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Lai CH, Ko KT, Fan PJ, Yu TA, Chang CF, Draczkowski P, Hsu STD. Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance. J Biol Chem 2024; 300:107230. [PMID: 38537699 PMCID: PMC11047754 DOI: 10.1016/j.jbc.2024.107230] [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: 12/22/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024] Open
Abstract
Arsenite-induced stress granule (SG) formation can be cleared by the ubiquitin-proteasome system aided by the ATP-dependent unfoldase p97. ZFAND1 participates in this pathway by recruiting p97 to trigger SG clearance. ZFAND1 contains two An1-type zinc finger domains (ZF1 and ZF2), followed by a ubiquitin-like domain (UBL); but their structures are not experimentally determined. To shed light on the structural basis of the ZFAND1-p97 interaction, we determined the atomic structures of the individual domains of ZFAND1 by solution-state NMR spectroscopy and X-ray crystallography. We further characterized the interaction between ZFAND1 and p97 by methyl NMR spectroscopy and cryo-EM. 15N spin relaxation dynamics analysis indicated independent domain motions for ZF1, ZF2, and UBL. The crystal structure and NMR structure of UBL showed a conserved β-grasp fold homologous to ubiquitin and other UBLs. Nevertheless, the UBL of ZFAND1 contains an additional N-terminal helix that adopts different conformations in the crystalline and solution states. ZFAND1 uses the C-terminal UBL to bind to p97, evidenced by the pronounced line-broadening of the UBL domain during the p97 titration monitored by methyl NMR spectroscopy. ZFAND1 binding induces pronounced conformational heterogeneity in the N-terminal domain of p97, leading to a partial loss of the cryo-EM density of the N-terminal domain of p97. In conclusion, this work paved the way for a better understanding of the interplay between p97 and ZFAND1 in the context of SG clearance.
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Affiliation(s)
- Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuang-Ting Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Ju Fan
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | - Tsun-Ai Yu
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Fon Chang
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | | | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; International Institute for Sustainability With Knotted Chiral Meta Matter (SKCM(2)), Hiroshima University, Higashihiroshima, Japan.
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2
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Tsai TY, Jhang WT, Hsu HK, Chan YT, Chang CF, Chen YR. Amyloid Modifier SERF1a Accelerates Alzheimer's Amyloid-β Fibrillization and Exacerbates the Cytotoxicity. ACS Chem Neurosci 2024; 15:479-490. [PMID: 38211979 DOI: 10.1021/acschemneuro.3c00403] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Alzheimer's disease (AD) is a devastating, progressive neurodegenerative disease affecting the elderly in the world. The pathological hallmark senile plaques are mainly composed of amyloid-β (Aβ), in which the main isoforms are Aβ40 and Aβ42. Aβ is prone to aggregate and ultimately forms amyloid fibrils in the brains of AD patients. Factors that alter the Aβ aggregation process have been considered to be potential targets for treatments of AD. Modifier of aggregation 4 (MOAG-4)/small EDRK-rich factor (SERF) was previously selected from a chemical mutagenesis screen and identified as an amyloid modifier that promotes amyloid aggregation for α-synuclein, huntingtin, and Aβ40. The interaction and effect of yeast ScSERF on Aβ40 were previously described. Here, we examined the human SERF1a effect on Aβ40 and Aβ42 fibrillization by the Thioflavin T assay and found that SERF1a accelerated Aβ fibrillization in a dose-dependent manner without changing the fibril amount and without incorporation. By Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM), we found that SERF1a altered the secondary structures and the morphology of Aβ fibrils. The electrospray ionization mass spectrometry (ESI-MS) and analytical ultracentrifugation (AUC) results showed that SERF1a binds to Aβ in a 1:1 stoichiometry. Moreover, the NMR study showed that SERF1a interacts with Aβ via its N-terminal region. Cytotoxicity assay demonstrated that SERF1a enhanced toxicity of Aβ intermediates, and the effect can be rescued by SERF1a antibody. Overall, our study provides the underlying molecular mechanism for the SERF1a effect on Aβ fibrillization and facilitates the therapeutic development of AD.
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Affiliation(s)
- Tien-Ying Tsai
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang District, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ting Jhang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hung-Kai Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Tsu Chan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 115, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 115, Taiwan
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3
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Hsu PH, Hazam PK, Huang YP, Yeh JC, Chen YR, Li CC, Chang CF, Liou JW, Chen JY. Optimization of sequence and chiral content enhances therapeutic potential of tilapia piscidin peptides. Eur J Med Chem 2024; 265:116083. [PMID: 38150960 DOI: 10.1016/j.ejmech.2023.116083] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 12/29/2023]
Abstract
Because antimicrobial peptides (AMPs) often exhibit broad-spectrum bactericidal potency, we sought to develop peptide-based antimicrobials for potential clinical use against drug-resistant pathogens. To accomplish this goal, we first optimized the amino acid sequence of a broad-spectrum AMP known as Tilapia Piscidin 4 (TP4). Then, we used the optimized sequence to create a pair of heterochiral variants (TP4-α and TP4-β) with different percentages of D-enantiomers, as poly-L peptides often exhibit poor pharmacokinetic profiles. The conformations of the peptide pair exhibited inverted chirality according to CD and NMR spectroscopic analyses. Both heterochiral peptides displayed enhanced stability and low hemolysis activities. Irrespective of their different d-enantiomer contents, both heterochiral peptides exhibited bactericidal activities in the presence of human serum or physiological enzymes. However, the peptide with higher d-amino acid content (TP4-β) caused better bacterial clearance when tested in mice infected with NDM-1 K. pneumoniae. In addition, we observed a relatively higher hydrogen bonding affinity in a simulation of the interaction between TP4-β and a model bacterial membrane. In sum, our results demonstrate that the current design strategy may be applicable for development of new molecules with enhanced stability and in vivo antimicrobial activity.
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Affiliation(s)
- Po-Hsien Hsu
- Institute of Fisheries Science, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei, 106, Taiwan
| | - Prakash Kishore Hazam
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd., Jiaushi, Ilan, 262, Taiwan
| | - Yi-Ping Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jih-Chao Yeh
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd., Jiaushi, Ilan, 262, Taiwan
| | - Yun-Ru Chen
- Academia Sinica Protein Clinic, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Section 2, Nankang District, Taipei, 115, Taiwan
| | - Chao-Chin Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - Je-Wen Liou
- Department of Biochemistry, School of Medicine, Tzu Chi University, 701, Sec.3, Chung-Yang Rd, Hualien, 970, Taiwan.
| | - Jyh-Yih Chen
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd., Jiaushi, Ilan, 262, Taiwan; The IEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, 402, Taiwan.
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4
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Wang CW, Tsai HY, Hsu C, Hsieh CC, Wang IS, Chang CF, Su NW. Structure-specific metabolism of flavonol molecules by Bacillus subtilis var. natto BCRC 80517. Food Chem 2024; 430:136975. [PMID: 37549625 DOI: 10.1016/j.foodchem.2023.136975] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Flavonols (3-hydroxy flavones) have been studied for their beneficial bioactivities for human health. Recently, we reported that a flavonoid phosphate synthetase (BsFPS) from Bacillus subtilis BCRC 80517 can transform several flavonoids into their phosphate conjugates, which become more water-soluble and thus increase the oral bioavailability. However, the in vivo metabolism of different flavonols has yet to be determined. Here, we investigated biotransformation of three flavonols (quercetin, kaempferol and fisetin) by B. subtilis BCRC 80517. C-ring cleavage products of quercetin and kaempferol, i.e., 2-protocatechuoyl-phloroglucinol carboxylic acid (2-PCPGCA), were produced, whereas two phosphate derivatives of fisetin (fisetin 4'-O-phosphate and fisetin 3'-O-phosphate) were generated by cultivation with B. subtilis BCRC 80517. Our results indicated that there are structure-specific metabolic pathways in B. subtilis toward different flavonols, where the 5-hydroxy group determines metabolic priority. Our findings provide new insights for developing bioproduction platform to produce flavonol phosphate derivatives for nutraceutical applications.
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Affiliation(s)
- Che-Wei Wang
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Ya Tsai
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Chen Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Ching-Chun Hsieh
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - I-Shu Wang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Nan-Wei Su
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan; Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan.
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5
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Hsu PH, Hazam PK, Huang YP, Yeh JC, Chen YR, Li CC, Chang CF, Liou JW, Chen JY. Sequential rearrangement and stereochemical reorganization to design an antimicrobial peptide with enhanced stability. Biomed Pharmacother 2024; 170:116088. [PMID: 38159380 DOI: 10.1016/j.biopha.2023.116088] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024] Open
Abstract
Antimicrobial peptides (AMPs) are natural molecules that function within the innate immune system to counteract pathogenic invasion and minimize the detrimental consequences of infection. However, utilizing these molecules for medical applications has been challenging. In this study, we selected a model AMP with poor stability, Tilapia Piscidin 4 (TP4), and modified its sequence and chirality (TP4-γ) to improve its potential for clinical application. The strategy of chirality inversion was inspired by the cereulide peptide, which has a DDLL enantiomer pattern and exhibits exceptional stability. Sequential substitution of key residues and selective chirality inversion yielded a less toxic peptide with enhanced stability and notable antimicrobial activity. In addition to its superior stability profile and antimicrobial activity, TP4-γ treatment reduced the level of LPS-induced nitric oxide (NO) release in a macrophage cell line. This reduction in NO release may reflect anti-inflammatory properties, as NO is widely known to promote inflammatory processes. Hence, our heterochiral peptide construct shows a more suitable pharmacokinetic profile than its parental compound, and further studies are warranted to develop the molecule for potential clinical application.
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Affiliation(s)
- Po-Hsien Hsu
- Institute of Fisheries Science, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei 106, Taiwan
| | - Prakash Kishore Hazam
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd., Jiaushi, Ilan 262, Taiwan
| | - Yi-Ping Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jih-Chao Yeh
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd., Jiaushi, Ilan 262, Taiwan
| | - Yun-Ru Chen
- Academia Sinica Protein Clinic, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Section 2, Nankang District, Taipei 115, Taiwan
| | - Chao-Chin Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - Je-Wen Liou
- Department of Biochemistry, School of Medicine, Tzu Chi University, 701, Section 3, Chung-Yang Rd, Hualien 970, Taiwan.
| | - Jyh-Yih Chen
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd., Jiaushi, Ilan 262, Taiwan; The iEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan.
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6
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Tsai TY, Chen CY, Lin TW, Lin TC, Chiu FL, Shih O, Chang MY, Lin YC, Su AC, Chen CM, Jeng US, Kuo HC, Chang CF, Chen YR. Author Correction: Amyloid modifier SERF1a interacts with polyQ-expanded huntingtin-exon 1 via helical interactions and exacerbates polyQ-induced toxicity. Commun Biol 2023; 6:1021. [PMID: 37814125 PMCID: PMC10562454 DOI: 10.1038/s42003-023-05389-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
Affiliation(s)
- Tien-Ying Tsai
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2. Nankang, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chun-Yu Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Wei Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Chang Lin
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Feng-Lan Chiu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
| | - Ming-Yun Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - An-Chung Su
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chiung-Mei Chen
- Department of Neurology, Linkou Chang Gung Memorial Hospital and College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan.
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Tsai TY, Chen CY, Lin TW, Lin TC, Chiu FL, Shih O, Chang MY, Lin YC, Su AC, Chen CM, Jeng US, Kuo HC, Chang CF, Chen YR. Amyloid modifier SERF1a interacts with polyQ-expanded huntingtin-exon 1 via helical interactions and exacerbates polyQ-induced toxicity. Commun Biol 2023; 6:767. [PMID: 37479809 PMCID: PMC10361993 DOI: 10.1038/s42003-023-05142-0] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Abnormal polyglutamine (polyQ) expansion and fibrillization occur in Huntington's disease (HD). Amyloid modifier SERF enhances amyloid formation, but the underlying mechanism is not revealed. Here, the fibrillization and toxicity effect of SERF1a on Htt-exon1 are examined. SERF1a enhances the fibrillization of and interacts with mutant thioredoxin (Trx)-fused Httex1. NMR studies with Htt peptides show that TrxHttex1-39Q interacts with the helical regions in SERF1a and SERF1a preferentially interacts with the N-terminal 17 residues of Htt. Time-course analysis shows that SERF1a induces mutant TrxHttex1 to a single conformation enriched of β-sheet. Co-expression of SERF1a and Httex1-polyQ in neuroblastoma and lentiviral infection of SERF1a in HD-induced polypotent stem cell (iPSC)-derived neurons demonstrates the detrimental effect of SERF1a in HD. Higher level of SERF1a transcript or protein is detected in HD iPSC, transgenic mice, and HD plasma. Overall, this study provides molecular mechanism for SERF1a and mutant Httex1 to facilitate therapeutic development for HD.
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Affiliation(s)
- Tien-Ying Tsai
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2. Nankang, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chun-Yu Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Wei Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Chang Lin
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Feng-Lan Chiu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
| | - Ming-Yun Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - An-Chung Su
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chiung-Mei Chen
- Department of Neurology, Linkou Chang Gung Memorial Hospital and College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan.
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Wang YL, Chang CY, Hsu NS, Lo IW, Lin KH, Chen CL, Chang CF, Wang ZC, Ogasawara Y, Dairi T, Maruyama C, Hamano Y, Li TL. N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry. Nat Commun 2023; 14:2528. [PMID: 37137912 PMCID: PMC10156733 DOI: 10.1038/s41467-023-38218-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N-O or O-S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.
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Affiliation(s)
- Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chin-Yuan Chang
- Department of Biology Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - I-Wen Lo
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Liang Chen
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Zhe-Chong Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Chitose Maruyama
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan
| | - Yoshimitsu Hamano
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan.
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan.
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
- Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.
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9
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Hsu C, Tsai HY, Chang CF, Yang CC, Su NW. Discovery of a novel phosphotransferase from Bacillus subtilis that phosphorylates a broad spectrum of flavonoids. Food Chem 2022; 400:134001. [DOI: 10.1016/j.foodchem.2022.134001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022]
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10
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Tsai HY, Chen MY, Hsu C, Kuan KY, Chang CF, Wang CW, Hsu CP, Su NW. Luteolin Phosphate Derivatives Generated by Cultivating Bacillus subtilis var. Natto BCRC 80517 with Luteolin. J Agric Food Chem 2022; 70:8738-8745. [PMID: 35795971 DOI: 10.1021/acs.jafc.2c03524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Luteolin (LUT), a plant-derived flavone, exhibits various bioactivities; however, the poor aqueous solubility hampers its applications. Here, we revealed bioconversion of LUT by Bacillus subtilis BCRC 80517, yielding three water-soluble phosphate conjugates. These derivatives were identified as luteolin 4'-O-phosphate (L4'P), luteolin 3'-O-phosphate (L3'P), and luteolin 7-O-phosphate (L7P) by LC-ESI-MS/MS and NMR. Besides, we found that Bacillus subtilis BCRC 80517 was able to convert different levels of LUT but showed a limited conversion rate. By observing bacterial morphology with transmission electron microscopy and confocal fluorescence microscopy, we found that LUT disrupted the bacterial membrane integrity, which explained the incomplete conversion. Additionally, we revealed a spontaneous intramolecular transesterification of L4'P to L3'P, the thermodynamically more stable form, under acidic conditions and proposed the possible mechanism involving a cyclic phosphate as the intermediate. This study provides insight into development of a potent structural modification strategy to enhance the solubility of LUT through biophosphorylation.
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Affiliation(s)
- Hsin-Ya Tsai
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Ming-Yu Chen
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan
| | - Chen Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Kai-Yuan Kuan
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Che-Wei Wang
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Physics Division, National Center for Theoretical Sciences, Taipei 106, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan
| | - Nan-Wei Su
- Department of Agricultural Chemistry, National Taiwan University, Taipei 106, Taiwan
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 106, Taiwan
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11
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Mariasina SS, Chang CF, Navalayeu TL, Chugunova AA, Efimov SV, Zgoda VG, Ivlev VA, Dontsova OA, Sergiev PV, Polshakov VI. Williams-Beuren Syndrome Related Methyltransferase WBSCR27: From Structure to Possible Function. Front Mol Biosci 2022; 9:865743. [PMID: 35782865 PMCID: PMC9240639 DOI: 10.3389/fmolb.2022.865743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Williams-Beuren syndrome (WBS) is a genetic disorder associated with the hemizygous deletion of several genes in chromosome 7, encoding 26 proteins. Malfunction of these proteins induce multisystemic failure in an organism. While biological functions of most proteins are more or less established, the one of methyltransferase WBSCR27 remains elusive. To find the substrate of methylation catalyzed by WBSCR27 we constructed mouse cell lines with a Wbscr27 gene knockout and studied the obtained cells using several molecular biology and mass spectrometry techniques. We attempted to pinpoint the methylation target among the RNAs and proteins, but in all cases neither a direct substrate has been identified nor the protein partners have been detected. To reveal the nature of the putative methylation substrate we determined the solution structure and studied the conformational dynamic properties of WBSCR27 in apo state and in complex with S-adenosyl-L-homocysteine (SAH). The protein core was found to form a canonical Rossman fold common for Class I methyltransferases. N-terminus of the protein and the β6–β7 loop were disordered in apo-form, but binding of SAH induced the transition of these fragments to a well-formed substrate binding site. Analyzing the structure of this binding site allows us to suggest potential substrates of WBSCR27 methylation to be probed in further research.
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Affiliation(s)
- Sofia S. Mariasina
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
- Institute of Functional Genomics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Sergey V. Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, Kazan, Russia
| | | | | | - Olga A. Dontsova
- Chemical Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Petr V. Sergiev
- Institute of Functional Genomics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Chemical Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vladimir I. Polshakov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Vladimir I. Polshakov,
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12
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Chen MH, Li YS, Hsu NS, Lin KH, Wang YL, Wang ZC, Chang CF, Lin JP, Chang CY, Li TL. Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04790] [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: 11/28/2022]
Affiliation(s)
- Mei-Hua Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Zhe-Chong Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Ping Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 115, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan
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13
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Maksimov EG, Laptev GY, Blokhin DS, Klochkov VV, Slonimskiy YB, Sluchanko NN, Friedrich T, Chang CF, Polshakov VI. NMR resonance assignment and backbone dynamics of a C-terminal domain homolog of orange carotenoid protein. Biomol NMR Assign 2021; 15:17-23. [PMID: 32939684 DOI: 10.1007/s12104-020-09976-1] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/11/2020] [Indexed: 05/15/2023]
Abstract
Photoprotection in cyanobacteria is mediated by the Orange Carotenoid Protein (OCP), a two-domain photoswitch which has multiple natural homologs of its N- and C-terminal domains. Recently, it was demonstrated that C-terminal domain homologs (CTDHs) of OCP are standalone carotenoproteins participating in multidirectional carotenoid transfer between membranes and proteins. Non-covalent embedment of a ketocarotenoid causes dimerization of the small 16-kDa water-soluble CTDH protein; however, dynamic interactions of CTDH with membranes and other proteins apparently require the monomeric state. Although crystallography recently provided static snapshots of the Anabaena CTDH (AnaCTDH) spatial structure in the apo-form, which predicted mobility of some putative functional segments, no crystallographic information on the holo-form of CTDH is presently available. In order to use NMR techniques to cope with the dynamics of the AnaCTDH protein, it was necessary to obtain 1H, 13C and 15N resonance assignments. AnaCTDH samples enriched with 13C and 15N isotopes were prepared using recombinant protein expression, and NMR resonance assignment was achieved for more than 90% of the residues. The obtained results revealed that the structure of AnaCTDH in solution and in the crystal are largely equivalent. Together with 15N NMR relaxation experiments, our data shed light on the AnaCTDH dynamics and provide the platform for the subsequent analysis of the holo-CTDH structure in solution, for the better understanding of light-triggered protein-protein interactions and the development of antioxidant nanocarriers for biomedical applications in the future.
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Affiliation(s)
- Eugene G Maksimov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
- A.N. Bach Institute of Biochemistry, Federal Research Center, "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia, 119071.
- Laboratory of Physical Chemistry of Biomembranes, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
| | - Gennady Yu Laptev
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Dmitriy S Blokhin
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya st., Kazan, Russia, 420008
| | - Vladimir V Klochkov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya st., Kazan, Russia, 420008
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center, "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia, 119071
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center, "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia, 119071
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
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14
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Lin MH, Huang YP, Chang CF, Hsu CH. NMR assignments of the macro domain from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Biomol NMR Assign 2021; 15:137-142. [PMID: 33486617 PMCID: PMC7826497 DOI: 10.1007/s12104-020-09996-x] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/11/2020] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2 is a novel pathogen causing pneumonia named COVID-19 and leading to a severe pandemic since the end of 2019. The genome of SARS-CoV-2 contains a macro domain that may play an important role in regulating ADP-ribosylation in host cells and initiating viral replication. Here, we report the 1H, 13C, and 15N resonance assignments of the SARS-CoV-2 macro domain. This work provides the ground for further structural deciphering and biophysical investigation in protein function and antiviral agent design.
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Affiliation(s)
- Meng-Hsuan Lin
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Yi-Ping Huang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Chun-Hua Hsu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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15
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Lin MH, Yu TA, Chang CF, Nishikawa Y, Hsu CH. NMR resonance assignments of the programmed cell death protein 5 (PDCD5) from Toxoplasma gondii. Biomol NMR Assign 2020; 14:277-280. [PMID: 32578164 DOI: 10.1007/s12104-020-09961-8] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Toxoplasmosis is a systematic protozoan disease caused by a tiny parasite Toxoplasma gondii. The infection can be dangerous for pregnant woman and people with weak immune systems. The secreted protein named TgPDCD5 (Programmed cell death protein 5 from Toxoplasma gondii) plays an important role in apoptosis-inducing effect on host cells. Here, we report the 1H, 13C, and 15N resonance assignments of TgPDCD5. This work provides the ground for further structural elucidate and biophysical investigation about protein function.
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Affiliation(s)
- Meng-Hsuan Lin
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Tsun-Ai Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yoshifumi Nishikawa
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Chun-Hua Hsu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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16
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Mariasina SS, Chang CF, Petrova OA, Efimov SV, Klochkov VV, Kechko OI, Mitkevich VA, Sergiev PV, Dontsova OA, Polshakov VI. Williams-Beuren syndrome-related methyltransferase WBSCR27: cofactor binding and cleavage. FEBS J 2020; 287:5375-5393. [PMID: 32255258 DOI: 10.1111/febs.15320] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/20/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022]
Abstract
Williams-Beuren syndrome, characterized by numerous physiological and mental problems, is caused by the heterozygous deletion of chromosome region 7q11.23, which results in the disappearance of 26 protein-coding genes. Protein WBSCR27 is a product of one of these genes whose biological function has not yet been established and for which structural information has been absent until now. Using NMR, we investigated the structural and functional properties of murine WBSCR27. For protein in the apo form and in a complex with S-(5'-adenosyl)-l-homocysteine (SAH), a complete NMR resonance assignment has been obtained and the secondary structure has been determined. This information allows us to attribute WBSCR27 to Class I methyltransferases. The interaction of WBSCR27 with the cofactor S-(5'-adenosyl)-l-methionine (SAM) and its metabolic products - SAH, 5'-deoxy-5'-methylthioadenosine (MTA) and 5'-deoxyadenosine (5'dAdo) - was studied by NMR and isothermal titration calorimetry. SAH binds WBSCR27 much tighter than SAM, leaving open the question of cofactor turnover in the methylation reaction. One possible answer to this question is the presence of weak but detectable nucleosidase activity for WBSCR27. We found that the enzyme catalyses the cleavage of the adenine moiety from SAH, MTA and 5'dAdo, similar to the action of bacterial SAH/MTA nucleosidases. We also found that the binding of SAM or SAH causes a significant change in the structure of WBSCR27 and in the conformational mobility of the protein fragments, which can be attributed to the substrate recognition site. This indicates that the binding of the cofactor modulates the folding of the substrate-recognizing region of the enzyme.
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Affiliation(s)
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Sergey V Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, Russia
| | | | - Olga I Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Petr V Sergiev
- M.V. Lomonosov Moscow State University, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga A Dontsova
- M.V. Lomonosov Moscow State University, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
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17
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Liu XH, Chang CF, Tjeng LH, Komarek AC, Wirth S. Large magnetoresistance effects in Fe 3O 4. J Phys Condens Matter 2019; 31:225803. [PMID: 30836348 DOI: 10.1088/1361-648x/ab0cf4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigated the magnetoresistance (MR) of a single crystal of magnetite, Fe3O4. In an effort to distinguish between different contributions to the MR the samples were prepared in two different initial magnetic states, i.e. by either zero-field or by field cooling from room temperature. The different magnetic structures in this sample have a dramatic effect on the magnetoresistance: for initially zero-field-cooled conditions a negative MR of about -20% is observed just below the Verwey transition at [Formula: see text] K. For decreasing temperature the MR increases, changes sign at ∼78 K and reaches a record positive value of ∼45% at around 50 K. This behavior is completely absent in the field-cooled sample. Magnetization measurements corroborate an alignment of the easy magnetization direction in applied magnetic fields below [Formula: see text] as a cause of the strong effects observed in both, magnetization and MR. Our results point to a complex interplay of structural and magnetocrystalline effects taking place upon cooling Fe3O4 through [Formula: see text].
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Affiliation(s)
- X H Liu
- Max-Planck-Institute for Chemical Physics of Solids, Nöthnitzer Str. 40, 01187 Dresden, Germany. State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, People's Republic of China
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18
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Mariasina SS, Petrova OA, Osterman IA, Sergeeva OV, Efimov SV, Klochkov VV, Sergiev PV, Dontsova OA, Huang TH, Chang CF, Polshakov VI. NMR assignments of the WBSCR27 protein related to Williams-Beuren syndrome. Biomol NMR Assign 2018; 12:303-308. [PMID: 29868988 DOI: 10.1007/s12104-018-9827-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Williams-Beuren syndrome is a genetic disorder characterized by physiological and mental abnormalities, and is caused by hemizygous deletion of several genes in chromosome 7. One of the removed genes encodes the WBSCR27 protein. Bioinformatic analysis of the sequence of WBSCR27 indicates that it belongs to the family of SAM-dependent methyltransferases. However, exact cellular functions of this protein or phenotypic consequences of its deficiency are still unknown. Here we report nearly complete 1H, 15N, and 13C chemical shifts assignments of the 26 kDa WBSCR27 protein from Mus musculus in complex with the cofactor S-adenosyl-L-methionine (SAM). Analysis of the assigned chemical shifts allowed us to characterize the protein's secondary structure and backbone dynamics. The topology of the protein's fold confirms the assumption that the WBSCR27 protein belongs to the family of class I methyltransferases.
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Affiliation(s)
- Sofia S Mariasina
- Faculty of Fundamental Medicine, Center for Magnetic Tomography and Spectroscopy, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Olga A Petrova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Ilya A Osterman
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga V Sergeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sergey V Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya, Kazan, Russia, 420008
| | - Vladimir V Klochkov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya, Kazan, Russia, 420008
| | - Petr V Sergiev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga A Dontsova
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Tai-Huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, Republic of China.
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Center for Magnetic Tomography and Spectroscopy, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
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19
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Hsu NS, Wang YL, Lin KH, Chang CF, Lyu SY, Hsu LJ, Liu YC, Chang CY, Wu CJ, Li TL. The Mesomeric Effect of Thiazolium on non-Kekulé Diradicals in Pichia stipitis
Transketolase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ning-Shian Hsu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
- Institute of Biochemistry and Molecular Biology; National Yang-Ming University; Taipei 112 Taiwan
| | - Yung-Lin Wang
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
- Institute of Biochemistry and Molecular Biology; National Yang-Ming University; Taipei 112 Taiwan
| | - Chi-Fon Chang
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Syue-Yi Lyu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Li-Jen Hsu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Yu-Chen Liu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Chang-Jer Wu
- Department of Food Science; National (Taiwan) Ocean University; Keelung 202 Taiwan
| | - Tsung-Lin Li
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
- Biotechnology Center; National Chung Hsing University; Taichung City 402 Taiwan
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20
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Hsu NS, Wang YL, Lin KH, Chang CF, Lyu SY, Hsu LJ, Liu YC, Chang CY, Wu CJ, Li TL. The Mesomeric Effect of Thiazolium on non-Kekulé Diradicals in Pichia stipitis
Transketolase. Angew Chem Int Ed Engl 2018; 57:1802-1807. [DOI: 10.1002/anie.201709799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/23/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ning-Shian Hsu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
- Institute of Biochemistry and Molecular Biology; National Yang-Ming University; Taipei 112 Taiwan
| | - Yung-Lin Wang
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
- Institute of Biochemistry and Molecular Biology; National Yang-Ming University; Taipei 112 Taiwan
| | - Chi-Fon Chang
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Syue-Yi Lyu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Li-Jen Hsu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Yu-Chen Liu
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
| | - Chang-Jer Wu
- Department of Food Science; National (Taiwan) Ocean University; Keelung 202 Taiwan
| | - Tsung-Lin Li
- Genomics Research Center; Academia Sinica; Taipei 115 Taiwan
- Biotechnology Center; National Chung Hsing University; Taichung City 402 Taiwan
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21
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Hsu C, Wu BY, Chang YC, Chang CF, Chiou TY, Su NW. Phosphorylation of Isoflavones by Bacillus subtilis BCRC 80517 May Represent Xenobiotic Metabolism. J Agric Food Chem 2018; 66:127-137. [PMID: 29231720 DOI: 10.1021/acs.jafc.7b04647] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The soy isoflavones daidzein (DAI) and genistein (GEN) have beneficial effects on human health. However, their oral bioavailability is hampered by their low aqueous solubility. Our previous study revealed two water-soluble phosphorylated conjugates of isoflavones, daidzein 7-O-phosphate and genistein 7-O-phosphate, generated via biotransformation by Bacillus subtilis BCRC80517 cultivated with isoflavones. In this study, two novel derivatives of isoflavones, daidzein 4'-O-phosphate and genistein 4'-O-phosphate, were identified by HPLC-ESI-MS/MS and 1H, 13C, and 31P NMR, and their biotransformation roadmaps were proposed. Primarily, isoflavone glucosides were deglycosylated and then phosphorylated predominantly into 7-O-phosphate conjugates with traces of 4'-O-phosphate conjugates. Inevitably, trace quantities of glucosides were converted into 6″-O-succinyl glucosides. GEN was more efficiently phosphorylated than DAI. Nevertheless, the presence of GEN prolonged the time until the exponential phase of cell growth, whereas the other isoflavones showed little effect on cell growth. Our findings provide new insights into the novel microbial phosphorylation of isoflavones involved in xenobiotic metabolism.
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Affiliation(s)
- Chen Hsu
- Laboratory of Food Chemistry, Department of Agricultural Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Bo-Yuan Wu
- Laboratory of Food Chemistry, Department of Agricultural Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Yu-Chuan Chang
- Laboratory of Food Chemistry, Department of Agricultural Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica , Taipei 11529, Taiwan
| | - Tai-Ying Chiou
- Laboratory of Food Science and Technology, Department of Biotechnology and Environmental Chemistry, Kitami Institute of Technology , Kitami 090-8507, Japan
| | - Nan-Wei Su
- Laboratory of Food Chemistry, Department of Agricultural Chemistry, National Taiwan University , Taipei 10617, Taiwan
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22
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Liang CT, Lin YS, Huang YC, Huang HL, Yang JQ, Wu TH, Chang CF, Huang SJ, Huang HB, Lin TH. Characterization of the interactions between inhibitor-1 and recombinant PP1 by NMR spectroscopy. Sci Rep 2018; 8:50. [PMID: 29311589 PMCID: PMC5758809 DOI: 10.1038/s41598-017-18383-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 07/21/2017] [Accepted: 12/11/2017] [Indexed: 11/16/2022] Open
Abstract
Inhibitor-1 is converted into a potent inhibitor of native protein phosphatase-1 (PP1) when Thr35 is phosphorylated by cAMP-dependent protein kinase (PKA). However, PKA-phosphorylated form of inhibitor-1 displayed a weak activity in inhibition of recombinant PP1. The mechanism for the impaired activity of PKA-phosphorylated inhibitor-1 toward inhibition of recombinant PP1 remained elusive. By using NMR spectroscopy in combination with site-directed mutagenesis and inhibitory assay, we found that the interaction between recombinant PP1 and the consensus PP1-binding motif of PKA-thiophosphorylated form of inhibitor-1 was unexpectedly weak. Unlike binding to native PP1, the subdomains 1 (residues around and including the phosphorylated Thr35) and 2 (the consensus PP1-binding motif) of PKA-thiophosphorylated form of inhibitor-1 do not exhibit a synergistic effect in inhibition of recombinant PP1. This finding implied that a slight structural discrepancy exists between native and recombinant PP1, resulting in PKA-thiophosphorylated form of inhibitor-1 displaying a different affinity to native and recombinant enzyme.
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Affiliation(s)
- Chu-Ting Liang
- Basic Research Division, Medical Research Department, Taipei Veterans General Hospital, Taipei, 11217, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 11221, Taiwan
| | - Yu-Shan Lin
- Department of Life Science, National Chung Cheng University, Chia-Yi, 62102, Taiwan
| | - Yi-Choang Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 11221, Taiwan
| | - Hsien-Lu Huang
- Department of Nutrition and Health Science, Fooyin University, Kaohsiung, 83102, Taiwan
| | - Jia-Qian Yang
- Department of Life Science, National Chung Cheng University, Chia-Yi, 62102, Taiwan
| | - Tsung-Hsien Wu
- Department of Life Science, National Chung Cheng University, Chia-Yi, 62102, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsien-Bin Huang
- Department of Life Science, National Chung Cheng University, Chia-Yi, 62102, Taiwan.
| | - Ta-Hsien Lin
- Basic Research Division, Medical Research Department, Taipei Veterans General Hospital, Taipei, 11217, Taiwan. .,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 11221, Taiwan. .,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 11221, Taiwan.
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23
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Lin TW, Chang CF, Chang YJ, Liao YH, Yu HM, Chen YR. Alzheimer's amyloid-β A2T variant and its N-terminal peptides inhibit amyloid-β fibrillization and rescue the induced cytotoxicity. PLoS One 2017; 12:e0174561. [PMID: 28362827 PMCID: PMC5376091 DOI: 10.1371/journal.pone.0174561] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/11/2017] [Indexed: 01/21/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common dementia affecting tens of million people worldwide. The primary neuropathological hallmark in AD is amyloid plaques composed of amyloid-β peptide (Aβ). Several familial mutations found in Aβ sequence result in early onset of AD. Previous studies showed that the mutations located at N-terminus of Aβ, such as the English (H6R) and Tottori (D7N) mutations, promote fibril formation and increase cytotoxicity. However, A2T mutant located at the very N-terminus of Aβ shows low-prevalence incidence of AD, whereas, another mutant A2V causes early onset of AD. To understand the molecular mechanism of the distinct effect and develop new potential therapeutic strategy, here, we examined the effect of full-length and N-terminal A2V/T variants to wild type (WT) Aβ40 by fibrillization assays and NMR studies. We found that full-length and N-terminal A2V accelerated WT fibrillization and induced large chemical shifts on the N-terminus of WT Aβ, whereas, full-length and N-terminal A2T retarded the fibrillization. We further examined the inhibition effect of various N-terminal fragments (NTFs) of A2T to WT Aβ. The A2T NTFs ranging from residue 1 to residue 7 to 10, but not 1 to 6 or shorter, are capable to retard WT Aβ fibrillization and rescue cytotoxicity. The results suggest that in the presence of full-length or specific N-terminal A2T can retard Aβ aggregation and the A2T NTFs can mitigate its toxicity. Our results provide a novel targeting site for future therapeutic development of AD.
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Affiliation(s)
- Tien-Wei Lin
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Jen Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hung Liao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hui-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
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24
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Zhang L, Zhao CX, Ji HX, He J, Chang CF, Hao HY, Li JG. [Effect of occupational lead exposure on the blood pressure of lead-exposed workers]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2016; 34:825-827. [PMID: 28043269 DOI: 10.3760/cma.j.issn.1001-9391.2016.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the effect of occupational lead exposure on blood pressure and pro-vide supportive evidence of health protection on lead - exposed workers. Methods: 612 workers (452 lead - ex-posed workers, 160 workers as control) were recruited in the battery factory. The blood lead concentration and blood pressure were detected by occupational health examination and biological monitoring. The relationship of blood lead concentration and blood pressure wasanalyzed. Results: The blood lead concentration in the exposed group (249.84±137.74) μg/L was higher than that of the control group (117.25±70.15) μg/L, and the differ-ence was statistically significant (P<0.01) . The difference of abnormal blood pressure and diastolic pressure among the exposed and the control group was statistically significant (P<0.05) . The abnormal blood pressure rate, systolic pressure rate and diastolic pressure rate in the 400~726 μg/L group was higher than that of the 6~199 μg/L and 200~399 μg/L group, and the difference was statistically significant (P<0.01) . Multiple lin-ear regression analysis showed that the influencing factors of the systolic pressure followed by sex, age, length of service and blood lead concentration, diastolic pressure followed by sex, age, smoke and blood lead concen-tration. Conclusion: These findings suggest that long - term occupational lead exposure may result in the in-crease of blood lead concentration.
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Affiliation(s)
- L Zhang
- Department of Epidemiology and Statistics, Hebei Medical University, Shijiazhuang 050017, China
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25
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Chou CY, Chu M, Chang CF, Yu T, Huang TH, Sakellariou D. High sensitivity high-resolution full range relaxometry using a fast mechanical sample shuttling device and a cryo-probe. J Biomol NMR 2016; 66:187-194. [PMID: 27744623 DOI: 10.1007/s10858-016-0066-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
Field-dependent NMR studies of bio-molecular systems using a sample shuttling hardware operating on a high-field NMR apparatus have provided valuable structural and dynamic information. We have recently published a design of a compact sample transportation device, called "field-cycler", which was installed in a commercial spectrometer and which provided highly precise positioning and stability during high speed shuttling. In this communication, we demonstrate the first use of a sample shuttling device on a commercial high field standard bore NMR spectrometer, equipped with a commercial triple resonance cryogenically cooled NMR probe. The performance and robustness of the hardware operating in 1D and 2D field cycling experiments, as well as the impact of the sample shuttling time on the signal intensity are discussed.
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Affiliation(s)
- Ching-Yu Chou
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-Sur-Yvette, France
- Laboratoire des Biomolécules, Département de Chimie, UMR7203 CNRS-UPMC-ENS, Ecole Normale Supérieure, 24 Rue Lhomond, 75005, Paris Cedex 05, France
- Field Cycling Technology Ltd., 10F., No.136, Chaiqiao Rd., Xiangshan, Hsinchu, 300, Taiwan, ROC
| | - Minglee Chu
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Tsunai Yu
- Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan, ROC
| | - Tai-Huang Huang
- Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan, ROC.
| | - Dimitris Sakellariou
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-Sur-Yvette, France
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26
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Huang YP, Cho CC, Chang CF, Hsu CH. NMR assignments of the macro domain from Middle East respiratory syndrome coronavirus (MERS-CoV). Biomol NMR Assign 2016; 10:245-8. [PMID: 26993639 PMCID: PMC7091117 DOI: 10.1007/s12104-016-9676-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/11/2016] [Indexed: 05/08/2023]
Abstract
The newly emerging human pathogen, Middle East respiratory syndrome coronavirus (MERS-CoV), contains a macro domain in the highly conserved N-terminal region of non-structural protein 3. Intense research has shown that macro domains bind ADP-ribose and other derivatives, but it still remains intangible about their exact function. In this study we report the preliminary structural analysis through solution NMR spectroscopy of the MERS-CoV macro domain. The near complete NMR assignments of MERS-CoV macro domain provide the basis for subsequent structural and biochemical investigation in the context of protein function.
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Affiliation(s)
- Yi-Ping Huang
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Chao-Cheng Cho
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
| | - Chun-Hua Hsu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
- Center for Systems Biology, National Taiwan University, Taipei, 10617, Taiwan.
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27
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Chen YH, Huang CW, Yeh PH, Chen JY, Lin TY, Chang CF, Wu WW. A solid-state cation exchange reaction to form multiple metal oxide heterostructure nanowires. Nanoscale 2016; 8:17039-17043. [PMID: 27714036 DOI: 10.1039/c6nr01287f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Metal oxide nanostructures have been investigated extensively due to their wide range of physical properties; zinc oxide is one of the most promising materials. It exhibits fascinating functional properties and various types of morphologies. In particular, ZnO heterostructures have attracted great attention because their performance can be modified and further improved by the addition of other materials. In this study, we successfully transformed ZnO nanowires (NWs) into multiple ZnO/Al2O3 heterostructure NWs via a solid-state cation exchange reaction. The experiment was carried out in situ via an ultrahigh vacuum transmission electron microscope (UHV-TEM), which was equipped with a video recorder. Moreover, we analyzed the structure and composition of the heterostructure NWs by Cs-corrected STEM equipped with EDS. Based on these experimental results, we inferred a cation exchange reaction ion path model. Additionally, we investigated the defects that appeared after the cation reaction, which resulted from the remaining zinc ions. These multiple heterostructure ZnO/Al2O3 NWs exhibited excellent UV sensing sensitivity and efficiency.
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Affiliation(s)
- Y H Chen
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - C W Huang
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - P H Yeh
- Department of Physics, Tam Kang University, New Taipei 251, Taiwan
| | - J Y Chen
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - T Y Lin
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - C F Chang
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - W W Wu
- Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan.
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28
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Chang CF, Yang J, Li XF, Zhao WM, Chen SS, Wang GP, Xu CS. [SPINK3: A novel growth factor that promotes rat liver regeneration]. Mol Biol (Mosk) 2016; 50:457-65. [PMID: 27414783 DOI: 10.7868/s0026898416030058] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/13/2015] [Indexed: 11/23/2022]
Abstract
Serine peptidase inhibitor, Kazal type 3 (SPINK3) is a trypsin inhibitor, and also a growth factor that has an identical structure to epidermal growth factor (EGF), which could combine with epidermal growth factor receptor (EGFR) to promote cell proliferation. To shed light on the role and regulation mechanism of SPINK3 in rat liver regeneration (LR), Rat Genome 230 2.0 assay was used to detect the expression profiles of LR genes after partial hepatectomy (PH). The results showed that Spink3 was significantly up-regulated at 2-24 h and 72-168 h after PH. In the present study, RT-PCR and immunoblotting were used to validate the assay results. Ingenuity Pathway Analysis 9.0 (IPA) software was used to build the SPINK3 signaling regulating LR and analyze the possible mechanism. And then the expression of cell proliferation-associated gene Ccna2 was examined by RT-PCR in normal rat liver cell line BRL-3A in which Spink3 was overexpressed. The results showed that Ccna2 was significantly up-regulated in BRL-3A in which Spink3 was over-expressed. SPINK3 combining with EGFR accelerated cell proliferation during rat liver regeneration via P38, PKC, JAK-STAT and AKT pathways. Thus, SPINK3 was likely to promote hepatocytes proliferation in LR through P38, PKC, JAK-STAT and AKT.
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Affiliation(s)
- C F Chang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, P.R. China.,College of Life Science, Henan Normal University, Xinxiang, 453007, P.R. China
| | - J Yang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, P.R. China.,College of Life Science, Henan Normal University, Xinxiang, 453007, P.R. China
| | - X F Li
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, P.R. China.,College of Life Science, Henan Normal University, Xinxiang, 453007, P.R. China
| | - W M Zhao
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, P.R. China.,College of Life Science, Henan Normal University, Xinxiang, 453007, P.R. China
| | - S S Chen
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, P.R. China.,College of Life Science, Henan Normal University, Xinxiang, 453007, P.R. China
| | - G P Wang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, P.R. China.,College of Life Science, Henan Normal University, Xinxiang, 453007, P.R. China
| | - C S Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, 453007, P.R. China.,College of Life Science, Henan Normal University, Xinxiang, 453007, P.R. China.,
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29
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Liang CT, Huang HB, Wang CC, Chen YR, Chang CF, Shiao MS, Chen YC, Lin TH. L17A/F19A Substitutions Augment the α-Helicity of β-Amyloid Peptide Discordant Segment. PLoS One 2016; 11:e0154327. [PMID: 27104649 PMCID: PMC4841593 DOI: 10.1371/journal.pone.0154327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/12/2016] [Indexed: 11/18/2022] Open
Abstract
β-amyloid peptide (Aβ) aggregation has been thought to be associated with the pathogenesis of Alzheimer’s disease. Recently, we showed that L17A/F19A substitutions may increase the structural stability of wild-type and Arctic-type Aβ40 and decrease the rates of structural conversion and fibril formation. However, the underlying mechanism for the increase of structural stability as a result of the alanine substitutions remained elusive. In this study, we apply nuclear magnetic resonance and circular dichroism spectroscopies to characterize the Aβ40 structure, demonstrating that L17A/F19A substitutions can augment the α-helicity of the residues located in the α/β-discordant segment (resides 15 to 23) of both wild-type and Arctic-type Aβ40. These results provide a structural basis to link the α-helicity of the α/β-discordant segment with the conformational conversion propensity of Aβ.
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Affiliation(s)
- Chu-Ting Liang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Basic Research Division, Medical Research Department, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
| | - Hsien-Bin Huang
- Department of Life Science and the Institute of Molecular Biology, National Chung Cheng University, Chiayi, Taiwan, R.O.C
| | - Chih-Ching Wang
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Yi-Ru Chen
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Department and Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan, R.O.C
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Ming-Shi Shiao
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Yi-Cheng Chen
- Department of Medicine, Mackay Medical College, Taipei, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
| | - Ta-Hsien Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Basic Research Division, Medical Research Department, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
- Structural Biology Program, National Yang-Ming University, Taipei, Taiwan, R.O.C
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University, Taipei, Taiwan, R.O.C
- * E-mail: (YCC); (THL)
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30
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Zhao WM, Qin YL, Niu ZP, Chang CF, Yang J, Li MH, Zhou Y, Xu CS. Branches of the NF-κB signaling pathway regulate proliferation of oval cells in rat liver regeneration. Genet Mol Res 2016; 15:gmr7750. [PMID: 27050988 DOI: 10.4238/gmr.15017750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The NF-kB (nuclear factor kB) pathway is involved in the proliferation of many cell types. To explore the mechanism of the NF-kB signaling pathway underlying the oval cell proliferation during rat liver regeneration, the Rat Genome 230 2.0 Array was used to detect expression changes of NF-kB signaling pathway-related genes in oval cells. The results revealed that the expression levels of many genes in the NF-kB pathway were significantly changed. This included 48 known genes and 16 homologous genes, as well as 370 genes and 85 homologous genes related to cell proliferation. To further understand the biological significance of these changes, an expression profile function was used to analyze the potential biological processes. The results showed that the NF-kB pathway promoted oval cell proliferation mainly through three signaling branches; the tumor necrosis factor alpha branch (TNF-a pathway), the growth factor branch, and the chemokine branch. An integrated statistics method was used to define the key genes in the NF-kB pathway. Seven genes were identified to play vital roles in the NF-kB pathway. To confirm these results, the protein content, including two key genes (TNF and FGF11) and two non-key genes (CCL2 and TNFRSF12A), were analyzed using two-dimensional gel electrophoresis and MALDI-TOF/TOF mass spectrometry. The results were generally consistent with those of the array data. To conclude, three branches and seven key genes were involved in the NF-kB signaling pathway that regulates oval cell proliferation during rat liver regeneration.
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Affiliation(s)
- W M Zhao
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China
| | - Y L Qin
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China
| | - Z P Niu
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China
| | - C F Chang
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China
| | - J Yang
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China
| | - M H Li
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China
| | - Y Zhou
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China.,College of Computer and Information Engineering, Henan Normal University, Xinxiang, Henan, China
| | - C S Xu
- College of Life Science, Henan Normal University, Xinxiang, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation, Henan Normal University, Xinxiang, China
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31
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Schock EN, Chang CF, Struve JN, Chang J, Brugmann SA. Using the talpid
2
as novel model for determining the cellular and molecular etiology of Oral-facial-digital syndrome. Cilia 2015. [PMCID: PMC4519141 DOI: 10.1186/2046-2530-4-s1-p41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Sabater L, Fang PJ, Chang CF, De Rache A, Prado E, Dejeu J, Garofalo A, Lin JH, Mergny JL, Defrancq E, Pratviel G. Cobalt(III)porphyrin to target G-quadruplex DNA. Dalton Trans 2015; 44:3701-7. [PMID: 25573281 DOI: 10.1039/c4dt03631j] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
G-quadruplex DNA ligands attract much attention because of their potential use in biology. Indeed they may interfere with G-quadrulex nucleic acid function in cells. Most of the G-quadruplex ligands so far reported (including also metal complexes) are large planar aromatic compounds that interact by π-π stacking with an external G-quartet of quadruplex. Porphyrins are well-known G-quadruplex ligands. We report herein a new porphyrin scaffold (meso-tetrakis(4-(N-methyl-pyridinium-2-yl)phenyl)porphyrin) able to strongly and selectively bind to G-quadruplex DNA. We show that even when this porphyrin is metallated with cobalt(III), i.e. it carries two water molecules as axial ligands on the cobalt ion, on each face of the porphyrin, the interaction occurs by a π-stacking-like mode with an external G-quartet of quadruplex DNA.
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Affiliation(s)
- Laurent Sabater
- CNRS, Laboratoire de Chimie de Coordination, 205 Route de Narbonne, BP 44099, F-31077 Toulouse, France.
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33
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Hsu CH, Chang CF, Liao YD, Wu SH, Chen C. Solution structure and base specificity of cytotoxic RC-RNase 2 from Rana catesbeiana. Arch Biochem Biophys 2015; 584:70-8. [PMID: 26302448 DOI: 10.1016/j.abb.2015.08.010] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 08/16/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
Abstract
Cytotoxic ribonucleases found in the oocytes and early embryos of frogs with antitumor activity are well-documented. RC-RNase 2, a cytotoxic ribonuclease isolated from oocytes of bullfrog Rana catesbeiana, consists of 105 residues linked with 4 disulfide bridges and belongs to the bovine pancreatic ribonuclease (RNase A) superfamily. Among the RC-RNases, the base preference for RNase 2 is UpG but CpG for RC-RNase 4; while RC-RNase possesses the base specificity of both UpG and CpG. Interestingly, RC-RNase 2 or 4 has much lower catalytic activity but only three-fold less cytotoxicity than RC-RNase. Here, we report the NMR solution structure of rRC-RNase 2, comprising three alpha-helices and two sets of antiparallel beta-sheets. The differences of side-chain conformations of subsite residues among RNase A, RC-RNase, RC-RNase 4 and rRNase 2 are related to their distinct catalytic activities and base preferences. Furthermore, the substrate-related residues in the base specificity among native RC-RNases are derived using the chemical shift perturbation on ligand binding.
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Affiliation(s)
- Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan; Genome and Systems Biology Degree Program, Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan.
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - You-Di Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chinpan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.
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Chang CF, Zhao WM, Mei JX, Zhou Y, Pan CY, Xu TT, Xu CS. Branches of NF-κb signaling pathway regulate hepatocyte proliferation in rat liver regeneration. Genet Mol Res 2015. [PMID: 26214444 DOI: 10.4238/2015.july.13.9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Previous studies have demonstrated that the nuclear factor κB (NF-κB) pathway is involved in promoting cell proliferation. To further explore the regulatory branches and their sequence in the NF-κB pathway in the promotion of hepatocyte proliferation at the transcriptional level during rat liver regeneration, Rat Genome 230 2.0 array was used to detect the expression changes of the isolated hepatocytes. We found that many genes involved in the NF-κB pathway (including 73 known genes and 19 homologous genes) and cell proliferation (including 484 genes and 104 homologous genes) were associated with liver regeneration. Expression profile function (Ep) was used to analyze the biological processes. It was revealed that the NF-κB pathway promoted hepatocyte proliferation through three branches. Several methods of integrated statistics were applied to extract and screen key genes in liver regeneration, and it indicated that eight genes may play a vital role in rat liver regeneration. To confirm the above predicted results, Ccnd1, Jun and Myc were analyzed using qRT-PCR, and the results were generally consistent with that of microarray data. It is concluded that 3 branches and 8 key genes involved in the NF-κB pathway regulate hepatocyte proliferation during rat liver regeneration.
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Affiliation(s)
- C F Chang
- College of Life Science, Henan Normal University, Xinxiang, China
| | - W M Zhao
- College of Life Science, Henan Normal University, Xinxiang, China
| | - J X Mei
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Y Zhou
- College of Life Science, Henan Normal University, Xinxiang, China
| | - C Y Pan
- College of Life Science, Henan Normal University, Xinxiang, China
| | - T T Xu
- College of Life Science, Henan Normal University, Xinxiang, China
| | - C S Xu
- College of Life Science, Henan Normal University, Xinxiang, China
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Chang CF, Yang J, Zhao WM, Li Y, Guo PJ, Li MH, Zhou Y, Xu CS. Gene expression profiling analysis of 5-hydroxytryptamine signaling pathway in rat regenerating liver and different types of liver cells. Genet Mol Res 2015; 14:3409-20. [PMID: 25966107 DOI: 10.4238/2015.april.15.4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We examined the gene expression profiles of the 5-hydroxytryptamine signaling pathway in the regenerating liver and 8 types of liver cells during rat liver regeneration, and explored expression differences in 5-hydroxytryptamine signaling pathway genes at the level of tissues and cells, as well as the role of the pathway on liver regeneration. Eight types of rat regenerating liver cells were isolated using Percoll density-gradient centrifugation and immunomagnetic bead methods. Rat Genome 230 2.0 Array was used to detect expression changes in 5-hydroxytryptamine signaling pathway genes. The results showed that 26, 47, 8, 21, 16, 19, 22, 27, and 20 genes changed significantly in hepatocytes, biliary epithelial cells, hepatic stellate cells, oval cells, sinusoidal endothelial cells, Kupffer cells, pit cells, dendritic cells, and the regenerating liver, respectively. Synthetic effects of 5-hydroxytryptamine signaling pathway genes in 8 types of liver cells showed that 26 genes were expressed significantly; the expression trends of 10 genes were the same in the regenerating liver, while others were different. Based on the gene expression profiles of the 8 types of liver cells, 5-hydroxytryptamine promoted hepatocyte proliferation through the RAS and STAT3 signaling pathways, proliferation and differentiation of sinusoidal endothelial cells through the STAT3 signaling pathway, and proliferation and apoptosis of pit cells through the AKT3 signaling pathway. There were large differences in genes involved in 5-hydroxytryptamine signaling at the tissue and cellular levels; thus, liver regeneration should be studied in-depth at the cellular level to reveal the molecular mechanism of liver regeneration.
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Affiliation(s)
- C F Chang
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
| | - J Yang
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
| | - W M Zhao
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
| | - Y Li
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
| | - P J Guo
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
| | - M H Li
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
| | - Y Zhou
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
| | - C S Xu
- Key Laboratory for Cell Differentiation Regulation, Xinxiang, Henan, China
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Polshakov VI, Eliseev BD, Frolova LY, Chang CF, Huang TH. Backbone (1)H, (13)C and (15)N resonance assignments of the human eukaryotic release factor eRF1. Biomol NMR Assign 2015; 9:37-42. [PMID: 24452424 DOI: 10.1007/s12104-014-9540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 01/04/2014] [Indexed: 06/03/2023]
Abstract
Eukaryotic translation termination is mediated by two interacting release factors, eukaryotic class 1 release factor (eRF1) and eukaryotic class 3 release factor (eRF3), which act cooperatively to ensure efficient stop codon recognition and fast polypeptide release. eRF1 consisting of three well-defined functional domains recognizes all three mRNA stop codons located in the A site of the small ribosomal subunit and triggers hydrolysis of the ester bond of peptidyl-tRNA in the peptidyl transfer center of the large ribosomal subunit. Nevertheless, various aspects of molecular mechanism of translation termination in eukaryotes remain unclear. Elucidation of the structure and dynamics of eRF1 in solution is essential for understanding molecular mechanism of its function in translation termination. To approach this problem, here we report NMR backbone signal assignments of the human eRF1 (437 a.a., 50 kDa).
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Affiliation(s)
- Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, 119991, Russia,
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Lo CJ, Chyan CL, Chen YC, Chang CF, Huang HB, Lin TH. Resonance assignments and secondary structure of apolipoprotein E C-terminal domain in DHPC micelles. Biomol NMR Assign 2015; 9:187-190. [PMID: 25239652 DOI: 10.1007/s12104-014-9571-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/02/2014] [Indexed: 06/03/2023]
Abstract
Human apolipoprotein E (apoE) has been known to play a key role in the transport of plasma cholesterol and lipoprotein metabolism. It is an apolipoprotein of 299 amino acids with a molecular mass, ~34 kDa. ApoE has three major isoforms, apoE2, apoE3, and apoE4 which differ only at residue 112 or 158. ApoE consists of two independently folded domains (N-terminal and C-terminal domain) separated by a hinge region. The N-terminal domain and C-terminal domain of apoE are responsible for the binding to receptor and to lipid, respectively. Since the high resolution structures of apoE in lipids are still unavailable to date, we therefore aim to resolve the structures in lipids by NMR. Here, we reported the resonance assignments and secondary structure distribution of the C-terminal domain of wild-type human apoE (residue 195-299) in the micelles formed by dihexanoylphosphatidylcholine. Our results may provide a novel structural model of apoE in micelles and may shed new light on the molecular mechanisms underlying the apoE related biological processes.
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Affiliation(s)
- Chi-Jen Lo
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan, ROC
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Lo CJ, Wang CC, Huang HB, Chang CF, Shiao MS, Chen YC, Lin TH. The Arctic mutation accelerates Aβ aggregation in SDS through reducing the helical propensity of residues 15-25. Amyloid 2015; 22:8-18. [PMID: 25376379 DOI: 10.3109/13506129.2014.980943] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations within the β-amyloid peptide (Aβ) sequence that cause early onset familial Alzheimer's disease (FAD) have been shown to promote Aβ aggregation. How these FAD-related mutants increase the aggregative ability of Aβ is not fully understood. Here, we characterized the effect of the Arctic variant (E22G) on the conformational stability of Aβ using various forms of spectroscopy and kinetic analyses, including nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, Fourier-transform infrared (FT-IR) spectroscopy and transmission electron microscopy (TEM). The E22G mutation in the Arctic variant reduced the α-helical propensity and conformational stability of Aβ on residues 15-25. This mutation also caused an increase in both α-helix-to-β-strand conversion and fibril nucleation rates. Our results suggest that the α-helical propensity of residues 15-25 may play a determinant role in the aggregative ability of Aβ. This may provide a structural basis for understanding the molecular mechanism of Aβ aggregation.
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Affiliation(s)
- Chi-Jen Lo
- Institute of Biochemistry & Molecular Biology, National Yang-Ming University , Taipei, Taiwan , ROC
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Huang SY, Chang CF, Fang PJ, Naik MT, Güntert P, Shih HM, Huang TH. The RING domain of human promyelocytic leukemia protein (PML). J Biomol NMR 2015; 61:173-180. [PMID: 25627356 DOI: 10.1007/s10858-015-9901-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Shu-Yu Huang
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, 11529, Taiwan, ROC
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Huang SY, Naik MT, Chang CF, Fang PJ, Wang YH, Shih HM, Huang TH. The B-box 1 dimer of human promyelocytic leukemia protein. J Biomol NMR 2014; 60:275-281. [PMID: 25355412 DOI: 10.1007/s10858-014-9869-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/20/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Shu-Yu Huang
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, 11529, Taiwan, ROC
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41
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Wang YS, Ko CH, Chang HT, Yang KJ, Chen YJ, Huang SJ, Fang PJ, Chang CF, Tzou DLM. ¹H, ¹³C and ¹⁵N backbone and side-chain resonance assignments of a family 36 carbohydrate binding module of xylanase from Paenibacillus campinasensis. Biomol NMR Assign 2014; 8:303-306. [PMID: 23835623 DOI: 10.1007/s12104-013-9505-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/29/2013] [Indexed: 06/02/2023]
Abstract
Paenibacillus campinasensis BL11 isolated from black liquor secretes multiple glycoside hydrolases (GHs) against all kinds of polysaccharides. GH consists of a catalytic module and non-catalytic carbohydrate-binding modules (CBMs), in which CBMs append to the catalytic module, mediating specific interactions with insoluble carbohydrates to promote the hydrolysis efficiency of the cognate enzyme. Endo-β-1,4-xylanase (XylX) is one of the GHs reveals high enzymatic activity in a wide range of pH and thermal endurance, suitable for bioconversion and bio-refinement applications. In this work, we report the resonance assignments of a family 36 CBM (characterized as CBM36) derived from XylX. Our investigations will facilitate molecular structure determination and molecular dynamics analysis of CBMs.
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Affiliation(s)
- Yu-Sheng Wang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan, ROC
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42
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Li YC, Chang CK, Chang CF, Cheng YH, Fang PJ, Yu T, Chen SC, Li YC, Hsiao CD, Huang TH. Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element. Nucleic Acids Res 2014; 42:8777-88. [PMID: 24990372 PMCID: PMC4117788 DOI: 10.1093/nar/gku572] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.
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Affiliation(s)
- Yi-Chuan Li
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Ya-Hsin Cheng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Pei-Ju Fang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Tsunai Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Sheng-Chia Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Yi-Ching Li
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Tai-huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan, ROC
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43
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Lee AYL, Chen YD, Chang YY, Lin YC, Chang CF, Huang SJ, Wu SH, Hsu CH. Structural basis for DNA-mediated allosteric regulation facilitated by the AAA+module of Lon protease. ACTA ACUST UNITED AC 2014; 70:218-30. [DOI: 10.1107/s139900471302631x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/23/2013] [Indexed: 01/07/2023]
Abstract
Lon belongs to a unique group of AAA+proteases that bind DNA. However, the DNA-mediated regulation of Lon remains elusive. Here, the crystal structure of the α subdomain of the Lon protease fromBrevibacillus thermoruber(Bt-Lon) is presented, together with biochemical data, and the DNA-binding mode is delineated, showing that Arg518, Arg557 and Arg566 play a crucial role in DNA binding. Electrostatic interactions contributed by arginine residues in the AAA+module are suggested to be important to DNA binding and allosteric regulation of enzymatic activities. Intriguingly, Arg557, which directly binds DNA in the α subdomain, has a dual role in the negative regulation of ATPase stimulation by DNA and in the domain–domain communication in allosteric regulation of Bt-Lon by substrate. In conclusion, structural and biochemical evidence is provided to show that electrostatic interaction in the AAA+module is important for DNA binding by Lon and allosteric regulation of its enzymatic activities by DNA and substrate.
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44
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Chang CK, Hou MH, Chang CF, Hsiao CD, Huang TH. The SARS coronavirus nucleocapsid protein--forms and functions. Antiviral Res 2014; 103:39-50. [PMID: 24418573 PMCID: PMC7113676 DOI: 10.1016/j.antiviral.2013.12.009] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/08/2013] [Accepted: 12/20/2013] [Indexed: 12/14/2022]
Abstract
Coronavirus N proteins share the same modular organization. Structures of SARS-CoV N protein provide insight into nucleocapsid formation. N protein binds to nucleic acid at multiple sites in a coupled-allostery manner. A RNP packaging model highlighting the importance of disorder and modularity is proposed.
The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. It is a protein with multifarious activities. In this article we will review our current understanding of the N protein structure and its interaction with nucleic acid. Highlights of the progresses include uncovering the modular organization, determining the structures of the structural domains, realizing the roles of protein disorder in protein–protein and protein–nucleic acid interactions, and visualizing the ribonucleoprotein (RNP) structure inside the virions. It was also demonstrated that N-protein binds to nucleic acid at multiple sites with a coupled-allostery manner. We propose a SARS-CoV RNP model that conforms to existing data and bears resemblance to the existing RNP structures of RNA viruses. The model highlights the critical role of modular organization and intrinsic disorder of the N protein in the formation and functions of the dynamic RNP capsid in RNA viruses. This paper forms part of a symposium in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Chung-ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Ming-Hon Hou
- Department of Life Science, National Chung Hsing University, Taichung 40254, Taiwan, ROC
| | - Chi-Fon Chang
- The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan, ROC
| | - Tai-huang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, ROC; The Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan, ROC; Department of Physics, National Taiwan Normal University, Taipei 11677, Taiwan, ROC.
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45
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Su MY, Chang CI, Chang CF. ¹H, ¹³C and ¹⁵N resonance assignments of the pyrin domain from human PYNOD. Biomol NMR Assign 2013; 7:141-143. [PMID: 22618865 DOI: 10.1007/s12104-012-9396-8] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/02/2012] [Indexed: 06/01/2023]
Abstract
PYNOD is a novel protein belonging to a large family of proteins containing the nucleotide-binding and oligomerization domain (NOD) involved in inflammation and apoptosis. Human PYNOD inhibits inflammatory response mediated by caspase-1 and apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC). Here we report the (1)H, (13)C and (15)N resonance assignments and secondary structure identification of the pyrin domain (PYD) of human PYNOD as the first step towards elucidating the structural basis of the anti-inflammatory activity of PYNOD.
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Affiliation(s)
- Ming-Yuan Su
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
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46
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de Jong S, Kukreja R, Trabant C, Pontius N, Chang CF, Kachel T, Beye M, Sorgenfrei F, Back CH, Bräuer B, Schlotter WF, Turner JJ, Krupin O, Doehler M, Zhu D, Hossain MA, Scherz AO, Fausti D, Novelli F, Esposito M, Lee WS, Chuang YD, Lu DH, Moore RG, Yi M, Trigo M, Kirchmann P, Pathey L, Golden MS, Buchholz M, Metcalf P, Parmigiani F, Wurth W, Föhlisch A, Schüßler-Langeheine C, Dürr HA. Speed limit of the insulator-metal transition in magnetite. Nat Mater 2013; 12:882-6. [PMID: 23892787 DOI: 10.1038/nmat3718] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 06/24/2013] [Indexed: 05/19/2023]
Abstract
As the oldest known magnetic material, magnetite (Fe3O4) has fascinated mankind for millennia. As the first oxide in which a relationship between electrical conductivity and fluctuating/localized electronic order was shown, magnetite represents a model system for understanding correlated oxides in general. Nevertheless, the exact mechanism of the insulator-metal, or Verwey, transition has long remained inaccessible. Recently, three-Fe-site lattice distortions called trimerons were identified as the characteristic building blocks of the low-temperature insulating electronically ordered phase. Here we investigate the Verwey transition with pump-probe X-ray diffraction and optical reflectivity techniques, and show how trimerons become mobile across the insulator-metal transition. We find this to be a two-step process. After an initial 300 fs destruction of individual trimerons, phase separation occurs on a 1.5±0.2 ps timescale to yield residual insulating and metallic regions. This work establishes the speed limit for switching in future oxide electronics.
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Affiliation(s)
- S de Jong
- 1] Stanford Institute for Energy and Materials Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA [2]
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47
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Chang CF, Hwang LP. Relaxation Studies of 2IZSZSpin Order in Liquid Benzene: Selection of Chemical Shift Anisotropy Parameters. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199100001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Hsu C, Ho HW, Chang CF, Wang ST, Fang TF, Lee MH, Su NW. Soy isoflavone-phosphate conjugates derived by cultivating Bacillus subtilis var. natto BCRC 80517 with isoflavone. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.05.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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49
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Su MY, Kuo CI, Chang CF, Chang CI. Three-dimensional structure of human NLRP10/PYNOD pyrin domain reveals a homotypic interaction site distinct from its mouse homologue. PLoS One 2013; 8:e67843. [PMID: 23861819 PMCID: PMC3701624 DOI: 10.1371/journal.pone.0067843] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/21/2013] [Indexed: 12/31/2022] Open
Abstract
NLRPs (Nucleotide-binding domain, leucine-rich repeat and pyrin domain containing proteins) are a family of pattern-recognition receptors (PRRs) that sense intracellular microbial components and endogenous stress signals. NLRP10 (also known as PYNOD) is a unique NLRP member characterized by a lack of the putative ligand-binding leucine-rich repeat domain. Recently, human NLRP10 has been shown to inhibit the self-association of ASC into aggregates and ASC-mediated procaspase-1 processing. However, such activities are not found in mouse NLRP10. Here we report the solution structure and dynamics of human NLRP10 pyrin domain (PYD), whose helix H3 and loop H2-H3 adopt a conformation distinct from those of mouse NLRP10. Docking studies show that human and mouse NLRP10 PYDs may interact differently with ASC PYD. These results provide a possible structural explanation for the contrasting effect of NLRP10 on ASC aggregation in human cells versus mouse models. Finally, we also provide evidence that in human NLRP10 the PYD domain may not interact with the NOD domain to regulate its intrinsic nucleotide hydrolysis activity.
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Affiliation(s)
- Ming-Yuan Su
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, Republic of China
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Chiao-I Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, Republic of China
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan, Republic of China
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50
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Chen SC, Chang CF, Fan PJ, Cheng YH, Yu T, Huang TH. (1)H, (13)C and (15)N resonance assignments of the C-terminal DNA-binding domain of RstA protein from Klebsiella pneumoniae. Biomol NMR Assign 2013; 7:85-88. [PMID: 22481468 DOI: 10.1007/s12104-012-9383-0] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/24/2012] [Indexed: 05/31/2023]
Abstract
Bacterial cells often use two-component signal transduction systems to regulate genes in response to environmental stimuli. The RstA/RstB system is a two-component regulatory system consisting of the membrane sensor, RstB, and its cognate response regulator RstA. The RstA of Klebsiella pneumoniae consists of a N-terminal receiver domain (NRD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of the response regulator induces a conformational change in the regulatory domain of RstA, which results in activation of the effector domain to regulate the downstream genes, including the ferrous iron transport system (Feo), at low-pH condition. Here we report the (1)H, (13)C and (15)N resonance assignments and secondary structure identification of the DBD of RstA from K. pneumoniae as a first step for unraveling the structural and functional relationship of the RstA/RstB two component system.
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Affiliation(s)
- Sheng-Chia Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan, ROC
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