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Lee JH, Park JY, Seo MD, Lee PC. Protein engineering of an oxidative cleavage-free pathway for crocetin-dialdehyde production in Escherichia coli. Metab Eng 2024; 88:137-147. [PMID: 39742954 DOI: 10.1016/j.ymben.2024.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 11/28/2024] [Accepted: 12/26/2024] [Indexed: 01/04/2025]
Abstract
The growing depletion of petroleum resources and the increasing demand for sustainable alternatives have spurred advancements in microorganism-based biofactories. Among high-value compounds, carotenoids are widely sought after in pharmaceuticals, cosmetics, and nutrition, making them prime candidates for microbial production. In this study, we engineered an efficient biosynthetic pathway in Escherichia coli for the production of the C20-carotenoid crocetin-dialdehyde. By bypassing traditional oxidative cleavage reactions mediated by carotenoid cleavage dioxygenases (CCDs), our approach reduces the enzymatic complexity of the pathway. Using the crystal structure of a CrtMLIKE enzyme identified in this study, we developed a mutant enzyme capable of condensing two C10-geranyl pyrophosphate molecules to form C20-phytoene. This intermediate was then desaturated and oxidized by CrtN and CrtP to produce crocetin-dialdehyde, achieving a yield of 1.13 mg/L. By reducing enzyme requirements from six to three and eliminating the need for CCDs, this pathway alleviates metabolic stress on the host and enhances the scalability of production for industrial applications. Overall, our research presents a streamlined and innovative approach to carotenoid biosynthesis, advancing sustainable production methods for short-chain carotenoids.
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Chae S, Lee HJ, Lee HE, Kim J, Jeong YJ, Lin Y, Kim HY, Leriche G, Ehrlich RS, Lingl SC, Seo MD, Lee YH, Yang J, Kim JI, Hoe HS. The dopamine analogue CA140 alleviates AD pathology, neuroinflammation, and rescues synaptic/cognitive functions by modulating DRD1 signaling or directly binding to Abeta. J Neuroinflammation 2024; 21:200. [PMID: 39129007 PMCID: PMC11317008 DOI: 10.1186/s12974-024-03180-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/17/2024] [Indexed: 08/13/2024] Open
Abstract
BACKGROUND We recently reported that the dopamine (DA) analogue CA140 modulates neuroinflammatory responses in lipopolysaccharide-injected wild-type (WT) mice and in 3-month-old 5xFAD mice, a model of Alzheimer's disease (AD). However, the effects of CA140 on Aβ/tau pathology and synaptic/cognitive function and its molecular mechanisms of action are unknown. METHODS To investigate the effects of CA140 on cognitive and synaptic function and AD pathology, 3-month-old WT mice or 8-month-old (aged) 5xFAD mice were injected with vehicle (10% DMSO) or CA140 (30 mg/kg, i.p.) daily for 10, 14, or 17 days. Behavioral tests, ELISA, electrophysiology, RNA sequencing, real-time PCR, Golgi staining, immunofluorescence staining, and western blotting were conducted. RESULTS In aged 5xFAD mice, a model of AD pathology, CA140 treatment significantly reduced Aβ/tau fibrillation, Aβ plaque number, tau hyperphosphorylation, and neuroinflammation by inhibiting NLRP3 activation. In addition, CA140 treatment downregulated the expression of cxcl10, a marker of AD-associated reactive astrocytes (RAs), and c1qa, a marker of the interaction of RAs with disease-associated microglia (DAMs) in 5xFAD mice. CA140 treatment also suppressed the mRNA levels of s100β and cxcl10, markers of AD-associated RAs, in primary astrocytes from 5xFAD mice. In primary microglial cells from 5xFAD mice, CA140 treatment increased the mRNA levels of markers of homeostatic microglia (cx3cr1 and p2ry12) and decreased the mRNA levels of a marker of proliferative region-associated microglia (gpnmb) and a marker of lipid-droplet-accumulating microglia (cln3). Importantly, CA140 treatment rescued scopolamine (SCO)-mediated deficits in long-term memory, dendritic spine number, and LTP impairment. In aged 5xFAD mice, these effects of CA140 treatment on cognitive/synaptic function and AD pathology were regulated by dopamine D1 receptor (DRD1)/Elk1 signaling. In primary hippocampal neurons and WT mice, CA140 treatment promoted long-term memory and dendritic spine formation via effects on DRD1/CaMKIIα and/or ERK signaling. CONCLUSIONS Our results indicate that CA140 improves neuronal/synaptic/cognitive function and ameliorates Aβ/tau pathology and neuroinflammation by modulating DRD1 signaling in primary hippocampal neurons, primary astrocytes/microglia, WT mice, and aged 5xFAD mice.
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Bang J, Park J, Lee SH, Jang J, Hwang J, Kamarov O, Park HJ, Lee SJ, Seo MD, Won HS, Seok SH, Kim JH. Nontraditional Roles of Magnesium Ions in Modulating Sav2152: Insight from a Haloacid Dehalogenase-like Superfamily Phosphatase from Staphylococcus aureus. Int J Mol Sci 2024; 25:5021. [PMID: 38732240 PMCID: PMC11084212 DOI: 10.3390/ijms25095021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infection has rapidly spread through various routes. A genomic analysis of clinical MRSA samples revealed an unknown protein, Sav2152, predicted to be a haloacid dehalogenase (HAD)-like hydrolase, making it a potential candidate for a novel drug target. In this study, we determined the crystal structure of Sav2152, which consists of a C2-type cap domain and a core domain. The core domain contains four motifs involved in phosphatase activity that depend on the presence of Mg2+ ions. Specifically, residues D10, D12, and D233, which closely correspond to key residues in structurally homolog proteins, are responsible for binding to the metal ion and are known to play critical roles in phosphatase activity. Our findings indicate that the Mg2+ ion known to stabilize local regions surrounding it, however, paradoxically, destabilizes the local region. Through mutant screening, we identified D10 and D12 as crucial residues for metal binding and maintaining structural stability via various uncharacterized intra-protein interactions, respectively. Substituting D10 with Ala effectively prevents the interaction with Mg2+ ions. The mutation of D12 disrupts important structural associations mediated by D12, leading to a decrease in the stability of Sav2152 and an enhancement in binding affinity to Mg2+ ions. Additionally, our study revealed that D237 can replace D12 and retain phosphatase activity. In summary, our work uncovers the novel role of metal ions in HAD-like phosphatase activity.
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Wang JM, Seok SH, Yoon WS, Kim JH, Seo MD. Crystal structure of the engineered endolysin mtEC340M. Acta Crystallogr F Struct Biol Commun 2023; 79:105-110. [PMID: 37132476 PMCID: PMC10167747 DOI: 10.1107/s2053230x23002583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/17/2023] [Indexed: 05/04/2023] Open
Abstract
Endolysins produced by bacteriophages play essential roles in the release of phage progeny by degrading the peptidoglycan layers of the bacterial cell wall. Bacteriophage-encoded endolysins have emerged as a new class of antibacterial agents to combat surging antibiotic resistance. The crystal structure of mtEC340M, an engineered endolysin EC340 from the PBEC131 phage that infects Escherichia coli, was determined. The crystal structure of mtEC340M at 2.4 Å resolution consists of eight α-helices and two loops. The three active residues of mtEC340M were predicted by structural comparison with peptidoglycan-degrading lysozyme.
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Kim HN, Park HJ, Lin Y, Cho T, Ryu KS, Won HS, Jin HE, Kim JH, Baek SH, Lee YH, Seo MD. Coiled-coil structure mediated inhibition of the cytotoxic huntingtin amyloid fibrils by an IP3 receptor fragment. Int J Biol Macromol 2023; 232:123412. [PMID: 36706883 DOI: 10.1016/j.ijbiomac.2023.123412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/05/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Disruption of cellular homeostasis by the aggregation of polyglutamine (polyQ) in the huntingtin protein (Htt) leads Huntington's disease (HD). Effective drugs for treating HD have not been developed, as the molecular mechanism underlying HD pathogenesis remains unclear. To develop strategies for inhibiting HD pathogenesis, the intermolecular interaction of Htt with IP3 receptor 1 (IP3R1) was investigated. Peptide (termed ICT60) corresponding to a coiled-coil motif in the C-terminus of IP3R1 was designed. Several biophysical approaches revealed the strong and specific binding of ICT60 to the N-terminal part of HttEx1. ICT60 inhibited not only amyloid formation by HttEx1, but also the cytotoxicity and cell-penetration ability of the amyloid fibrils of HttEx1. The importance of coiled-coil structure was verified by charge-manipulated variants. The coiled-coil structures of ICT60-KK and -EE were partially and largely disrupted, respectively. ICT60 wild-type and -KK inhibited amyloid formation by HttEx1-46Q, whereas ICT60-EE did not block amyloidogenesis. Similarly, the cytotoxicity and cell-penetration ability of the amyloid fibrils of HttEx1-46Q were efficiently inhibited by ICT60 wild-type and ICT60-KK, but not by ICT60-EE. We propose a mechanical model explaining how an IP3 receptor-inspired molecule can modulate cytotoxic amyloid formation by Htt, providing a molecular basis for developing therapeutics to treat HD.
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Park K, Yoo HS, Oh CK, Lee JR, Chung HJ, Kim HN, Kim SH, Kee KM, Kim TY, Kim M, Kim BG, Ra JS, Myung K, Kim H, Han SH, Seo MD, Lee Y, Kim DW. Reciprocal interactions among Cobll1, PACSIN2, and SH3BP1 regulate drug resistance in chronic myeloid leukemia. Cancer Med 2022; 11:4005-4020. [PMID: 35352878 PMCID: PMC9636508 DOI: 10.1002/cam4.4727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Cobll1 affects blast crisis (BC) progression and tyrosine kinase inhibitor (TKI) resistance in chronic myeloid leukemia (CML). PACSIN2, a novel Cobll1 binding protein, activates TKI‐induced apoptosis in K562 cells, and this activation is suppressed by Cobll1 through the interaction between PACSIN2 and Cobll1. PACSIN2 also binds and inhibits SH3BP1 which activates the downstream Rac1 pathway and induces TKI resistance. PACSIN2 competitively interacts with Cobll1 or SH3BP1 with a higher affinity for Cobll1. Cobll1 preferentially binds to PACSIN2, releasing SH3BP1 to promote the SH3BP1/Rac1 pathway and suppress TKI‐mediated apoptosis and eventually leading to TKI resistance. Similar interactions among Cobll1, PACSIN2, and SH3BP1 control hematopoiesis during vertebrate embryogenesis. Clinical analysis showed that most patients with CML have Cobll1 and SH3BP1 expression at the BC phase and BC patients with Cobll1 and SH3BP1 expression showed severe progression with a higher blast percentage than those without any Cobll1, PACSIN2, or SH3BP1 expression. Our study details the molecular mechanism of the Cobll1/PACSIN2/SH3BP1 pathway in regulating drug resistance and BC progression in CML.
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Kim KH, Kim JO, Park JY, Seo MD, Park SG. Antibody-Drug Conjugate Targeting c-Kit for the Treatment of Small Cell Lung Cancer. Int J Mol Sci 2022; 23:ijms23042264. [PMID: 35216379 PMCID: PMC8875948 DOI: 10.3390/ijms23042264] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths. Small cell lung cancer (SCLC) accounts for 15–25% of all lung cancers. It exhibits a rapid doubling time and a high degree of invasiveness. Additionally, overexpression of c-Kit occurs in 70% of SCLC patients. In this study, we evaluated an antibody-drug conjugate (ADC) that targets c-Kit, which is a potential therapeutic agent for SCLC. First, we generated and characterized 4C9, a fully human antibody that targets c-Kit and specifically binds to SCLC cells expressing c-Kit with a binding affinity of KD = 5.5 × 10−9 M. Then, we developed an ADC using DM1, a microtubule inhibitor, as a payload. 4C9-DM1 efficiently induced apoptosis in SCLC with an IC50 ranging from 158 pM to 4 nM. An in vivo assay using a xenograft mouse model revealed a tumor growth inhibition (TGI) rate of 45% (3 mg/kg) and 59% (5 mg/kg) for 4C9-DM1 alone. Combination treatment with 4C9-DM1 plus carboplatin/etoposide or lurbinectedin resulted in a TGI rate greater than 90% compared with the vehicle control. Taken together, these results indicate that 4C9-DM1 is a potential therapeutic agent for SCLC treatment.
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Kim SR, Jeong MS, Mun SH, Cho J, Seo MD, Kim H, Lee J, Song JH, Ko HJ. Antiviral Activity of Chrysin against Influenza Virus Replication via Inhibition of Autophagy. Viruses 2021; 13:1350. [PMID: 34372556 PMCID: PMC8310364 DOI: 10.3390/v13071350] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/23/2022] Open
Abstract
Influenza viruses cause respiratory infections in humans and animals, which have high morbidity and mortality rates. Although several drugs that inhibit viral neuraminidase are used to treat influenza infections, the emergence of resistant viruses necessitates the urgent development of new antiviral drugs. Chrysin (5,7-dihydroxyflavone) is a natural flavonoid that exhibits antiviral activity against enterovirus 71 (EV71) by inhibiting viral 3C protease activity. In this study, we evaluated the antiviral activity of chrysin against influenza A/Puerto Rico/8/34 (A/PR/8). Chrysin significantly inhibited A/PR/8-mediated cell death and the replication of A/PR/8 at concentrations up to 2 μM. Viral hemagglutinin expression was also markedly decreased by the chrysin treatment in A/PR/8-infected cells. Through the time course experiment and time-of-addition assay, we found that chrysin inhibited viral infection at the early stages of the replication cycle. Additionally, the nucleoprotein expression of A/PR/8 in A549 cells was reduced upon treatment with chrysin. Regarding the mechanism of action, we found that chrysin inhibited autophagy activation by increasing the phosphorylation of mammalian target of rapamycin (mTOR). We also confirmed a decrease in LC3B expression and LC3-positive puncta levels in A/PR/8-infected cells. These results suggest that chrysin exhibits antiviral activity by activating mTOR and inhibiting autophagy to inhibit the replication of A/PR/8 in the early stages of infection.
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Son SH, Do JM, Yoo JN, Lee HW, Kim NK, Yoo HS, Gee MS, Kim JH, Seong JH, Inn KS, Seo MD, Lee JK, Kim NJ. Identification of ortho catechol-containing isoflavone as a privileged scaffold that directly prevents the aggregation of both amyloid β plaques and tau-mediated neurofibrillary tangles and its in vivo evaluation. Bioorg Chem 2021; 113:105022. [PMID: 34098397 DOI: 10.1016/j.bioorg.2021.105022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/03/2021] [Accepted: 05/23/2021] [Indexed: 12/15/2022]
Abstract
In this study, polyhydroxyisoflavones that directly prevent the aggregation of both amyloid β (Aβ) and tau were expediently synthesized via divergent Pd(0)-catalyzed Suzuki-Miyaura coupling and then biologically evaluated. By preliminary structure-activity relationship studies using thioflavin T (ThT) assays, an ortho-catechol containing isoflavone scaffold was proven to be crucial for preventing both Aβ aggregation and tau-mediated neurofibrillary tangle formation. Additional TEM experiment confirmed that ortho-catechol containing isoflavone 4d significantly prevented the aggregation of both Aβ and tau. To investigate the mode of action (MOA) of 4d, which possesses an ortho-catechol moiety, 1H-15N HSQC NMR analysis was thoroughly performed and the result indicated that 4d could directly inhibit both the formation of Aβ42 fibrils and the formation of tau-derived neurofibrils, probably through the catechol-mediated nucleation of tau. Finally, 4d was demonstrated to alleviate cognitive impairment and pathologies related to Alzheimer's disease in a 5XFAD transgenic mouse model.
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Park HJ, Kim HN, Kim CY, Seo MD, Baek SH. Synergistic Protection by Isoquercitrin and Quercetin against Glutamate-Induced Oxidative Cell Death in HT22 Cells via Activating Nrf2 and HO-1 Signaling Pathway: Neuroprotective Principles and Mechanisms of Dendropanax morbifera Leaves. Antioxidants (Basel) 2021; 10:antiox10040554. [PMID: 33918248 PMCID: PMC8066007 DOI: 10.3390/antiox10040554] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 01/18/2023] Open
Abstract
Dendropanax morbifera leaves (DML) have long been used as traditional medicine to treat diverse symptoms in Korea. Ethyl acetate-soluble extracts of DML (DMLE) rescued HT22 mouse hippocampal neuronal cells from glutamate (Glu)-induced oxidative cell death; however, the protective compounds and mechanisms remain unknown. Here, we aimed to identify the neuroprotective ingredients and mechanisms of DMLE in the Glu-HT22 cell model. Five antioxidant compounds were isolated from DMLE and characterized as chlorogenic acid, hyperoside, isoquercitrin, quercetin, and rutin by spectroscopic methods. Isoquercitrin and quercetin significantly inhibited Glu-induced oxidative cell death by restoring intracellular reactive oxygen species (ROS) levels and mitochondrial superoxide generation, Ca2+ dysregulation, mitochondrial dysfunction, and nuclear translocation of apoptosis-inducing factor. These two compounds significantly increased the expression levels of nuclear factor erythroid-2-related factor 2 (Nrf2) and heme oxygenase 1 (HO-1) in the presence or absence of Glu treatment. Combinatorial treatment of the five compounds based on the equivalent concentrations in DMLE showed that significant protection was found only in the cells cotreated with isoquercitrin and quercetin, both of whom showed prominent synergism, as assessed by drug–drug interaction analysis. These findings suggest that isoquercitrin and quercetin are the active principles representing the protective effects of DMLE, and these effects were mediated by the Nrf2/HO-1 pathway.
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Kim JO, Kim HN, Kim KH, Baek EJ, Park JY, Ha K, Heo DR, Seo MD, Park SG. Development and characterization of a fully human antibody targeting SCF/c-kit signaling. Int J Biol Macromol 2020; 159:66-78. [PMID: 32437800 DOI: 10.1016/j.ijbiomac.2020.05.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/23/2022]
Abstract
CD117/c-kit, a tyrosine kinase receptor, plays a critical role in hematopoiesis, pigmentation, and fertility. The overexpression and activation of c-kit are thought to promote tumor growth and have been reported in various cancers, including leukemia, glioblastoma and mastocytosis. To disrupt the SCF/c-kit signaling axis in cancer, we generated a c-kit antagonist human antibody (NN2101) that binds to domain 2/3 of c-kit. This completely blocked the SCF-mediated phosphorylation of c-kit and inhibited TF-1 cell proliferation, erythroleukemia. In addition, the examination of binding affinity using surface plasmon resonance (SPR) assay showed that NN2101 can bind to c-kit of monkeys (KD = 2.92 × 10-10 M), rats (KD = 1.68 × 10-6 M), mice (KD = 11.5 × 10-9 M), and humans (KD = 2.83 × 10-12 M). We showed that NN2101 does not cause antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. The immunogenicity of NN2101 was similar to that of bevacizumab. Furthermore, the crystal structure of NN2101 Fab was determined and the structure of NN2101 Fab:c-kit complex was modeled. Structural information, as well as mutagenesis results, revealed that NN2101 can bind to the SCF-binding regions of c-kit. Collectively, we generated a c-kit neutralizing human antibody (NN2101) for the treatment of erythroleukemia and characterized its biophysical properties. NN2101 can potentially be used as a therapeutic antibody to treat different cancers.
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Yoon WS, Seok SH, Won HS, Cho T, Lee SJ, Seo MD. Structural changes of antitoxin HigA from Shigella flexneri by binding of its cognate toxin HigB. Int J Biol Macromol 2019; 130:99-108. [PMID: 30797012 DOI: 10.1016/j.ijbiomac.2019.02.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022]
Abstract
In toxin-antitoxin systems, many antitoxin proteins that neutralize their cognate toxin proteins also bind to DNA to repress transcription, and the DNA-binding affinity of the antitoxin is affected by its toxin. We solved crystal structures of the antitoxin HigA (apo-SfHigA) and its complex with the toxin HigB (SfHigBA) from Shigella flexneri. The apo-SfHigA shows a distinctive V-shaped homodimeric conformation with sequestered N-domains having a novel fold. SfHigBA appears as a heterotetramer formed by N-terminal dimerization of SfHigB-bound SfHigA molecules. The conformational change in SfHigA upon SfHigB binding is mediated by rigid-body movements of its C-domains, which accompanied an overall conformational change from wide V-shaped to narrow V-shaped dimer. Consequently, the two putative DNA-binding helices (α7 in each subunit) are repositioned to a conformation more compatible with canonical homodimeric DNA-binding proteins containing HTH motifs. Collectively, this study demonstrates a conformational change in an antitoxin protein, which occurs upon toxin binding and is responsible for regulating antitoxin DNA binding.
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Kim HN, Seok SH, Lee YS, Won HS, Seo MD. Crystal structure and functional characterization of SF216 from Shigella flexneri. FEBS Lett 2017; 591:3692-3703. [PMID: 28983914 DOI: 10.1002/1873-3468.12873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022]
Abstract
Shigella flexneri is a Gram-negative anaerobic bacterium that causes highly infectious bacterial dysentery in humans. Here, we solved the crystal structure of SF216, a hypothetical protein from the S. flexneri 5a strain M90T, at 1.7 Å resolution. The crystal structure of SF216 represents a homotrimer stabilized by intersubunit interactions and ion-mediated electrostatic interactions. Each subunit consists of three β-strands and five α-helices with the β-β-β-α-α-α-α-α topology. Based on the structural information, we also demonstrate that SF216 shows weak ribonuclease activity by a fluorescence quenching assay. Furthermore, we identify potential druggable pockets (putative hot spots) on the surface of the SF216 structure by computational mapping.
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Sim DW, Lu Z, Won HS, Lee SN, Seo MD, Lee BJ, Kim JH. Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins. Molecules 2017; 22:molecules22081347. [PMID: 28809779 PMCID: PMC6152068 DOI: 10.3390/molecules22081347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 02/05/2023] Open
Abstract
A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology. Among these technologies, solution NMR is a powerful tool for studying protein-protein, protein-ligand interactions and protein dynamics at a wide range of time scales as well as structure determination of membrane proteins. This review provides general and useful guideline for membrane protein sample preparation and the choice of membrane-mimetic media, which are the key step for successful structural analysis. Furthermore, this review provides an opportunity to look at recent applications of solution NMR to structural studies on α-helical membrane proteins through some success stories.
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Sim DW, Choi JW, Kim JH, Ryu KS, Kim M, Yu HW, Jo KS, Kim EH, Seo MD, Jeon YH, Lee BJ, Kim YP, Won HS. C-terminal dimerization of apo-cyclic AMP receptor protein validated in solution. FEBS Lett 2017; 591:1064-1070. [PMID: 28245055 DOI: 10.1002/1873-3468.12613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/28/2017] [Accepted: 02/23/2017] [Indexed: 11/07/2022]
Abstract
Although cyclic AMP receptor protein (CRP) has long served as a typical example of effector-mediated protein allostery, mechanistic details into its regulation have been controversial due to discrepancy between the known crystal structure and NMR structure of apo-CRP. Here, we report that the recombinant protein corresponding to its C-terminal DNA-binding domain (CDD) forms a dimer. This result, together with structural information obtained in the present NMR study, is consistent with the previous crystal structure and validates its relevance also in solution. Therefore, our findings suggest that dissociation of the CDD may be critically involved in cAMP-induced allosteric activation of CRP.
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Kim J, Seok SH, Hong E, Yoo TH, Seo MD, Ryu Y. Crystal structure and characterization of esterase Est25 mutants reveal improved enantioselectivity toward (S)-ketoprofen ethyl ester. Appl Microbiol Biotechnol 2016; 101:2333-2342. [PMID: 27915377 DOI: 10.1007/s00253-016-7989-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/25/2016] [Accepted: 11/05/2016] [Indexed: 11/25/2022]
Abstract
Esterases comprise a group of enzymes that catalyze the cleavage and synthesis of ester bonds. They are important in biotechnological applications owing to their enantioselectivity, regioselectivity, broad substrate specificity, and the fact that they do not require cofactors. In a previous study, we isolated the esterase Est25 from a metagenomic library. Est25 showed catalytic activity toward the (R,S)-ketoprofen ethyl ester but had low enantioselectivity toward the (S)-ketoprofen ethyl ester. Because (S)-ketoprofen has stronger anti-inflammatory effects and fewer side effects than (R)-ketoprofen, enantioselectivity of this esterase is important. In this study, we generated Est25 mutants with improved enantioselectivity toward the (S)-ketoprofen ethyl ester; improved enantioselectivity of mutants was established by analysis of their crystal structures. The enantioselectivity of mutants was influenced by substitution of Phe72 and Leu255. Substituting these residues changed the size of the binding pocket and the entrance hole that leads to the active site. The enantioselectivity of Est25 (E = 1.1 ± 0.0) was improved in the mutants F72G (E = 1.9 ± 0.2), L255W (E = 16.1 ± 1.1), and F72G/L255W (E = 60.1 ± 0.5). Finally, characterization of Est25 mutants was performed by determining the optimum reaction conditions, thermostability, effect of additives, and substrate specificity after substituting Phe72 and Leu255.
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Lee KY, Choi HS, Choi HS, Chung KY, Lee BJ, Maeng HJ, Seo MD. Quercetin Directly Interacts with Vitamin D Receptor (VDR): Structural Implication of VDR Activation by Quercetin. Biomol Ther (Seoul) 2016; 24:191-8. [PMID: 26902087 PMCID: PMC4774501 DOI: 10.4062/biomolther.2015.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 08/26/2015] [Accepted: 09/09/2015] [Indexed: 11/23/2022] Open
Abstract
The vitamin D receptor (VDR) is a member of the nuclear receptor (NR) superfamily. The VDR binds to active vitamin D3 metabolites, which stimulates downstream transduction signaling involved in various physiological activities such as calcium homeostasis, bone mineralization, and cell differentiation. Quercetin is a widely distributed flavonoid in nature that is known to enhance transactivation of VDR target genes. However, the detailed molecular mechanism underlying VDR activation by quercetin is not well understood. We first demonstrated the interaction between quercetin and the VDR at the molecular level by using fluorescence quenching and saturation transfer difference (STD) NMR experiments. The dissociation constant (Kd) of quercetin and the VDR was 21.15 ± 4.31 μM, and the mapping of quercetin subsites for VDR binding was performed using STD-NMR. The binding mode of quercetin was investigated by a docking study combined with molecular dynamics (MD) simulation. Quercetin might serve as a scaffold for the development of VDR modulators with selective biological activities.
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Chae YJ, Cho KH, Yoon IS, Noh CK, Lee HJ, Park Y, Ji E, Seo MD, Maeng HJ. Vitamin D Receptor-Mediated Upregulation of CYP3A4 and MDR1 by Quercetin in Caco-2 cells. PLANTA MEDICA 2016; 82:121-130. [PMID: 26366751 DOI: 10.1055/s-0035-1557898] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To examine whether quercetin interacts with vitamin D receptor, we investigated the effects of quercetin on vitamin D receptor activity in human intestinal Caco-2 cells. The effects of quercetin on the expression of the vitamin D receptor target genes, vitamin D3 24-hydroxylase, cytochrome P450 3A4, multidrug resistance protein 1, and transient receptor potential vanilloid type 6 were measured using quantitative polymerase chain reaction. The vitamin D receptor siRNA was used to assess the involvement of the vitamin D receptor. Vitamin D receptor activation using a vitamin D responsive element-mediated cytochrome P450 3A4 reporter gene assay was investigated in Caco-2 cells transfected with human vitamin D receptor. We also studied the magnitude of the vitamin D receptor activation and/or synergism between 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3] and quercetin-like flavonoids. Slight but significant increases in the mRNA expression of cytochrome P450 3A4, vitamin D3 24-hydroxylase, multidrug resistance protein 1, and transient receptor potential vanilloid type 6 were observed after 3 days of continual quercetin treatment. The silencing effect of vitamin D receptor by vitamin D receptor siRNA in Caco-2 cells significantly attenuated the induction of the vitamin D receptor target genes. Moreover, quercetin significantly enhanced cytochrome P450 3A4 reporter activity in Caco-2 cells in a dose-dependent manner, and the expression of exogenous vitamin D receptor further stimulated the vitamin D receptor activity. Quercetin-like flavonoids such as kaempferol stimulated the vitamin D receptor activity in a manner similar to that seen with quercetin. Taken together, the data indicates that quercetin upregulates cytochrome P450 3A4 and multidrug resistance protein 1 expression in Caco-2 cells likely via a vitamin D receptor-dependent pathway.
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Sim DW, Lee YS, Seo MD, Won HS, Kim JH. A simple guide to the structural study on membrane proteins in detergents using solution NMR. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2015. [DOI: 10.6564/jkmrs.2015.19.3.137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lee YS, Kim JH, Seo MD, Ryu KS, Kim EH, Won HS. Oxidation-induced conformational change of Hsp33, monitored by NMR. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2015. [DOI: 10.6564/jkmrs.2015.19.3.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Lee YS, Lee J, Ryu KS, Lee Y, Jung TG, Jang JH, Sim DW, Kim EH, Seo MD, Lee KW, Won HS. Semi-Empirical Structure Determination of Escherichia coli Hsp33 and Identification of Dynamic Regulatory Elements for the Activation Process. J Mol Biol 2015; 427:3850-61. [DOI: 10.1016/j.jmb.2015.09.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 11/27/2022]
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Kim YI, Song JH, Kwon BE, Kim HN, Seo MD, Park K, Lee S, Yeo SG, Kweon MN, Ko HJ, Chang SY. Pros and cons of VP1-specific maternal IgG for the protection of Enterovirus 71 infection. Vaccine 2015; 33:6604-10. [PMID: 26529069 DOI: 10.1016/j.vaccine.2015.10.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 10/06/2015] [Accepted: 10/24/2015] [Indexed: 12/13/2022]
Abstract
Enterovirus 71 (EV71) causes hand, foot, and mouth diseases and can result in severe neurological disorders when it infects the central nervous system. Thus, there is a need for the development of effective vaccines against EV71 infection. Here we report that viral capsid protein 1 (VP1), one of the main capsid proteins of EV71, efficiently elicited VP1-specific immunoglobulin G (IgG) in the serum of mice immunized with recombinant VP1. The VP1-specific IgG produced in female mice was efficiently transferred to their offspring, conferring protection against EV71 infection immediately after birth. VP1-specific antibody can neutralize EV71 infection and protect host cells. VP1-specific maternal IgG in offspring was maintained for over 6 months. However, the pre-existence of VP1-specific maternal IgG interfered with the production of VP1-specific IgG antibody secreting cells by active immunization in offspring. Therefore, although our results showed the potential for VP1-specific maternal IgG protection against EV71 in neonatal mice, other strategies must be developed to overcome the hindrance of maternal IgG in active immunization. In this study, we developed an effective and feasible animal model to evaluate the protective efficacy of humoral immunity against EV71 infection using a maternal immunity concept.
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Kim HN, Seok SH, Chung KY, Won HS, Son WS, Seo MD. Expression, purification and structural characterization of the type 1-specific ATP binding site of IP3 receptor (IP3R1-ATPA). Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lee YS, Yoon WS, Chung I, Chung KY, Won HS, Seo MD. Backbone NMR Assignments of an Uncharacterized Protein, SF1002 from Shigella flexneri 5a M90T. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2015. [DOI: 10.6564/jkmrs.2015.19.1.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kim DK, Yun Y, Kim HR, Seo MD, Chung KY. Different conformational dynamics of various active states of β-arrestin1 analyzed by hydrogen/deuterium exchange mass spectrometry. J Struct Biol 2015; 190:250-9. [DOI: 10.1016/j.jsb.2015.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/26/2015] [Accepted: 04/07/2015] [Indexed: 01/14/2023]
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