provided by the rare amino acid, Sec.
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Affiliation(s)
- Moon-Jung Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea
| | - Byung Cheon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea.
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Lee EH, Lee K, Hwang KY, Kim HY. Essential role of the C-terminal helical domain in active site formation of selenoprotein MsrA from Clostridium oremlandii. PLoS One 2015; 10:e0117836. [PMID: 25692691 PMCID: PMC4333827 DOI: 10.1371/journal.pone.0117836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/02/2015] [Indexed: 11/18/2022] Open
Abstract
We previously determined the crystal structures of 1-Cys type selenoprotein MsrA from Clostridium oremlandii (CoMsrA). The overall structure of CoMsrA is unusual, consisting of two domains, the N-terminal catalytic domain and the C-terminal distinct helical domain which is absent from other known MsrA structures. Deletion of the helical domain almost completely abolishes the catalytic activity of CoMsrA. In this study, we determined the crystal structure of the helical domain-deleted (ΔH-domain) form of CoMsrA at a resolution of 1.76 Å. The monomer structure is composed of the central rolled mixed β-sheet surrounded by α-helices. However, there are significant conformational changes in the N- and C-termini and loop regions of the ΔH-domain protein relative to the catalytic domain structure of full-length CoMsrA. The active site structure in the ΔH-domain protein completely collapses, thereby causing loss of catalytic activity of the protein. Interestingly, dimer structures are observed in the crystal formed by N-terminus swapping between two molecules. The ΔH-domain protein primarily exists as a dimer in solution, whereas the full-length CoMsrA exists as a monomer. Collectively, this study provides insight into the structural basis of the essential role of the helical domain of CoMsrA in its catalysis.
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Affiliation(s)
- Eun Hye Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kitaik Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Republic of Korea
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Kim MJ, Jeong J, Jeong J, Hwang KY, Lee KJ, Kim HY. Mechanism of 1-Cys type methionine sulfoxide reductase A regeneration by glutaredoxin. Biochem Biophys Res Commun 2015; 457:567-71. [PMID: 25600814 DOI: 10.1016/j.bbrc.2015.01.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 01/08/2015] [Indexed: 10/24/2022]
Abstract
Glutaredoxin (Grx), a major redox regulator, can act as a reductant of methionine sulfoxide reductase A (MsrA). However, the biochemical mechanisms involved in MsrA activity regeneration by Grx remain largely unknown. In this study, we investigated the regeneration mechanism of 1-Cys type Clostridium oremlandii MsrA (cMsrA) lacking a resolving Cys residue in a Grx-dependent assay. Kinetic analysis showed that cMsrA could be reduced by both monothiol and dithiol Grxs as efficiently as by in vitro reductant dithiothreitol. Our data revealed that the catalytic Cys sulfenic acid intermediate is not glutathionylated in the presence of the substrate, and that Grx instead directly formed a complex with cMsrA. Mass spectrometry analysis identified a disulfide bond between the N-terminal catalytic Cys of the active site of Grx and the catalytic Cys of cMsrA. This mixed disulfide bond could be resolved by glutathione. Based on these findings, we propose a model for regeneration of 1-Cys type cMsrA by Grx that involves no glutathionylation on the catalytic Cys of cMsrA. This mechanism contrasts with that of the previously known 1-Cys type MsrB.
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Affiliation(s)
- Moon-Jung Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea
| | - Jaeho Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Jihye Jeong
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea.
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Jia Y, Kim JH, Nam B, Kim J, Lee JH, Kim KO, Hwang KY, Lee SJ. The dipeptide H-Trp-Arg-OH (WR) Is a PPARα agonist and reduces hepatic lipid accumulation in lipid-loaded H4IIE cells. Appl Biochem Biotechnol 2014; 175:1211-20. [PMID: 25377249 DOI: 10.1007/s12010-014-1302-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 10/15/2014] [Indexed: 12/17/2022]
Abstract
Dipeptides absorbed by the intestinal epithelium are delivered to circulation, but their metabolic roles are not yet clearly understood. We investigated the biological activities of a dietary dipeptide, H-Trp-Arg-OH (WR), on the regulation of peroxisome proliferator-activated receptor (PPAR) α activity. Reporter gene assays revealed that WR dose-dependently induced PPARα transactivation. Surface plasmon resonance experiments demonstrated that WR interacts directly with the PPARα ligand binding domain, and time-resolved fluorescence energy transfer analyses revealed recruitment of a co-activator peptide, fluorescein-PGC1α, to PPARα, confirming the direct binding of WR to PPARα and occurrence of conformational changes. WR induced cellular fatty acid uptake and the expression of PPARα response genes in fatty acid oxidation, thus reducing intracellular triglyceride accumulation in lipid-loaded hepatocytes. In conclusion, the dietary dipeptide WR activates PPARα and reduces hepatic lipid accumulation in lipid-loaded hepatocytes.
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Affiliation(s)
- Yaoyao Jia
- Department of Biotechnology, Graduate School of Biotechnology, Korea University, Room 410, College of Life Sciences & Biotechnology EAST Bldg, Anam-5-ga, 136-713, Seoul, Republic of Korea
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Kim KH, Hong SK, Hwang KY, Kim EE. Structure of mouse muskelin discoidin domain and biochemical characterization of its self-association. ACTA ACUST UNITED AC 2014; 70:2863-74. [PMID: 25372678 DOI: 10.1107/s139900471401894x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/21/2014] [Indexed: 01/29/2023]
Abstract
Muskelin is an intracellular kelch-repeat protein comprised of discoidin, LisH, CTLH and kelch-repeat domains. It is involved in cell adhesion and the regulation of cytoskeleton dynamics as well as being a component of a putative E3 ligase complex. Here, the first crystal structure of mouse muskelin discoidin domain (MK-DD) is reported at 1.55 Å resolution, which reveals a distorted eight-stranded β-barrel with two short α-helices at one end of the barrel. Interestingly, the N- and C-termini are not linked by the disulfide bonds found in other eukaryotic discoidin structures. A highly conserved MIND motif appears to be the determinant for MK-DD specific interaction together with the spike loops. Analysis of interdomain interaction shows that MK-DD binds the kelch-repeat domain directly and that this interaction depends on the presence of the LisH domain.
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Affiliation(s)
- Kook Han Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Seung Kon Hong
- Biomedical Research Institute, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seoul 136-701, Republic of Korea
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
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48
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Kim HS, Kwak GH, Lee K, Jo CH, Hwang KY, Kim HY. Structural and biochemical analysis of a type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum. Arch Biochem Biophys 2014; 560:10-9. [DOI: 10.1016/j.abb.2014.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/27/2014] [Accepted: 07/10/2014] [Indexed: 12/12/2022]
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Lee EH, Kim HY, Hwang KY. The GSH- and GSSG-bound structures of glutaredoxin from Clostridium oremlandii. Arch Biochem Biophys 2014; 564:20-5. [PMID: 25218089 DOI: 10.1016/j.abb.2014.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/25/2014] [Accepted: 09/01/2014] [Indexed: 12/21/2022]
Abstract
Glutaredoxin (Grx) is a major redox enzyme that reduces disulfide bonds using glutathione (GSH) as an electron donor. The anaerobic bacterium Clostridium oremlandii possesses a selenocysteine-containing Grx (cGrx1) and a cysteine-containing homolog (cGrx2). Here, the crystal structure of the GSSG-bound form of cGrx2 was determined for the first time at a resolution of 1.95Å. In addition, its monothiol variant cGrx2/C15S in complex with GSH was also determined at a resolution of 1.58Å. cGrx2 is a monomeric protein with an overall structure that consists of the typical thioredoxin fold composed of four α-helices and four β-strands. Two ligands, GSH and GSSG, share a conserved binding site consisting of CPYC, TVP, and CDD motifs. The cysteinyl and γ-glutamyl moieties show similar binding interactions in the two structures, whereas the glycine moiety shows different interactions. Interestingly, the structures revealed that only one GSH moiety of GSSG is sufficient for its binding to the protein. The GSSG-bound structure of cGrx2 was obtained as an oxidized form with a disulfide bond at the CPYC motif. Comparison of the GSH-binding mode in cGrx2 to other known Grxs revealed similarities as well as some diversity.
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Affiliation(s)
- Eun Hye Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Republic of Korea.
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.
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Hwang E, Cheong HK, Hwang KY, Cheong C. Structural Studies on the SARAH Domain from MST and RASSF Family Proteins. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314091888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Although the recent progress towards the molecular biology of the Hippo signaling pathway, the mechanistic and structural information in this area remains elusive. Intriguingly, RASSFs function both positively and negatively depending on the events in the diverse cellular signals, by the interaction with MSTs through their SARAH domains. The precise mechanism of these sophisticated regulations of cell growth and apoptosis is still largely unknown. Here, we determined the 3D structures of SARAH domains as MST1-RASSF5 heterodimer and MST2 homodimer by X-ray crystallography. Although the structure of MST2 homodimer showed very similar to the previously reported MST1 homodimer, MST1-RASSF5 showed a distinct feature with flexible N-terminal extension of MST1 SARAH domain and a hydrophobic core stabilized by the aromatic interactions. Comparison of the interfaces and computational alanine scanning indicates the more extensive interactions in the dimer interface in MST1-RASSF5 heterodimer than those of homodimer. Monitoring the structural stability by urea denaturation indicated MSTs-RASSFs heterodimers are substantially more stable than MSTs homodimer. These results provide a 3D structural explanation for the preferential binding of MSTs-RASSFs SARAH domains which is a key mechanism of regulation in the Hippo pathway.
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