23 results on '"Ying-Chih Chi"'
Search Results
2. Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease
- Author
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Zhiming Wang, Jeremy Rahkola, Jasmina S. Redzic, Ying-Chih Chi, Norman Tran, Todd Holyoak, Hongjin Zheng, Edward Janoff, and Elan Eisenmesser
- Subjects
Science - Abstract
Pathogenic IgA1 metalloproteases block the initial host immune response by cleaving host IgA1. Using cryoEM, the authors here provide structural insights into the substrate recognition mechanism of Streptococcus pneumoniae IgA1 protease, and develop a protease-inhibiting antibody.
- Published
- 2020
- Full Text
- View/download PDF
3. Discovery and substrate specificity engineering of nucleotide halogenases
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Jie Ni, Jingyuan Zhuang, Yiming Shi, Ying-Chih Chiang, and Gui-Juan Cheng
- Subjects
Science - Abstract
Abstract C2′-halogenation has been recognized as an essential modification to enhance the drug-like properties of nucleotide analogs. The direct C2ʹ-halogenation of the nucleotide 2′-deoxyadenosine-5′-monophosphate (dAMP) has recently been achieved using the Fe(II)/α-ketoglutarate-dependent nucleotide halogenase AdaV. However, the limited substrate scope of this enzyme hampers its broader applications. In this study, we report two halogenases capable of halogenating 2ʹ-deoxyguanosine monophosphate (dGMP), thereby expanding the family of nucleotide halogenases. Computational studies reveal that nucleotide specificity is regulated by the binding pose of the phosphate group. Based on these findings, we successfully engineered the substrate specificity of these halogenases by mutating second-sphere residues. This work expands the toolbox of nucleotide halogenases and provides insights into the regulation mechanism of nucleotide specificity.
- Published
- 2024
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- View/download PDF
4. Targeting HR Repair as a Synthetic Lethal Approach to Increase DNA Damage Sensitivity by a RAD52 Inhibitor in BRCA2-Deficient Cancer Cells
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Yi-Tsen Kuo, Wei-Che Tseng, Ching Yuh Chern, Shou-Jhen Liou, Chin-Chuan Chen, Ying-Chih Chi, Ya-Chen Chiu, Yi-Chen Li, Pei-Ya Lin, Shih-Ting Tseng, Chi-Yuan Chen, Shu-Fang Cheng, Wen-Chih Lee, and Chu-An Wang
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0301 basic medicine ,endocrine system diseases ,DNA Repair ,Apoptosis ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,Tumor Cells, Cultured ,Biology (General) ,skin and connective tissue diseases ,Homologous Recombination ,Spectroscopy ,Chemistry ,BRCA-deficient ,General Medicine ,female genital diseases and pregnancy complications ,Computer Science Applications ,Gene Expression Regulation, Neoplastic ,030220 oncology & carcinogenesis ,Female ,Curcumin ,QH301-705.5 ,DNA damage ,DNA repair ,RAD52 inhibitor ,Mice, Nude ,Antineoplastic Agents ,Breast Neoplasms ,Irinotecan ,Catalysis ,Article ,Inorganic Chemistry ,03 medical and health sciences ,medicine ,Animals ,Humans ,Physical and Theoretical Chemistry ,QD1-999 ,Molecular Biology ,neoplasms ,Cell Proliferation ,BRCA2 Protein ,Organic Chemistry ,BRCA mutation ,Cancer ,medicine.disease ,Xenograft Model Antitumor Assays ,Rad52 DNA Repair and Recombination Protein ,030104 developmental biology ,Cell culture ,synthetic lethal ,Cancer cell ,Mutation ,Cancer research ,Topoisomerase I Inhibitors ,Ovarian cancer ,DNA Damage - Abstract
BRCA mutation, one of the most common types of mutations in breast and ovarian cancer, has been suggested to be synthetically lethal with depletion of RAD52. Pharmacologically inhibiting RAD52 specifically eradicates BRCA-deficient cancer cells. In this study, we demonstrated that curcumin, a plant polyphenol, sensitizes BRCA2-deficient cells to CPT-11 by impairing RAD52 recombinase in MCF7 cells. More specifically, in MCF7-siBRCA2 cells, curcumin reduced homologous recombination, resulting in tumor growth suppression. Furthermore, a BRCA2-deficient cell line, Capan1, became resistant to CPT-11 when BRCA2 was reintroduced. In vivo, xenograft model studies showed that curcumin combined with CPT-11 reduced the growth of BRCA2-knockout MCF7 tumors but not MCF7 tumors. In conclusion, our data indicate that curcumin, which has RAD52 inhibitor activity, is a promising candidate for sensitizing BRCA2-deficient cells to DNA damage-based cancer therapies.
- Published
- 2021
5. Validation of bioactive components from traditional Chinese medicine for lifespan extension
- Author
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Chih-Ching Wu, Jiann-Jong Shen, Shu-Ling Yang, Tong-Hong Wang, Shu-Huei Wang, Wen-Chih Lee, Chia-Jen Wang, Tsong-Long Hwang, Yann-Lii Leu, Chun-Hao Feng, Chun-Yu Lai, Shu-Fang Cheng, Sien-Hung Yang, Ying-Chih Chi, Chi-Yuan Chen, Chin-Chuan Chen, Wei-Che Tseng, and Cheng-Hsin Kuo
- Subjects
Computer science ,Traditional Chinese medicine ,Extension (predicate logic) ,Data science - Abstract
In long history of traditional Chinese medicine (TCM), some single herb and complex formulas have been recorded to increase lifespan in TCM pharmacopeia. However, the mechanism of these TCMs increasing lifespan is insufficient. Here, we collected a list of TCMs from pharmacopeias for lifespan extension. By utilizing the mother enrichment program (MEP), we systematically screened these TCMs and identified a single TCM herb, Psoralea corylifolia, that increases lifespan in Saccharomyces cerevisiae. Next, twenty-two pure compounds were isolated from P. corylifolia, and one of the compounds, corylin, was shown to extend the replicative lifespan (RLS) by targeting the Gtr1 protein. Furthermore, in HUVECs, the RNA sequencing data showed that corylin ameliorated cellular senescence. Finally, corylin reduced the risk of death of mice fed a high-fat diet. Taken together, these findings demonstrate that corylin has long-term benefits for longevity and could be a potential treatment for age-related disease.
- Published
- 2021
6. The flavonoid corylin exhibits lifespan extension properties in mouse
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Tong-Hong Wang, Wei-Che Tseng, Yann-Lii Leu, Chi-Yuan Chen, Wen-Chih Lee, Ying-Chih Chi, Shu-Fang Cheng, Chun-Yu Lai, Chen-Hsin Kuo, Shu-Ling Yang, Sien-Hung Yang, Jiann-Jong Shen, Chun-Hao Feng, Chih-Ching Wu, Tsong-Long Hwang, Chia-Jen Wang, Shu-Huei Wang, and Chin-Chuan Chen
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Flavonoids ,Mammals ,Mice ,Multidisciplinary ,Longevity ,General Physics and Astronomy ,Animals ,Endothelial Cells ,General Chemistry ,Medicine, Chinese Traditional ,General Biochemistry, Genetics and Molecular Biology - Abstract
In the long history of traditional Chinese medicine, single herbs and complex formulas have been suggested to increase lifespan. However, the identification of single molecules responsible for lifespan extension has been challenging. Here, we collected a list of traditional Chinese medicines with potential longevity properties from pharmacopeias. By utilizing the mother enrichment program, we systematically screened these traditional Chinese medicines and identified a single herb, Psoralea corylifolia, that increases lifespan in Saccharomyces cerevisiae. Next, twenty-two pure compounds were isolated from Psoralea corylifolia. One of the compounds, corylin, was found to extend the replicative lifespan in yeast by targeting the Gtr1 protein. In human umbilical vein endothelial cells, RNA sequencing data showed that corylin ameliorates cellular senescence. We also examined an in vivo mammalian model, and found that corylin extends lifespan in mice fed a high-fat diet. Taken together, these findings suggest that corylin may promote longevity.
- Published
- 2020
7. Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease
- Author
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Todd Holyoak, Norman Tran, Jeremy T Rahkola, Zhiming Wang, Ying-Chih Chi, Edward N. Janoff, Elan Z. Eisenmesser, Jasmina S. Redzic, and Hongjin Zheng
- Subjects
0301 basic medicine ,Models, Molecular ,Proteases ,Science ,General Physics and Astronomy ,chemical and pharmacologic phenomena ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Virulence factor ,Article ,Microbiology ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,fluids and secretions ,stomatognathic system ,Catalytic Domain ,Streptococcus pneumoniae ,medicine ,Secretion ,Protease Inhibitors ,030212 general & internal medicine ,chemistry.chemical_classification ,Metalloproteinase ,Bacterial structural biology ,Multidisciplinary ,biology ,Cryoelectron Microscopy ,Serine Endopeptidases ,Antibodies, Monoclonal ,General Chemistry ,030104 developmental biology ,Enzyme ,chemistry ,Enzyme mechanisms ,biology.protein ,Biocatalysis ,Antibody ,Protein Binding - Abstract
Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since their discovery nearly 30 years ago despite the potential for developing vaccines that target these enzymes to block infection. Here we show through a series of cryo-electron microscopy single particle reconstructions how the Streptococcus pneumoniae IgA1 protease facilitates IgA1 substrate recognition and how this can be inhibited. Specifically, the Streptococcus pneumoniae IgA1 protease subscribes to an active-site-gated mechanism where a domain undergoes a 10.0 Å movement to facilitate cleavage. Monoclonal antibody binding inhibits this conformational change, providing a direct means to block infection at the host interface. These structural studies explain decades of biological and biochemical studies and provides a general strategy to block Streptococcus pneumoniae IgA1 protease activity to potentially prevent infection., Pathogenic IgA1 metalloproteases block the initial host immune response by cleaving host IgA1. Using cryoEM, the authors here provide structural insights into the substrate recognition mechanism of Streptococcus pneumoniae IgA1 protease, and develop a protease-inhibiting antibody.
- Published
- 2020
8. Structure basis for the modulation of CXC chemokine receptor 3 by antagonist AMG487
- Author
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Haizhan Jiao, Bin Pang, Ying-Chih Chiang, Qiang Chen, Qi Pan, Ruobing Ren, and Hongli Hu
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Cytology ,QH573-671 - Published
- 2023
- Full Text
- View/download PDF
9. Streptococcus pneumoniaeIgA1 protease: A metalloprotease that can catalyze in a split mannerin vitro
- Author
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Jeremy T Rahkola, Thomas S. Roberts, Agnieszka A. Kendrick, Michael J. Holliday, Elan Z. Eisenmesser, Ying-Chih Chi, Edward N. Janoff, and Natasia Paukovich
- Subjects
0301 basic medicine ,Metalloproteinase ,Proteases ,Architecture domain ,030106 microbiology ,Protein domain ,Biology ,medicine.disease_cause ,Biochemistry ,Virulence factor ,Bacterial cell structure ,respiratory tract diseases ,Microbiology ,Serine ,03 medical and health sciences ,030104 developmental biology ,Streptococcus pneumoniae ,medicine ,Molecular Biology - Abstract
IgA1 proteases (IgA1P) from diverse pathogenic bacteria specifically cleave human immunoglobulin A1 (IgA1) at the hinge region, thereby thwarting protective host immune responses. Streptococcus pneumoniae (S. pneumoniae) IgA1P shares no sequence conservation with serine or cysteine types of IgA1Ps or other known proteins, other than a conserved HExxH Zn-binding motif (1604-1608) found in metalloproteases. We have developed a novel expression system to produce the mature S. pneumoniae IgA1P and we have discovered that this form is both attached to the bacterial cell surface and released in its full form. Our data demonstrate that the S. pneumoniae IgA1P comprises two distinct regions that associate to form an active metalloprotease, the first such example of a metalloprotease that can be split in vitro and recombined to form an active enzyme. By capitalizing on this novel domain architecture, we show that the N-terminal region of S. pneumoniae IgA1P comprises the primary binding region for IgA1, although the C-terminal region of S. pneumoniae IgA1P is necessary for cleavage of IgA1. Our findings lend insight into the protein domain architecture of the S. pneumoniae IgA1P and function of this important virulence factor for S. pneumoniae infection.
- Published
- 2017
10. Streptococcus pneumoniae G5 domains bind different ligands
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Jasmina S. Redzic, Kirk C. Hansen, Natasia Paukovich, Elan Z. Eisenmesser, Aaron Issaian, Jeremy T Rahkola, Ying-Chih Chi, Edward N. Janoff, and Ashley Blue
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Models, Molecular ,Full‐Length Papers ,Context (language use) ,medicine.disease_cause ,Ligands ,Biochemistry ,Bacterial Adhesion ,03 medical and health sciences ,Bacterial Proteins ,Streptococcus pneumoniae ,Hydrolase ,medicine ,Cell adhesion ,Molecular Biology ,Nuclear Magnetic Resonance, Biomolecular ,030304 developmental biology ,0303 health sciences ,biology ,Chemistry ,030302 biochemistry & molecular biology ,Biofilm ,Ligand (biochemistry) ,biology.organism_classification ,Small molecule ,3. Good health ,Biophysics ,Bacteria - Abstract
Many bacterial pathogens express small G5 domains that exist in the context of various membrane-anchored proteins and these G5 domains have been associated with colonization, cellular adhesion, and biofilm formation. However, despite over a decade since the computational prediction of these G5 domains, many remain uncharacterized, particularly those from Streptococcus pneumoniae. Of five previously predicted G5 domains we found that four of these, all derived from S. pneumoniae, are independently folded modules. As one of these exhibits extreme line broadening due to self-association, we were able to use NMR solution studies to probe the potential ligand interactions of the remaining three G5 domains. None of these G5 domains engage N-acetylglucosamine (NAG) as previously predicted but do interact with other small molecules that may modulate adherence to both bacteria and host cells. Specifically, while all G5 domains tested engage Zn, only one of these G5 domains engage heparin. NMR solution structural studies of the IgA1 Protease G5 (IgA1P-G5) and endo-beta-N-acetylglucosaminidase-D G5 (ENDD-G5) also facilitated identification of the ligand binding sites and confirm the typical G5 fold that comprises two connected β-sheets with no canonical core. NMR relaxation experiments indicate flexibility on both ends and within the connecting regions between the β-sheets. Our studies thus establish a basis for future biological experiments to test whether the ligands presented here are involved in bacterial adherence, either to bacteria or to host cells.
- Published
- 2019
11. Residue Histidine 50 Plays a Key Role in Protecting α-Synuclein from Aggregation at Physiological pH
- Author
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Ying-Chih Chi, Geoffrey S. Armstrong, David N. M. Jones, Chang-Wei Liu, and Elan Z. Eisenmesser
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animal diseases ,Mutant ,Buffers ,Protein aggregation ,Biochemistry ,chemistry.chemical_compound ,Residue (chemistry) ,Neurobiology ,Electrochemistry ,Humans ,Histidine ,Nuclear Magnetic Resonance, Biomolecular ,Molecular Biology ,Alpha-synuclein ,Chemistry ,fungi ,food and beverages ,Parkinson Disease ,Cell Biology ,Hydrogen-Ion Concentration ,nervous system diseases ,Glutamine ,nervous system ,Amino Acid Substitution ,Unfolded Protein Response ,alpha-Synuclein ,Unfolded protein response ,Synuclein - Abstract
α-Synuclein (αSyn) aggregation is involved in the pathogenesis of Parkinson disease (PD). Recently, substitution of histidine 50 in αSyn with a glutamine, H50Q, was identified as a new familial PD mutant. Here, nuclear magnetic resonance (NMR) studies revealed that the H50Q substitution causes an increase of the flexibility of the C-terminal region. This finding provides direct evidence that this PD-causing mutant can mediate long range effects on the sampling of αSyn conformations. In vitro aggregation assays showed that substitution of His-50 with Gln, Asp, or Ala promotes αSyn aggregation, whereas substitution with the positively charged Arg suppresses αSyn aggregation. Histidine carries a partial positive charge at neutral pH, and so our result suggests that positively charged His-50 plays a role in protecting αSyn from aggregation under physiological conditions.
- Published
- 2014
12. Streptococcus pneumoniae IgA1 protease: A metalloprotease that can catalyze in a split manner in vitro
- Author
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Ying-Chih, Chi, Jeremy T, Rahkola, Agnieszka A, Kendrick, Michael J, Holliday, Natasia, Paukovich, Thomas S, Roberts, Edward N, Janoff, and Elan Z, Eisenmesser
- Subjects
Streptococcus pneumoniae ,Bacterial Proteins ,Protein Domains ,Virulence Factors ,Amino Acid Motifs ,Serine Endopeptidases ,Articles ,Catalysis ,respiratory tract diseases - Abstract
IgA1 proteases (IgA1P) from diverse pathogenic bacteria specifically cleave human immunoglobulin A1 (IgA1) at the hinge region, thereby thwarting protective host immune responses. Streptococcus pneumoniae (S. pneumoniae) IgA1P shares no sequence conservation with serine or cysteine types of IgA1Ps or other known proteins, other than a conserved HExxH Zn‐binding motif (1604‐1608) found in metalloproteases. We have developed a novel expression system to produce the mature S. pneumoniae IgA1P and we have discovered that this form is both attached to the bacterial cell surface and released in its full form. Our data demonstrate that the S. pneumoniae IgA1P comprises two distinct regions that associate to form an active metalloprotease, the first such example of a metalloprotease that can be split in vitro and recombined to form an active enzyme. By capitalizing on this novel domain architecture, we show that the N‐terminal region of S. pneumoniae IgA1P comprises the primary binding region for IgA1, although the C‐terminal region of S. pneumoniae IgA1P is necessary for cleavage of IgA1. Our findings lend insight into the protein domain architecture of the S. pneumoniae IgA1P and function of this important virulence factor for S. pneumoniae infection.
- Published
- 2016
13. The Catalytic Determinants of Streptococcal Pneumoniae IgA1 Protease are Formed by Multiple Domains
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Edward N. Janoff, Agnieszka A. Kendrick, Ying-Chih Chi, Jeremy T Rahkola, and Elan Z. Eisenmesser
- Subjects
Serotype ,Metalloproteinase ,Protease ,biology ,medicine.drug_class ,medicine.medical_treatment ,Antibiotics ,Biophysics ,medicine.disease_cause ,biology.organism_classification ,Virology ,Microbiology ,Streptococcus pneumoniae ,medicine ,biology.protein ,CTD ,Antibody ,Bacteria - Abstract
Streptococcus pneumoniae (SPN) is a gram-positive bacterium which causes non-invasive infections, such as otitis media, as well as invasive diseases like pneumonia and meningitis. Despite the development of bacterial antibiotics and vaccines, exposure to SPN still leads to diseases in young, elderly, and immunocompromised individuals. Current vaccines have serious limitations due to the serotype variability and genomic plasticity of the bacterium and therefore, an ever-increasing frequency of multidrug-resistant strains have been reported. Immunoglobulin A1 (IgA1) represents 90% of the IgA within the human respiratory tract and multiple bacterial pathogens, including SPN, can produce an IgA1-specific protease (IgA1P) to inactivate this major component of mucosal immunity. IgA1P cleaves IgA1 at the hinge region and leads to removal of the Fc domain of IgA1, which is recognized by host clearance mechanisms. Because of the universal expression among different serotypes of SPN, IgA1P has been shown to be a potential target for new vaccine development. SPN IgA1P is unique with no sequence conservation to any other known protein, other than a conserved HExxH Zn-binding motif found in many metalloproteases. We have discovered that the SPN IgA1P released from cells is active and our biochemical studies have revealed that the SPN IgA1P contains a well-folded C-terminal domain (CTD) that houses the third Zn coordinating residue, Glu1628. Furthermore, our data illustrates that the N-terminal domain (NTD) is primarily responsible for engaging IgA1 and the CTD does not have detectable affinity for IgA1 by itself. However, the CTD does play a role in facilitating the binding and is essential for the catalytic activity. Our discoveries shed light on the mechanistic details of this novel metalloprotease and potentially help in developing better vaccines.
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- 2016
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- View/download PDF
14. JNK signaling pathway is required for bFGF-mediated surface cadherin downregulation on HUVEC
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Chia-Jen Wang, Woei-Yau Kao, Wei-Hwa Chen, Jen-Chine Wu, Ying-Chih Chi, Horng-Chin Yan, and Wei-Teing Chen
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MAPK/ERK pathway ,Cell signaling ,Angiogenesis ,Basic fibroblast growth factor ,Down-Regulation ,Neovascularization, Physiologic ,Cell Communication ,Biology ,Adherens junction ,chemistry.chemical_compound ,Downregulation and upregulation ,Cell Adhesion ,Humans ,RNA, Messenger ,Receptor, Fibroblast Growth Factor, Type 1 ,Enzyme Inhibitors ,Cell adhesion ,Cells, Cultured ,Anthracenes ,Cadherin ,Infant, Newborn ,JNK Mitogen-Activated Protein Kinases ,Adherens Junctions ,Cell Biology ,Cadherins ,Cell biology ,chemistry ,cardiovascular system ,Fibroblast Growth Factor 2 ,ras Guanine Nucleotide Exchange Factors ,Endothelium, Vascular ,Protein Processing, Post-Translational ,Signal Transduction - Abstract
Angiogenesis, the process of new blood vessel formation, is important in wound healing, inflammation, tumorigenesis and metastases. During this process, it is a critical step of the loosening of cellular interactions between endothelial cells, which are dependent on the architecture of adherens junction constructed by homophilic interactions of cell surface cadherins. Several studies suggested that the dynamic changes of cadherins are necessary during angiogenesis. However, the mechanism of cadherins regulation on endothelial cells requires further delineation. Here, we showed that basic fibroblast growth factor (bFGF), a pivotal pro-angiogenic factor, can downregulate typical cadherins (E-, N-, P- and VE-cadherin) expression on the surface of human umbilical vein endothelial cells (HUVECs) via FGF receptor 1 (FGFR1) signaling. The bFGF-mediated surface cadherin downregulation was significantly reversed only when the HUVECs were treated with JNK inhibitor (SP600125), but not ERK (PD98059) or p38 inhibitor (SB203580). Infecting HUVECs with a dominant negative H-Ras mutant (Ras(S17N)) interferes bFGF-mediated cadherin downregulation, and the result suggests that bFGF attenuates surface cadherin expression on HUVECs via FGFR1 and intracellular Ras-JNK signaling. However, after growth factors withdrawal, FGFR1 blockade or JNK inhibition for 16 h, cadherins were re-expressed on cell surface of HUVECs. But the mRNA or total protein of cadherins had no significant change, suggesting that the effect of bFGF on cadherin expression may work through a post-translational control. Our data first suggest that JNK participates in bFGF-mediated surface cadherin downregulation. Loss of surface cadherins may affect the cell-cell interaction between endothelial cells and facilitate angiogenesis.
- Published
- 2008
15. Subject Index Vol. 10, 2003
- Author
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Mei-Sue Chen, Jen-Hwey Chiu, Hsing I. Chen, Wann-Cherng Perng, Jianning Wei, Chien-Hung Chen, Ya-Chen Liu, Małgorzata Szereda-Przestaszewska, Hong-Jen Lee, Sumio Sugano, Shu-Min Lin, Ann-Ping Tsou, Stephen C. Fowler, Chu-Wen Yang, Annelies Hauspie, Nada H. Khattar, Jen-Chine Wu, Wei-Kuang Liu, Richard B. Markham, David Camerini, Rong Chen, Christine Neuveut, Yi-Da Chung, Seng-Sheen Fan, Chien-Wen Hou, Chien-Huang Lin, Meng-Chun Hu, Carl Denef, Chin-Pyng Wu, Chien-Ying Liu, Marcin Rozalski, Ing-Cherng Guo, Yi-Ting Chen, Chen-Kung Chou, Y.S. Chan, Wei-Teing Chen, Luo-Hwa Miau, Jin-Tun Lin, Chain Fa Su, Chia-Hua Kuo, Laura De Marchis, Mei-Ling Chang, Chih-Ten Yu, Cezary Watala, Yu-Lun Liao, Eve Seuntjens, Vivian C. Yang, Di Sha, Wen-Hsin Huang, Horng-Chyuan Lin, Chun-Chung Lee, D.K.Y. Shum, Yu-Chi Chuang, Jung-Yaw Lin, Wan-An Lu, Jacek Golanski, Ben Berkhout, Cheng-Deng Kuo, Hsin-Yi Ho, Kerry Wu, Vincent J. Blanch, Wen-Chang Chang, Jang-Yen Wu, Chun-Hua Wang, Daniel Cupac, Kou-Gi Shyu, David Wang, Wen-Hsin Chang, Han-Pin Kuo, Ching-Hung Lin, Che-Yi Chao, Sharon Bargo, Chia-Chu Tsai, Jui-Fen Lin, K.K.L. Yung, Ru Ping Lee, Michael M.C. Lai, Beata Kopczyńska, June L. Traicoff, Wei-Ting Chao, Yutaka Suzuku, Charlotte S. Kaetzel, Kuan-Teh Jeang, Ying Jin, Kun-Ze Lee, Ying-Chih Chi, Robert M. Scoggins, Shankung Lin, Bao-Wei Wang, Shang Jyh Kao, Rodolfo E. Zamora, Britten L. Ginsburg, I-Jung Lu, Heng Wu, Ding-Shinn Chen, Bon Chu Chung, Hang Chang, Boguslawa Luzak, Yu-Ling Sung, Albert M. Wu, Wen-Chih Lee, C.H. Lai, Dennis J. Templeton, Yu-Chia Su, P.C. Joost Haasnoot, Jin-Yuan Su, Hugo Vankelecom, Daniel Fu-Chang Tsai, Fu-Chiu Yu, L.W. Chen, John T. Kung, Ling-Ling Chiou, Hsuan-Shu Lee, F.X. Zhang, Sarah J. Plummer, Guan-Tarn Huang, Pei-Ming Yang, Shih-Wei Chou, Horng-Chin Yan, Li-Chi Ku, Yun-Hen Liu, Samuel H.H. Chan, Ji-Chuu Hwang, Jin-Chuan Sheu, Ching-jang Huang, Shiow-Chwen Tsai, and Graham Casey
- Subjects
Index (economics) ,Endocrinology, Diabetes and Metabolism ,Biochemistry (medical) ,Clinical Biochemistry ,Statistics ,Pharmacology (medical) ,Subject (documents) ,Cell Biology ,General Medicine ,Molecular Biology ,Mathematics - Published
- 2003
16. Contents Vol. 10, 2003
- Author
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Jin-Chuan Sheu, Hong-Jen Lee, Ching-jang Huang, Chien-Hung Chen, Fu-Chiu Yu, Shiow-Chwen Tsai, Pei-Ming Yang, Li-Chi Ku, Chia-Hua Kuo, Graham Casey, Ji-Chuu Hwang, Ya-Chen Liu, Seng-Sheen Fan, Chien-Wen Hou, Rodolfo E. Zamora, Y.S. Chan, Sarah J. Plummer, Jen-Chine Wu, Chien-Ying Liu, Bon Chu Chung, Mei-Sue Chen, Chen-Kung Chou, Horng-Chyuan Lin, Guan-Tarn Huang, Hsing I. Chen, Wei-Teing Chen, Laura De Marchis, F.X. Zhang, Cezary Watala, Jung-Yaw Lin, Yi-Ting Chen, D.K.Y. Shum, Nada H. Khattar, Kerry Wu, Mei-Ling Chang, Charlotte S. Kaetzel, Che-Yi Chao, Ing-Cherng Guo, Chin-Pyng Wu, Vincent J. Blanch, Beata Kopczyńska, Ben Berkhout, Yu-Lun Liao, Jui-Fen Lin, Wen-Hsin Huang, Cheng-Deng Kuo, Daniel Cupac, K.K.L. Yung, David Wang, Han-Pin Kuo, Wei-Ting Chao, Yutaka Suzuku, Yu-Chia Su, Chun-Hua Wang, Kun-Ze Lee, Ying-Chih Chi, Yu-Chi Chuang, P.C. Joost Haasnoot, I-Jung Lu, Albert M. Wu, Ding-Shinn Chen, Dennis J. Templeton, Ching-Hung Lin, Wen-Chih Lee, Jin-Yuan Su, C.H. Lai, Hugo Vankelecom, Britten L. Ginsburg, Wen-Hsin Chang, Heng Wu, Bao-Wei Wang, Shang Jyh Kao, Wan-An Lu, Jin-Tun Lin, Daniel Fu-Chang Tsai, Wei-Kuang Liu, Hang Chang, Boguslawa Luzak, Chih-Ten Yu, Hsin-Yi Ho, Yu-Ling Sung, Shu-Min Lin, Sharon Bargo, Wen-Chang Chang, Annelies Hauspie, Michael M.C. Lai, L.W. Chen, Yi-Da Chung, John T. Kung, Ling-Ling Chiou, Hsuan-Shu Lee, Jianning Wei, Chu-Wen Yang, David Camerini, June L. Traicoff, Marcin Rozalski, Vivian C. Yang, Jacek Golanski, Di Sha, Małgorzata Szereda-Przestaszewska, Robert M. Scoggins, Shankung Lin, Ru Ping Lee, Rong Chen, Yun-Hen Liu, Meng-Chun Hu, Samuel H.H. Chan, Ann-Ping Tsou, Stephen C. Fowler, Richard B. Markham, Shih-Wei Chou, Carl Denef, Jen-Hwey Chiu, Kuan-Teh Jeang, Chien-Huang Lin, Ying Jin, Horng-Chin Yan, Chain Fa Su, Eve Seuntjens, Sumio Sugano, Chun-Chung Lee, Wann-Cherng Perng, Christine Neuveut, Kou-Gi Shyu, Chia-Chu Tsai, Jang-Yen Wu, and Luo-Hwa Miau
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Endocrinology, Diabetes and Metabolism ,Biochemistry (medical) ,Clinical Biochemistry ,Pharmacology (medical) ,Cell Biology ,General Medicine ,Molecular Biology - Published
- 2003
17. The Protective Effect of Adenosine Triphosphate-MgCl2 on Ischemia-Reperfusion Lung Injury Is Leukocyte Dependent
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Wei-Teing Chen, Wen-Hsin Huang, David Wang, Fu-Chiu Yu, Ying-Chih Chi, Jen-Chine Wu, Kerry Wu, Wann-Cherng Perng, Chin-Pyng Wu, and Horng-Chin Yan
- Subjects
Endocrinology, Diabetes and Metabolism ,Biochemistry (medical) ,Clinical Biochemistry ,Pharmacology (medical) ,Cell Biology ,General Medicine ,Molecular Biology - Published
- 2003
18. ABPCaps: A Novel Capsule Network-Based Method for the Prediction of Antibacterial Peptides
- Author
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Lantian Yao, Yuxuan Pang, Jingting Wan, Chia-Ru Chung, Jinhan Yu, Jiahui Guan, Clement Leung, Ying-Chih Chiang, and Tzong-Yi Lee
- Subjects
antibacterial peptide ,capsule network ,feature extraction ,deep learning ,antibiotic resistance ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Biology (General) ,QH301-705.5 ,Physics ,QC1-999 ,Chemistry ,QD1-999 - Abstract
The emergence of drug resistance among pathogens has become a major challenge to human health on a global scale. Among them, antibiotic resistance is already a critical issue, and finding new therapeutic agents to address this problem is therefore urgent. One of the most promising alternatives to antibiotics are antibacterial peptides (ABPs), i.e., short peptides with antibacterial activity. In this study, we propose a novel ABP recognition method, called ABPCaps. It integrates a convolutional neural network (CNN), a long short-term memory (LSTM), and a new type of neural network named the capsule network. The capsule network can extract critical features automatically from both positive and negative samples, leading to superior performance of ABPCaps over all baseline models built on hand-crafted peptide descriptors. Evaluated on independent test sets, ABPCaps achieves an accuracy of 93.33% and an F1-score of 91.34%, and consistently outperforms the baseline models in other extensive experiments as well. Our study demonstrates that the proposed ABPCaps, built on the capsule network method, is a valuable addition to the current state-of-the-art in the field of ABP recognition and has significant potential for further development.
- Published
- 2023
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19. Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism
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Yufei Han, Qian Zhuang, Bo Sun, Wenping Lv, Sheng Wang, Qingjie Xiao, Bin Pang, Youli Zhou, Fuxing Wang, Pengliang Chi, Qisheng Wang, Zhen Li, Lizhe Zhu, Fuping Li, Dong Deng, Ying-Chih Chiang, Zhenfei Li, and Ruobing Ren
- Subjects
Science - Abstract
Steroid 5α-reductase 2 (SRD5A2), a testosterone metabolism enzyme, is implicated in human disease. Structural and biochemical analyses of PbSRD5A, a bacterial homolog, reveal SRD5A2 substrate binding pocket and provide framework for the design of new drugs targeting this enzyme.
- Published
- 2021
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- View/download PDF
20. Defining a Link with Autosomal-Dominant Polycystic Kidney Disease in Mice with Congenitally Low Expression of Pkd1
- Author
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Si Tse Jiang, Chi-Kuang Leo Wang, Hsiu Kuan Lin, Yuan Yow Chiou, Hung Li, Ying Chih Chi, Ellian Wang, Ming Jer Tang, and Yuan Ta Lin
- Subjects
medicine.medical_specialty ,Receptors, Vasopressin ,TRPP Cation Channels ,Blotting, Western ,Autosomal dominant polycystic kidney disease ,Cre recombinase ,Apoptosis ,Biology ,urologic and male genital diseases ,Article ,Pathology and Forensic Medicine ,Mice ,Epidermal growth factor ,Internal medicine ,medicine ,Polycystic kidney disease ,In Situ Nick-End Labeling ,Animals ,Cyst ,Mice, Knockout ,Polycystic Kidney Diseases ,Aquaporin 2 ,PKD1 ,Epidermal Growth Factor ,urogenital system ,Reverse Transcriptase Polymerase Chain Reaction ,Proteins ,medicine.disease ,Immunohistochemistry ,female genital diseases and pregnancy complications ,ErbB Receptors ,Disease Models, Animal ,Endocrinology ,Targeted Mutation ,Mutation ,Intercellular Signaling Peptides and Proteins ,Sodium-Potassium-Exchanging ATPase ,Kidney disease ,Heparin-binding EGF-like Growth Factor - Abstract
Mouse models for autosomal-dominant polycystic kidney disease (ADPKD), derived from homozygous targeted disruption of Pkd1 gene, generally die in utero or perinatally because of systemic defects. We introduced a loxP site and a loxP-flanked mc1-neo cassette into introns 30 and 34, respectively, of the Pkd1 locus to generate a conditional, targeted mutation. Significantly, before excision of the floxed exons and mc1-neo from the targeted locus by Cre recombinase, mice homozygous for the targeted allele appeared normal at birth but developed polycystic kidney disease with a slower progression than that of Pkd-null mice. Further, the homozygotes continued to produce low levels of full-length Pkd1-encoded protein, suggesting that slight Pkd1 expression is sufficient for renal cyst formation in ADPKD. In this viable model, up-regulation of heparin-binding epidermal growth factor-like growth factor accompanied increased epidermal growth factor receptor signaling, which may be involved in abnormal proliferation of the cyst-lining epithelia. Increased apoptosis in cyst epithelia was only observed in the later period that correlated with the cyst regression. Abnormalities in Na(+)/K(+)-ATPase, aquaporin-2, and vasopressin V2 receptor expression were also identified. This mouse model may be suitable for further studies of progression and therapeutic interventions of ADPKD.
- Published
- 2006
21. The protective effect of adenosine triphosphate-MgCl2 on ischemia-reperfusion lung injury is leukocyte dependent
- Author
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Horng-Chin Yan, Wann-Cherng Perng, Chin-Pyng Wu, David Wang, Ying-Chih Chi, Fu-Chiu Yu, Kerry Wu, Jen-Chine Wu, Wen-Hsin Huang, and Wei-Teing Chen
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inorganic chemicals ,Male ,medicine.medical_specialty ,Endocrinology, Diabetes and Metabolism ,Clinical Biochemistry ,Ischemia ,Vascular permeability ,Lung injury ,Capillary Permeability ,Rats, Sprague-Dawley ,chemistry.chemical_compound ,Adenosine Triphosphate ,In vivo ,medicine.artery ,Internal medicine ,medicine ,Leukocytes ,Animals ,Pharmacology (medical) ,Pulmonary Wedge Pressure ,Molecular Biology ,Lung ,business.industry ,Biochemistry (medical) ,Cell Biology ,General Medicine ,medicine.disease ,Adenosine ,Rats ,Perfusion ,Endocrinology ,medicine.anatomical_structure ,chemistry ,Anesthesia ,Reperfusion Injury ,Pulmonary artery ,business ,Adenosine triphosphate ,Bronchoalveolar Lavage Fluid ,medicine.drug - Abstract
Adenosine triphosphate (ATP)-MgCl(2) attenuates ischemia-reperfusion (I-R)-induced lung injury in rats. A previous study indirectly suggests that Mg(2+)-dependent ecto-ATPases on the surface of leukocytes are responsible for the hydrolysis of ATP-MgCl(2) to adenosine, which then contributes to the protective effect of ATP-MgCl(2). This study investigated the role of leukocytes in I-R injury and the protective effect of ATP-MgCl(2) in our buffer-perfused isolated rat lung model. After isolating the lung blood flow of adult male Sprague-Dawley rats, the lungs were perfused through the pulmonary artery cannula with a physiologic salt solution containing human serum albumin. The protective effect of ATP-MgCl(2) pretreatment with or without leukocytes was investigated. Capillary permeability (K(fc)), lung weight gain (LWG), lung wet weight/body weight ratio (LW/BW), lung lavage protein concentration (LPC) and pulmonary artery pressure (PAP) were measured. I-R produced a significant increase in K(fc), LWG, LW/BW, LPC, and PAP. The increases in these indices were significantly attenuated by pretreatment with ATP-MgCl(2) (1 x 10(-6)M) together with leukocytes (2.9 x 10(6)/ml in the perfusate) but not with ATP-MgCl(2) alone. Our data suggest that I-R-induced acute lung injury is not dependent on circulating leukocytes. Pretreatment with ATP-MgCl(2) plus leukocytes but not ATP-MgCl(2) alone had protective effects against I-R lung injury. Whether these findings occur in vivo could not be determined in this study. In our isolated lung red blood cell-free perfusate system, the protective effect of ATP-MgCl(2) requires the presence of leukocytes.
- Published
- 2003
22. Exploring the Chemical Space of CYP17A1 Inhibitors Using Cheminformatics and Machine Learning
- Author
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Tianshi Yu, Tianyang Huang, Leiye Yu, Chanin Nantasenamat, Nuttapat Anuwongcharoen, Theeraphon Piacham, Ruobing Ren, and Ying-Chih Chiang
- Subjects
CYP17A1 ,prostate cancer ,cheminformatics ,quantitative structure–activity relationship ,Murcko scaffold ,Organic chemistry ,QD241-441 - Abstract
Cytochrome P450 17A1 (CYP17A1) is one of the key enzymes in steroidogenesis that produces dehydroepiandrosterone (DHEA) from cholesterol. Abnormal DHEA production may lead to the progression of severe diseases, such as prostatic and breast cancers. Thus, CYP17A1 is a druggable target for anti-cancer molecule development. In this study, cheminformatic analyses and quantitative structure–activity relationship (QSAR) modeling were applied on a set of 962 CYP17A1 inhibitors (i.e., consisting of 279 steroidal and 683 nonsteroidal inhibitors) compiled from the ChEMBL database. For steroidal inhibitors, a QSAR classification model built using the PubChem fingerprint along with the extra trees algorithm achieved the best performance, reflected by the accuracy values of 0.933, 0.818, and 0.833 for the training, cross-validation, and test sets, respectively. For nonsteroidal inhibitors, a systematic cheminformatic analysis was applied for exploring the chemical space, Murcko scaffolds, and structure–activity relationships (SARs) for visualizing distributions, patterns, and representative scaffolds for drug discoveries. Furthermore, seven total QSAR classification models were established based on the nonsteroidal scaffolds, and two activity cliff (AC) generators were identified. The best performing model out of these seven was model VIII, which is built upon the PubChem fingerprint along with the random forest algorithm. It achieved a robust accuracy across the training set, the cross-validation set, and the test set, i.e., 0.96, 0.92, and 0.913, respectively. It is anticipated that the results presented herein would be instrumental for further CYP17A1 inhibitor drug discovery efforts.
- Published
- 2023
- Full Text
- View/download PDF
23. Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).
- Author
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Ying-Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing-Ke Weng, and Yi Wang
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Substrate permissiveness has long been regarded as the raw materials for the evolution of new enzymatic functions. In land plants, hydroxycinnamoyltransferase (HCT) is an essential enzyme of the phenylpropanoid metabolism. Although essential enzymes are normally associated with high substrate specificity, HCT can utilize a variety of non-native substrates. To examine the structural and dynamic basis of substrate permissiveness in this enzyme, we report the crystal structure of HCT from Selaginella moellendorffii and molecular dynamics (MD) simulations performed on five orthologous HCTs from several major lineages of land plants. Through altogether 17-μs MD simulations, we demonstrate the prevalent swing motion of an arginine handle on a submicrosecond timescale across all five HCTs, which plays a key role in native substrate recognition by these intrinsically promiscuous enzymes. Our simulations further reveal how a non-native substrate of HCT engages a binding site different from that of the native substrate and diffuses to reach the catalytic center and its co-substrate. By numerically solving the Smoluchowski equation, we show that the presence of such an alternative binding site, even when it is distant from the catalytic center, always increases the reaction rate of a given substrate. However, this increase is only significant for enzyme-substrate reactions heavily influenced by diffusion. In these cases, binding non-native substrates 'off-center' provides an effective rationale to develop substrate permissiveness while maintaining the native functions of promiscuous enzymes.
- Published
- 2018
- Full Text
- View/download PDF
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