1
|
Puri S, Liu CY, Hu IC, Lai CH, Hsu STD, Lyu PC. Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions. Biochem Biophys Res Commun 2023; 672:81-88. [PMID: 37343318 DOI: 10.1016/j.bbrc.2023.06.021] [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: 05/29/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
CP74 is an engineered circular permutant of a deep trefoil knotted SpoU-TrmD (SPOUT) RNA methyl transferase protein YbeA from E. coli. We have previously established that the circular permutation unties the knotted topology of YbeA and CP74 forms a domain-swapped dimer with a large dimeric interface of ca. 4600 Å2. To understand the impact of domain-swapping and the newly formed hinge region joining the two folded domains on the folding and stability of CP74, the five equally spaced tryptophan residues were individually substituted into phenylalanine to monitor their conformational and stability changes by a battery of biophysical tools. Far-UV circular dichroism, intrinsic fluorescence, and small-angle X-ray scattering dictated minimal global conformational perturbations to the native structures in the tryptophan variants. The structures of the tryptophan variants also showed the conservation of the domain-swapped ternary structure with the exception that the W72F exhibited significant asymmetry in the α-helix 5. Comparative global thermal and chemical stability analyses indicated the pivotal role of W100 in the folding of CP74 followed by W19 and W72. Solution-state NMR spectroscopy and hydrogen-deuterium exchange mass spectrometry further revealed the accumulation of a native-like intermediate state in which the hinge region made important contributions to maintain the domain-swapped ternary structure of CP74.
Collapse
Affiliation(s)
- Sarita Puri
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Yu Liu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - I-Chen Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima, 739-8527, Japan.
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| |
Collapse
|
2
|
Lyu PC, Zhu WY, Lu HY. [State of recurrent IgG4-related sclerosing cholangitis during the course of hormone therapy: a case report]. Zhonghua Gan Zang Bing Za Zhi 2023; 31:538-541. [PMID: 37365032 DOI: 10.3760/cma.j.cn501113-20230401-00138] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Affiliation(s)
- P C Lyu
- Department of infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - W Y Zhu
- Department of infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - H Y Lu
- Department of infectious Diseases, Peking University First Hospital, Beijing 100034, China
| |
Collapse
|
3
|
Lyu PC, Wu L. [Diagnosis and differential diagnosis of arrhythmogenic cardiomyopathy]. Zhonghua Nei Ke Za Zhi 2022; 61:1069-1073. [PMID: 36008305 DOI: 10.3760/cma.j.cn112138-20211019-00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- P C Lyu
- Department of Cardiology, Peking University First Hospital, Beijing 100034, China
| | - L Wu
- Department of Cardiology, Peking University First Hospital, Beijing 100034, China
| |
Collapse
|
4
|
Huang PJ, Huang CY, Li YX, Liu YC, Chu LJ, Yeh YM, Cheng WH, Chen RM, Lee CC, Chen LC, Lin HC, Chiu SF, Lin WN, Lyu PC, Tang P, Huang KY. Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death. Biomedicines 2021; 9:biomedicines9121817. [PMID: 34944632 PMCID: PMC8698965 DOI: 10.3390/biomedicines9121817] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent non-viral sexually transmitted infection worldwide. Metronidazole (MTZ) is the mainstay of anti-trichomonal chemotherapy; however, drug resistance has become an increasingly worrying issue. Additionally, the molecular events of MTZ-induced cell death in T. vaginalis remain elusive. To gain insight into the differential expression of genes related to MTZ resistance and cell death, we conducted RNA-sequencing of three paired MTZ-resistant (MTZ-R) and MTZ-sensitive (MTZ-S) T. vaginalis strains treated with or without MTZ. Comparative transcriptomes analysis identified that several putative drug-resistant genes were exclusively upregulated in different MTZ-R strains, such as ATP-binding cassette (ABC) transporters and multidrug resistance pumps. Additionally, several shared upregulated genes among all the MTZ-R transcriptomes were not previously identified in T. vaginalis, such as 5′-nucleotidase surE and Na+-driven multidrug efflux pump, which are a potential stress response protein and a multidrug and toxic compound extrusion (MATE)-like protein, respectively. Functional enrichment analysis revealed that purine and pyrimidine metabolisms were suppressed in MTZ-S parasites upon drug treatment, whereas the endoplasmic reticulum-associated degradation (ERAD) pathway, proteasome, and ubiquitin-mediated proteolysis were strikingly activated, highlighting the novel pathways responsible for drug-induced stress. Our work presents the most detailed analysis of the transcriptional changes and the regulatory networks associated with MTZ resistance and MTZ-induced signaling, providing insights into MTZ resistance and cell death mechanisms in trichomonads.
Collapse
Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City 333, Taiwan;
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
| | - Ching-Yun Huang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei City 114, Taiwan; (C.-Y.H.); (S.-F.C.)
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
| | - Yu-Xuan Li
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
| | - Yi-Chung Liu
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan; (Y.-C.L.); (P.-C.L.)
| | - Lichieh-Julie Chu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City 333, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
| | - Wei-Hung Cheng
- Department of Medical Laboratory Science, College of Medicine, I-Shou University, Kaohsiung City 824, Taiwan;
| | - Ruei-Ming Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City 114, Taiwan; (R.-M.C.); (H.-C.L.)
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City 333, Taiwan; (Y.-M.Y.); (C.-C.L.)
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan City 333, Taiwan
| | - Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City 252, Taiwan;
| | - Hsin-Chung Lin
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City 114, Taiwan; (R.-M.C.); (H.-C.L.)
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan
| | - Shu-Fang Chiu
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei City 114, Taiwan; (C.-Y.H.); (S.-F.C.)
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
- Department of Inspection, Taipei City Hospital, Renai Branch, Taipei City 114, Taiwan
| | - Wei-Ning Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 242, Taiwan;
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan; (Y.-C.L.); (P.-C.L.)
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City 333, Taiwan; (Y.-X.L.); (L.-J.C.); (P.T.)
| | - Kuo-Yang Huang
- Host-Parasite Interactions Laboratory, National Defense Medical Center, Taipei City 114, Taiwan
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City 114, Taiwan
- Correspondence: ; Tel.: +886-2-87923100 (ext. 18564)
| |
Collapse
|
5
|
Hsieh WT, Hsu MH, Lin WJ, Xiao YC, Lyu PC, Liu YC, Lin WY, Kuo YH, Chung JG. Ergosta-7, 9 (11), 22-trien-3β-ol Interferes with LPS Docking to LBP, CD14, and TLR4/MD-2 Co-Receptors to Attenuate the NF-κB Inflammatory Pathway In Vitro and Drosophila. Int J Mol Sci 2021; 22:ijms22126511. [PMID: 34204506 PMCID: PMC8234490 DOI: 10.3390/ijms22126511] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
Ergosta-7, 9 (11), 22-trien-3β-ol (EK100) was isolated from Cordyceps militaris, which has been used as a traditional anti-inflammatory medicine. EK100 has been reported to attenuate inflammatory diseases, but its anti-inflammatory mechanism is still unclear. We were the first to investigate the effect of EK100 on the Toll-like receptor 4 (TLR4)/nuclear factor of the κ light chain enhancer of B cells (NF-κB) signaling in the lipopolysaccharide (LPS)-stimulated RAW264.7 cells and the green fluorescent protein (GFP)-labeled NF-κB reporter gene of Drosophila. EK100 suppressed the release of the cytokine and attenuated the mRNA and protein expression of pro-inflammatory mediators. EK100 inhibited the inhibitor kappa B (IκB)/NF-κB signaling pathway. EK100 also inhibited phosphatidylinositol-3-kinase (PI3K)/Protein kinase B (Akt) signal transduction. Moreover, EK100 interfered with LPS docking to the LPS-binding protein (LBP), transferred to the cluster of differentiation 14 (CD14), and bonded to TLR4/myeloid differentiation-2 (MD-2) co-receptors. Compared with the TLR4 antagonist, resatorvid (CLI-095), and dexamethasone (Dexa), EK100 suppressed the TLR4/AKT signaling pathway. In addition, we also confirmed that EK100 attenuated the GFP-labeled NF-κB reporter gene expression in Drosophila. In summary, EK100 might alter LPS docking to LBP, CD14, and TLR4/MD-2 co-receptors, and then it suppresses the TLR4/NF-κB inflammatory pathway in LPS-stimulated RAW264.7 cells and Drosophila.
Collapse
Affiliation(s)
- Wen-Tsong Hsieh
- Department of Pharmacology, China Medical University, Taichung 40402, Taiwan
- Chinese Medicine Research Center, China Medical University, Taichung 40402, Taiwan;
- Correspondence: ; Tel.: +886-4-22053366 (ext. 2221); Fax: +886-4-22053764
| | - Min-Hsien Hsu
- Department of Neurology, Chang Bing Show-Chwan Memorial Hospital, Changhua 505, Taiwan;
| | - Wen-Jen Lin
- Graduate Institute of Biomedicine Science, China Medical University, Taichung 40402, Taiwan;
| | - Yi-Cheng Xiao
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan;
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 300044, Taiwan;
| | - Yi-Chung Liu
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli 350, Taiwan;
| | - Wei-Yong Lin
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan;
| | - Yueh-Hsiung Kuo
- Chinese Medicine Research Center, China Medical University, Taichung 40402, Taiwan;
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung 40402, Taiwan
| | - Jing-Gung Chung
- Department of Biological Science and Technology, China Medical University, Taichung 40402, Taiwan;
| |
Collapse
|
6
|
Wu CY, Hu IC, Yang YC, Ding WC, Lai CH, Lee YZ, Liu YC, Cheng HC, Lyu PC. An essential role of acetyl coenzyme A in the catalytic cycle of insect arylalkylamine N-acetyltransferase. Commun Biol 2020; 3:441. [PMID: 32796911 PMCID: PMC7427786 DOI: 10.1038/s42003-020-01177-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
Acetyl coenzyme A (Ac-CoA)-dependent N-acetylation is performed by arylalkylamine N-acetyltransferase (AANAT) and is important in many biofunctions. AANAT catalyzes N-acetylation through an ordered sequential mechanism in which cofactor (Ac-CoA) binds first, with substrate binding afterward. No ternary structure containing AANAT, cofactor, and substrate was determined, meaning the details of substrate binding and product release remain unclear. Here, two ternary complexes of dopamine N-acetyltransferase (Dat) before and after N-acetylation were solved at 1.28 Å and 1.36 Å resolution, respectively. Combined with the structures of Dat in apo form and Ac-CoA bound form, we addressed each stage in the catalytic cycle. Isothermal titration calorimetry (ITC), crystallography, and nuclear magnetic resonance spectroscopy (NMR) were utilized to analyze the product release. Our data revealed that Ac-CoA regulates the conformational properties of Dat to form the catalytic site and substrate binding pocket, while the release of products is facilitated by the binding of new Ac-CoA.
Collapse
Affiliation(s)
- Chu-Ya Wu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - I-Chen Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Chen Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wei-Cheng Ding
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chih-Hsuan Lai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Instrumentation Center, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Chung Liu
- Institute of Population Sciences, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Hui-Chun Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Department of Medical Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| |
Collapse
|
7
|
Chuang HC, Chang CC, Teng CF, Hsueh CH, Chiu LL, Hsu PM, Lee MC, Hsu CP, Chen YR, Liu YC, Lyu PC, Tan TH. MAP4K3/GLK Promotes Lung Cancer Metastasis by Phosphorylating and Activating IQGAP1. Cancer Res 2019; 79:4978-4993. [DOI: 10.1158/0008-5472.can-19-1402] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/04/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022]
|
8
|
Ko KT, Hu IC, Huang KF, Lyu PC, Hsu STD. Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer. Structure 2019; 27:1224-1233.e4. [DOI: 10.1016/j.str.2019.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/01/2019] [Accepted: 04/05/2019] [Indexed: 11/28/2022]
|
9
|
Huang PJ, Lin HH, Lee CC, Chiu LY, Wu SM, Yeh YM, Tang P, Chiu CH, Lyu PC, Tsai PC. CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts. BMC Med Genomics 2019; 12:99. [PMID: 31296206 PMCID: PMC6624176 DOI: 10.1186/s12920-019-0510-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND CoMut plot is widely used in cancer research publications as a visual summary of mutational landscapes in cancer cohorts. This summary plot can inspect gene mutation rate and sample mutation burden with their relevant clinical details, which is a common first step for analyzing the recurrence and co-occurrence of gene mutations across samples. The cBioPortal and iCoMut are two web-based tools that allow users to create intricate visualizations from pre-loaded TCGA and ICGC data. For custom data analysis, only limited command-line packages are available now, making the production of CoMut plots difficult to achieve, especially for researchers without advanced bioinformatics skills. To address the needs for custom data and TCGA/ICGC data comparison, we have created CoMutPlotter, a web-based tool for the production of publication-quality graphs in an easy-of-use and automatic manner. RESULTS We introduce a web-based tool named CoMutPlotter to lower the barriers between complex cancer genomic data and researchers, providing intuitive access to mutational profiles from TCGA/ICGC projects as well as custom cohort studies. A wide variety of file formats are supported by CoMutPlotter to translate cancer mutation profiles into biological insights and clinical applications, which include Mutation Annotation Format (MAF), Tab-separated values (TSV) and Variant Call Format (VCF) files. CONCLUSIONS In summary, CoMutPlotter is the first tool of its kind that supports VCF file, the most widely used file format, as its input material. CoMutPlotter also provides the most-wanted function for comparing mutation patterns between custom cohort and TCGA/ICGC project. Contributions of COSMIC mutational signatures in individual samples are also included in the summary plot, which is a unique feature of our tool. CoMutPlotter is freely available at http://tardis.cgu.edu.tw/comutplotter .
Collapse
Affiliation(s)
- Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Hou-Hsien Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Ling-Ya Chiu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shao-Min Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
| | - Pei-Chien Tsai
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan. .,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.
| |
Collapse
|
10
|
Affiliation(s)
- Ping-Chiang Lyu
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan.
| |
Collapse
|
11
|
Hsing EW, Shiah SG, Peng HY, Chen YW, Chuu CP, Hsiao JR, Lyu PC, Chang JY. TNF-α-induced miR-450a mediates TMEM182 expression to promote oral squamous cell carcinoma motility. PLoS One 2019; 14:e0213463. [PMID: 30893332 PMCID: PMC6426234 DOI: 10.1371/journal.pone.0213463] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 10/11/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
Distant metastasis leads oral cancer patients into a poor survival rate and a high recurrence stage. During tumor progression, dysregulated microRNAs (miRNAs) have been reported to involve tumor initiation and modulate oral cancer malignancy. MiR-450a was significantly upregulated in oral squamous cell carcinoma (OSCC) patients without functional reports. This study was attempted to uncover the molecular mechanism of novel miR-450a in OSCC. Mir-450a expression was examined by quantitative RT-PCR, both in OSCC cell lines and patients. Specific target of miR-450a was determined by software prediction, luciferase reporter assay, and correlation with target protein expression. The functions of miR-450a and TMEM182 were accessed by adhesion and transwell invasion analyses. Determination of the expression and cellular localization of TMEM182 was examined by RT-PCR and by immunofluorescence staining. The signaling pathways involved in regulation of miR-450a were investigated using the kinase inhibitors. Overexpression of miR-450a in OSCC cells impaired cell adhesion ability and induced invasiveness, which demonstrated the functional role of miR-450a as an onco-miRNA. Interestingly, tumor necrosis factor alpha (TNF-α)-mediated expression of TMEM182 was regulated by miR-450a induction. MiR-450a-reduced cellular adhesion was abolished by TMEM182 restoration. Furthermore, the oncogenic activity of TNF-α/miR-450a/TMEM182 axis was primarily through activating extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway. ERK1/2 inhibitor prevented the TNF-α-induced miR-450a expression and enhanced adhesion ability. Our data suggested that TNF-α-induced ERK1/2-dependent miR-450a against TMEM182 expression exerted a great influence on increasing OSCC motility. Overall, our results provide novel molecular insights into how TNF-α contributes to oral carcinogenesis through miR-450a that targets TMEM182.
Collapse
Affiliation(s)
- En-Wei Hsing
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
- Structural Biology Program, Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shine-Gwo Shiah
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Hsuan-Yu Peng
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Ya-Wen Chen
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chih-Pin Chuu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Jenn-Ren Hsiao
- Department of Otolaryngology, Head and Neck Collaborative Oncology Group, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Chiang Lyu
- Structural Biology Program, Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jang-Yang Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- * E-mail:
| |
Collapse
|
12
|
Fan CY, Huang SY, Chou MY, Lyu PC. De novo protein sequencing, humanization and in vitro effects of an antihuman CD34 mouse monoclonal antibody. Biochem Biophys Rep 2016; 9:51-60. [PMID: 28955989 PMCID: PMC5614552 DOI: 10.1016/j.bbrep.2016.11.006] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/08/2023] Open
Abstract
QBEND/10 is a mouse immunoglobulin lambda-chain monoclonal antibody with strict specificity against human hematopoietic progenitor cell antigen CD34. Our in vitro study showed that QBEND/10 impairs the tube formation of human umbilical vein endothelial cells (HUVECs), suggesting that the antibody may be of potential benefit in blocking tumor angiogenesis. We provided a de novo protein sequencing method through tandem mass spectrometry to identify the amino acid sequences in the variable heavy and light chains of QBEND/10. To reduce immunogenicity for clinical applications, QBEND/10 was further humanized using the resurfacing approach. We demonstrate that the de novo sequenced and humanized QBEND/10 retains the biological functions of the parental mouse counterpart, including the binding kinetics to CD34 and blockage of the tube formation of the HUVECs.
Collapse
Affiliation(s)
- Chia-Yu Fan
- Institute of Bioinformatics and Structural Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | | | - Min-Yuan Chou
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| |
Collapse
|
13
|
Cheng YY, Cheng CS, Lee TR, Chang WSW, Lyu PC. A clamp-like orientation of basic residues set in a parallelogram is essential for heparin binding. FEBS Lett 2016; 590:3089-97. [PMID: 27531580 DOI: 10.1002/1873-3468.12361] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/29/2016] [Accepted: 08/05/2016] [Indexed: 11/06/2022]
Abstract
While the majority of studies have focused on the biological roles of heparin-binding proteins, relatively little is known about their key residues and structural elements responsible for heparin interaction. In this study, we employed the IgG-binding domain B1 of Streptococcal protein G as a miniature scaffold to investigate how certain positively charged residues within the β-sheet conformation become favorable for heparin binding. By performing a series of arginine substitution mutations followed by gain-of-heparin-binding analysis, we deduced that a clamp-like orientation with discontinuous basic residues separated by ~ 5 Å with ~ 100° interior angle is advantageous for high heparin affinity.
Collapse
Affiliation(s)
- Yi-Yun Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Tian-Ren Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Wun-Shaing Wayne Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan.
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan. .,Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan.
| |
Collapse
|
14
|
Dwivedi AK, Singh R, Singh A, Wei KH, Wu CY, Lyu PC, Lin HC. Novel Water-Soluble Cyclodextrin-Based Conjugated Polymer for Selective Host–Guest Interactions of Cationic Surfactant CTAB and Reverse FRET with Rhodamine B Tagged Adamantyl Guest. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00789] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Atul Kumar Dwivedi
- Department
of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Ravinder Singh
- Department
of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Ashutosh Singh
- Department
of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Kung-Hwa Wei
- Department
of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Chu-Ya Wu
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Ping-Chiang Lyu
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Hong-Cheu Lin
- Department
of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| |
Collapse
|
15
|
Huang SH, Law CH, Kuo PH, Hu RY, Yang CC, Chung TW, Li JM, Lin LH, Liu YC, Liao EC, Tsai YT, Wei YS, Lin CC, Chang CW, Chou HC, Wang WC, Chang MDT, Wang LH, Kung HJ, Chan HL, Lyu PC. Retraction: MMP-13 is involved in oral cancer cell metastasis. Oncotarget 2016; 7:48851. [PMID: 27885991 PMCID: PMC5217056 DOI: 10.18632/oncotarget.10823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
16
|
Su GC, Yeh HY, Lin SW, Chung CI, Huang YS, Liu YC, Lyu PC, Chi P. Role of the RAD51-SWI5-SFR1 Ensemble in homologous recombination. Nucleic Acids Res 2016; 44:6242-51. [PMID: 27131790 PMCID: PMC5291256 DOI: 10.1093/nar/gkw375] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/25/2016] [Indexed: 12/22/2022] Open
Abstract
During DNA double-strand break and replication fork repair by homologous recombination, the RAD51 recombinase catalyzes the DNA strand exchange reaction via a helical polymer assembled on single-stranded DNA, termed the presynaptic filament. Our published work has demonstrated a dual function of the SWI5-SFR1 complex in RAD51-mediated DNA strand exchange, namely, by stabilizing the presynaptic filament and maintaining the catalytically active ATP-bound state of the filament via enhancement of ADP release. In this study, we have strived to determine the basis for physical and functional interactions between Mus musculus SWI5-SFR1 and RAD51. We found that SWI5-SFR1 preferentially associates with the oligomeric form of RAD51. Specifically, a C-terminal domain within SWI5 contributes to RAD51 interaction. With specific RAD51 interaction defective mutants of SWI5-SFR1 that we have isolated, we show that the physical interaction is indispensable for the stimulation of the recombinase activity of RAD51. Our results thus help establish the functional relevance of the trimeric RAD51-SWI5-SFR1 complex and provide insights into the mechanistic underpinnings of homology-directed DNA repair in mammalian cells.
Collapse
Affiliation(s)
- Guan-Chin Su
- Institute of Biochemical Sciences, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chan-I Chung
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yu-Shan Huang
- National Synchrotron Radiation Research Center, No.101, Hsin-Ann Road, Hsinchu, Science Park, Hsinchu 30076, Taiwan
| | - Yi-Chung Liu
- Institute of Population Sciences, National Health Research Institutes, NO. 35 Keyan, Road, Zhunan, Miaoli County 35053, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| |
Collapse
|
17
|
Tu CH, Lin WH, Peng YH, Hsu T, Wu JS, Chang CY, Lu CT, Lyu PC, Shih C, Jiaang WT, Wu SY. Pyrazolylamine Derivatives Reveal the Conformational Switching between Type I and Type II Binding Modes of Anaplastic Lymphoma Kinase (ALK). J Med Chem 2016; 59:3906-19. [PMID: 27031565 DOI: 10.1021/acs.jmedchem.6b00106] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Most anaplastic lymphoma kinase (ALK) inhibitors adopt a type I binding mode, but only limited type II ALK structural studies are available. Herein, we present the structure of ALK in complex with N1-(3-4-[([5-(tert-butyl)-3-isoxazolyl]aminocarbonyl)amino]-3-methylphenyl-1H-5-pyrazolyl)-4-[(4-methylpiperazino)methyl]benzamide (5a), a novel ALK inhibitor adopting a type II binding mode. It revealed binding of 5a resulted in the conformational change and reposition of the activation loop, αC-helix, and juxtamembrane domain, which are all important domains for the autoinhibition mechanism and downstream signal pathway regulation of ALK. A structure-activity relationship study revealed that modifications to the structure of 5a led to significant differences in the ALK potency and altered the protein structure of ALK. To the best of our knowledge, this is the first structural biology study to directly observe how changes in the structure of a small molecule can regulate the switch between the type I and type II binding modes and induce dramatic conformational changes.
Collapse
Affiliation(s)
- Chih-Hsiang Tu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University , 101, Sect. 2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Yi-Hui Peng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Tsu Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chun-Yu Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Cheng-Tai Lu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University , 101, Sect. 2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Weir-Torn Jiaang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| |
Collapse
|
18
|
Tseng KL, Lee YZ, Chen YR, Lyu PC. 1H, 15N and 13C resonance assignments of light organ-associated fatty acid-binding protein of Taiwanese fireflies. Biomol NMR Assign 2016; 10:71-74. [PMID: 26373428 DOI: 10.1007/s12104-015-9640-0] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
Fatty acid-binding proteins (FABPs) are a family of proteins that modulate the transfer of various fatty acids in the cytosol and constitute a significant portion in many energy-consuming cells. The ligand binding properties and specific functions of a particular type of FABP seem to be diverse and depend on the respective binding cavity as well as the cell type from which this protein is derived. Previously, a novel FABP (lcFABP; lc: Luciola cerata) was identified in the light organ of Taiwanese fireflies. The lcFABP was proved to possess fatty acids binding capabilities, especially for fatty acids of length C14-C18. However, the structural details are unknown, and the structure-function relationship has remained to be further investigated. In this study, we finished the (1)H, (15)N and (13)C chemical shift assignments of (15)N/(13)C-enriched lcFABP by solution NMR spectroscopy. In addition, the secondary structure distribution was revealed based on the backbone N, H, Cα, Hα, C and side chain Cβ assignments. These results can provide the basis for further structural exploration of lcFABP.
Collapse
Affiliation(s)
- Kai-Li Tseng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Yun-Ru Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC.
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan, ROC.
| |
Collapse
|
19
|
Huang SH, Law CH, Kuo PH, Hu RY, Yang CC, Chung TW, Li JM, Lin LH, Liu YC, Liao EC, Tsai YT, Wei YS, Lin CC, Chang CW, Chou HC, Wang WC, Chang MDT, Wang LH, Kung HJ, Chan HL, Lyu PC. MMP-13 is involved in oral cancer cell metastasis. Oncotarget 2016; 7:17144-61. [PMID: 26958809 PMCID: PMC4941377 DOI: 10.18632/oncotarget.7942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/31/1969] [Indexed: 12/20/2022] Open
Abstract
The oral cancer cell line OC3-I5 with a highly invasive ability was selected and derived from an established OSCC line OC3. In this study, we demonstrated that matrix metalloproteinases protein MMP-13 was up-regulated in OC3-I5 than in OC3 cells. We also observed that expression of epithelial-mesenchymal transition (EMT) markers including Twist, p-Src, Snail1, SIP1, JAM-A, and vinculin were increased in OC3-I5 compared to OC3 cells, whereas E-cadherin expression was decreased in the OC3-I5 cells. Using siMMP-13 knockdown techniques, we showed that siMMP-13 not only reduced the invasion and migration, but also the adhesion abilities of oral cancer cells. In support of the role of MMP-13 in metastasis, we used MMP-13 expressing plasmid-transfected 293T cells to enhance MMP-13 expression in the OC3 cells, transplanting the MMP-13 over expressing OC3 cells into nude mice led to enhanced lung metastasis. In summary, our findings show that MMP-13 promotes invasion and metastasis in oral cancer cells, suggesting altered expression of MMP-13 may be utilized to impede the process of metastasis.
Collapse
Affiliation(s)
- Shun-Hong Huang
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ching-Hsuan Law
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Hsueh Kuo
- Department of Medical Sciences and Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ren-Yu Hu
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ching-Chieh Yang
- Department of Radiation Oncology, Chi-Mei Medical Center, Tainan, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ting-Wen Chung
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ji-Min Li
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Li-Hsun Lin
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Chung Liu
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Institute of Population Sciences, National Health Research Institutes, Miaoli County, Taiwan
| | - En-Chi Liao
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Ting Tsai
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Shan Wei
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Chen Lin
- Institute of Biomedical Science, National Chung Hsing University, Taichung, Taiwan.,Institute of Biomedical Science and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan.,Department of Medical Research and Education, Taichung Veterans General Hospital, Taichung, Taiwan.,Division of Chest Medicine. Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Chien-Wen Chang
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Taiwan
| | - Hsiu-Chuan Chou
- Department of Applied Science, National Hsinchu University of Education, Hsinchu, Taiwan
| | - Wen-Ching Wang
- Department of Medical Sciences and Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Margaret Dah-Tsyr Chang
- Department of Medical Sciences and Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Lu-Hai Wang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Hong-Lin Chan
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Sciences and Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Department of Medical Sciences and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Sciences and Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| |
Collapse
|
20
|
Wang LW, Liu YN, Lyu PC, Jackson SE, Hsu STD. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori. J Phys Condens Matter 2015; 27:354106. [PMID: 26290953 DOI: 10.1088/0953-8984/27/35/354106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.
Collapse
Affiliation(s)
- Liang-Wei Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan. Institute of Biochemical Science, National Taiwan University, Taipei 116, Taiwan. Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | | | | | | | | |
Collapse
|
21
|
Chien CTH, Wang LW, Liu YN, Hsu BD, Lyu PC, Hsu STD. NMR assignments of a hypothetical pseudo-knotted protein HP0242 from Helicobacter pylori. Biomol NMR Assign 2014; 8:287-289. [PMID: 23824732 DOI: 10.1007/s12104-013-9502-6] [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: 03/27/2013] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Many knotted proteins have been discovered recently, but the folding process of which remains elusive. HP0242 is a hypothetical protein from Helicobacter pylori, which is a model system for studying the folding pathway of a knotted protein. In this study, we report the (1)H, (13)C, and (15)N chemical shift assignments of HP0242. The results will enable us to further investigate HP0242 by NMR experiments.
Collapse
|
22
|
Lin LH, Chang SJ, Hu RY, Lin MW, Lin ST, Huang SH, Lyu PC, Chou HC, Lai ZY, Chuang YJ, Chan HL. Biomarker discovery for neuroendocrine cervical cancer. Electrophoresis 2014; 35:2039-45. [DOI: 10.1002/elps.201400014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 03/20/2014] [Accepted: 04/02/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Li-Hsun Lin
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Shing-Jyh Chang
- Gynecologic Oncology Section, Department of Obstetrics and Gynecology; Hsinchu Mackay Memorial Hospital; Hsinchu Taiwan
| | - Ren-Yu Hu
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Meng-Wei Lin
- Department of Applied Science; National Hsinchu University of Education; Hsinchu Taiwan
| | - Szu-Ting Lin
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Shun-Hong Huang
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Ping-Chiang Lyu
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Hsiu-Chuan Chou
- Department of Applied Science; National Hsinchu University of Education; Hsinchu Taiwan
| | - Zih-Yin Lai
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Yung-Jen Chuang
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Hong-Lin Chan
- Department of Medical Sciences; Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| |
Collapse
|
23
|
Wey MT, Lyu PC, Kan LS. Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
24
|
Lee TR, Lee HY, Huang SH, Chan HT, Lyu PC, Chan HL. Comparative proteomics analysis of normal and memory-deficient Drosophila melanogaster heads. Zool Stud 2013. [DOI: 10.1186/1810-522x-52-10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Learning and memory are extremely complex and dynamic processes. Proteins that participate in memory formation are strictly regulated by various pathways and may require protein synthesis and/or post-translational modifications. To examine the formation of memory, Drosophila was genetically engineered with the mutated memory-related gene, Amn
X8
, which induces normal learning and memory behavior within the first 30 min of training. However, the process through which learning occurred could not be retained after the 30 min of training, indicating that these mutants possessed deficits in middle-term memory. A proteomics platform based on two-dimensional differential gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry was employed to examine the head proteome alterations between the wild-type 2u strain and the memory-deficient mutant Amn
X8
strain.
Results
The results indicated that 30 differentially expressed head proteins that mainly function in metabolic pathways and cell structure/cytoskeleton proteins were involved in memory formation. A bioinformatics analysis demonstrated that mitochondrial proteins had critical roles in modulating this process.
Conclusions
This is the first study of a comparative head proteomics analysis of a memory mutant strain and a normal control fruit fly strain. The fundamental proteomics analysis provides potential candidates for further elucidation of the biological mechanism of the memory formation process in Drosophila.
Collapse
|
25
|
Peng YH, Shiao HY, Tu CH, Liu PM, Hsu JTA, Amancha PK, Wu JS, Coumar MS, Chen CH, Wang SY, Lin WH, Sun HY, Chao YS, Lyu PC, Hsieh HP, Wu SY. Protein Kinase Inhibitor Design by Targeting the Asp-Phe-Gly (DFG) Motif: The Role of the DFG Motif in the Design of Epidermal Growth Factor Receptor Inhibitors. J Med Chem 2013; 56:3889-903. [DOI: 10.1021/jm400072p] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi-Hui Peng
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chih-Hsiang Tu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
- Institute of Bioinformatics
and Structural Biology, National Tsing Hua University, 101, Sect.
2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Pang-Min Liu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - John Tsu-An Hsu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Prashanth Kumar Amancha
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School
of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014,
India
| | - Chun-Hwa Chen
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Sing-Yi Wang
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hsu-Yi Sun
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Yu-Sheng Chao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics
and Structural Biology, National Tsing Hua University, 101, Sect.
2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| |
Collapse
|
26
|
Lin ST, Lo YW, Chang SJ, Wang WC, Chang MDT, Lyu PC, Chen YW, Chou HC, Chan HL. Redox-proteomic analysis of doxorubicin resistance-induced altered thiol activity in uterine carcinoma. J Pharm Biomed Anal 2013; 78-79:1-8. [DOI: 10.1016/j.jpba.2013.01.028] [Citation(s) in RCA: 5] [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] [Received: 11/30/2012] [Revised: 01/16/2013] [Accepted: 01/19/2013] [Indexed: 10/27/2022]
|
27
|
Lee CC, Chen YPP, Yao TJ, Ma CY, Lo WC, Lyu PC, Tang CY. GI-POP: A combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. Gene 2013; 518:114-23. [DOI: 10.1016/j.gene.2012.11.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
|
28
|
Tseng TS, Cheng CS, Hsu STD, Shih MF, He PL, Lyu PC. Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster. PLoS One 2013; 8:e54187. [PMID: 23349821 PMCID: PMC3551606 DOI: 10.1371/journal.pone.0054187] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/07/2012] [Indexed: 11/19/2022] Open
Abstract
Drosophila melanogaster crammer is a novel cathepsin inhibitor involved in long-term memory formation. A molten globule-to-ordered structure transition is required for cathepsin inhibition. This study reports the use of alanine scanning to probe the critical residues in the two hydrophobic cores and the salt bridges of crammer in the context of disorder-to-order transition and cathepsin inhibition. Alanine substitution of the aromatic residues W9, Y12, F16, Y20, Y32, and W53 within the hydrophobic cores, and charged residues E8, R28, R29, and E67 in the salt bridges considerably decrease the ability of crammer to inhibit Drosophila cathepsin B (CTSB). Far-UV circular dichroism (CD), intrinsic fluorescence, and nuclear magnetic resonance (NMR) spectroscopies show that removing most of the aromatic and charged side-chains substantially reduces thermostability, alters pH-dependent helix formation, and disrupts the molten globule-to-ordered structure transition. Molecular modeling indicates that W53 in the hydrophobic Core 2 is essential for the interaction between crammer and the prosegment binding loop (PBL) of CTSB; the salt bridge between R28 and E67 is critical for the appropriate alignment of the α-helix 4 toward the CTSB active cleft. The results of this study show detailed residue-specific dissection of folding transition and functional contributions of the hydrophobic cores and salt bridges in crammer, which have hitherto not been characterized for cathepsin inhibition by propeptide-like cysteine protease inhibitors. Because of the involvements of cathepsin inhibitors in neurodegenerative diseases, these structural insights can serve as a template for further development of therapeutic inhibitors against human cathepsins.
Collapse
Affiliation(s)
- Tien-Sheng Tseng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Min-Fang Shih
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Pei-Lin He
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
- * E-mail:
| |
Collapse
|
29
|
Stephen P, Cheng KC, Lyu PC. Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites. PLoS One 2012; 7:e50488. [PMID: 23226294 PMCID: PMC3511584 DOI: 10.1371/journal.pone.0050488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 10/22/2012] [Indexed: 11/20/2022] Open
Abstract
Glucoamylases, containing starch-binding domains (SBD), have a wide range of scientific and industrial applications. Random mutagenesis and DNA shuffling of the gene encoding a starch-binding domain have resulted in only minor improvements in the affinities of the corresponding protein to their ligands, whereas circular permutation of the RoCBM21 substantially improved its binding affinity and selectivity towards longer-chain carbohydrates. For the study reported herein, we used a standard soluble ligand (amylose EX-I) to characterize the functional and structural aspects of circularly permuted RoCBM21 (CP90). Site-directed mutagenesis and the analysis of crystal structure reveal the dimerisation and an altered binding path, which may be responsible for improved affinity and altered selectivity of this newly created starch-binding domain. The functional and structural characterization of CP90 suggests that it has significant potential in industrial applications.
Collapse
Affiliation(s)
- Preyesh Stephen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Kuo-Chang Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
- * E-mail:
| |
Collapse
|
30
|
Lin ST, Chou HC, Chang SJ, Chen YW, Lyu PC, Wang WC, Chang MDT, Chan HL. Proteomic analysis of proteins responsible for the development of doxorubicin resistance in human uterine cancer cells. J Proteomics 2012; 75:5822-47. [DOI: 10.1016/j.jprot.2012.07.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 07/16/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
|
31
|
Chen CP, Chen YH, Chern SR, Chang SJ, Tsai TL, Li SH, Chou HC, Lo YW, Lyu PC, Chan HL. Placenta proteome analysis from Down syndrome pregnancies for biomarker discovery. Mol Biosyst 2012; 8:2360-72. [PMID: 22777171 DOI: 10.1039/c2mb25081k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Down syndrome is one of the most frequent chromosomal disorders, with a prevalence of approximately 1/500 to 1/800, depending on the maternal age distribution of the pregnant population. However, few reliable protein biomarkers have been used in the diagnosis of this disease. Recent progress in quantitative proteomics has offered opportunities to discover biomarkers for tracking the progression and for understanding the molecular mechanisms of Down syndrome. In the present study, placental samples were analyzed by fluorescence two-dimensional differential gel electrophoresis (2D-DIGE) and differentially expressed proteins were identified by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In total, 101 proteins have been firmly identified representing 80 unique gene products. These proteins mainly function in cytoskeleton structure and regulation (such as vimentin and Profilin-1). Additionally, our quantitative proteomics approach has identified numerous previously reported Down syndrome markers, such as myelin protein. Here we present several Down syndrome biomarkers including galectin-1, ataxin-3 and sprouty-related EVH1 domain-containing protein 2 (SPRED2), which have not been reported elsewhere and may be associated with the progression and development of the disease. In summary, we report a comprehensive placenta-based proteomics approach for the identification of potential biomarkers for Down syndrome, in which serum amyloid P-component (APCS) and ataxin-3 have been shown to be up-regulated in the maternal peripheral plasma of Down syndrome cases. The potential of utilizing these markers for the prognosis and screening of Down syndrome warrants further investigation.
Collapse
Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Abstract
Aspergillus species are industrially and agriculturally important as fermentors and as producers of various secondary metabolites. Among them, fungal polyketides such as lovastatin and melanin are considered a gold mine for bioactive compounds. We used a phylogenomic approach to investigate the distribution of iterative polyketide synthases (PKS) in eight sequenced Aspergilli and classified over 250 fungal genes. Their genealogy by the conserved ketosynthase (KS) domain revealed three large groups of nonreducing PKS, one group inside bacterial PKS, and more than 9 small groups of reducing PKS. Polyphyly of nonribosomal peptide synthase (NRPS)-PKS genes raised questions regarding the recruitment of the elegant conjugation machinery. High rates of gene duplication and divergence were frequent. All data are accessible through our web database at http://metabolomics.jp/wiki/Category:PK.
Collapse
Affiliation(s)
- Shu-Hsi Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | | | | | | |
Collapse
|
33
|
Affiliation(s)
- Tian-Ren Lee
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Shun-Hong Huang
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Chi-Ching Lee
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Hsiao-Yun Lee
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Hsin-Tzu Chan
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Kuo-Sen Lin
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Hong-Lin Chan
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| | - Ping-Chiang Lyu
- Department of Medical Sciences; National Tsing Hua University; Hsinchu Taiwan
- Institute of Bioinformatics and Structural Biology; National Tsing Hua University; Hsinchu Taiwan
| |
Collapse
|
34
|
Cheng CS, Chen WT, Chen YW, Chen CH, Luo YC, Lyu PC, Yin HS. Substitution of asparagine 76 by a tyrosine residue induces domain swapping in Helicobacter pylori phosphopantetheine adenylyltransferase. J Biomol Struct Dyn 2012; 30:488-502. [PMID: 22694317 DOI: 10.1080/07391102.2012.682213] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Phosphopantetheine adenylyltransferase (PPAT) catalyses the penultimate step in coenzyme A biosynthesis in bacteria and is therefore a candidate target for antibacterial drug development. We randomly mutated the residues in the Helicobacter pylori PPAT sequence to identify those that govern protein folding and ligand binding, and we describe the crystal structure of one of these mutants (I4V/N76Y) that contains the mutations I4 → V and N76 → Y. Unlike other PPATs, which are homohexamers, I4V/N76Y is a domain-swapped homotetramer. The protomer structure of this mutant is an open conformation in which the 65 C-terminal residues are intertwined with those of a neighbouring protomer. Despite structural differences between wild-type PPAT and IV4/N76Y, they had similar ligand-binding properties. ATP binding to these two proteins was enthalpically driven, whereas that for Escherichia coli PPAT is entropically driven. The structural packing of the subunits may affect the thermal denaturation of wild-type PPAT and I4V/N76Y. Mutations in hinge regions often induce domain swapping, i.e. the spatial exchange of portions of adjacent protomers, but residues 4 and 76 of H. pylori PPAT are not located in or near to the hinge region. However, one or both of these residues is responsible for the large conformational change in the C-terminal region of each protomer. To identify the residue(s) responsible, we constructed the single-site mutant, N76Y, and found a large displacement of α-helix 4, which indicated that its flexibility allowed the domain swap to occur.
Collapse
Affiliation(s)
- Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, and College of Life Sciences, National Tsing Hua University, Hsinchu, 300, Taiwan
| | | | | | | | | | | | | |
Collapse
|
35
|
Abstract
Circular permutation (CP) is a protein structural rearrangement phenomenon, through which nature allows structural homologs to have different locations of termini and thus varied activities, stabilities and functional properties. It can be applied in many fields of protein research and bioengineering. The limitation of applying CP lies in its technical complexity, high cost and uncertainty of the viability of the resulting protein variants. Not every position in a protein can be used to create a viable circular permutant, but there is still a lack of practical computational tools for evaluating the positional feasibility of CP before costly experiments are carried out. We have previously designed a comprehensive method for predicting viable CP cleavage sites in proteins. In this work, we implement that method into an efficient and user-friendly web server named CPred (CP site predictor), which is supposed to be helpful to promote fundamental researches and biotechnological applications of CP. The CPred is accessible at http://sarst.life.nthu.edu.tw/CPred.
Collapse
Affiliation(s)
- Wei-Cheng Lo
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | | | | | | | | | | |
Collapse
|
36
|
Lee CC, Lo WC, Lai SM, Chen YPP, Tang CY, Lyu PC. Metabolic classification of microbial genomes using functional probes. BMC Genomics 2012; 13:157. [PMID: 22537274 PMCID: PMC3355368 DOI: 10.1186/1471-2164-13-157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 04/27/2012] [Indexed: 11/29/2022] Open
Abstract
Background Microorganisms able to grow under artificial culture conditions comprise only a small proportion of the biosphere's total microbial community. Until recently, scientists have been unable to perform thorough analyses of difficult-to-culture microorganisms due to limitations in sequencing technology. As modern techniques have dramatically increased sequencing rates and rapidly expanded the number of sequenced genomes, in addition to traditional taxonomic classifications which focus on the evolutionary relationships of organisms, classifications of the genomes based on alternative points of view may help advance our understanding of the delicate relationships of organisms. Results We have developed a proteome-based method for classifying microbial species. This classification method uses a set of probes comprising short, highly conserved amino acid sequences. For each genome, in silico translation is performed to obtained its proteome, based on which a probe-set frequency pattern is generated. Then, the probe-set frequency patterns are used to cluster the proteomes/genomes. Conclusions Features of the proposed method include a high running speed in challenge of a large number of genomes, and high applicability for classifying organisms with incomplete genome sequences. Moreover, the probe-set clustering method is sensitive to the metabolic phenotypic similarities/differences among species and is thus supposed potential for the classification or differentiation of closely-related organisms.
Collapse
Affiliation(s)
- Chi-Ching Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | | | | | | | | |
Collapse
|
37
|
Chan HT, Lee TR, Huang SH, Lee HY, Sang TK, Chan HL, Lyu PC. Proteomic analysis of a drosophila IBMPFD model reveals potential pathogenic mechanisms. Mol Biosyst 2012; 8:1730-41. [PMID: 22481368 DOI: 10.1039/c2mb25037c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IBMPFD, Inclusion body myopathy associated with Paget's disease of bone and frontotemporal dementia, is a hereditary degenerative disorder due to single missense mutations in VCP (Valosin-Containing Protein). The mechanisms of how mutations of VCP lead to IBMPFD remain mysterious. Here we utilize two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry to study the IBMPFD disorder at the protein level. With this set-up, we are able to employ comparative proteomics to analyze IBMPFD disease using Drosophila melanogaster as our disease model organism. Head proteome of transgenic D. melanogaster expressing wild type VCP is compared, respectively, with the head proteome of transgenic mutant type VCPs that correspond to human IBMPFD disease alleles (TER94(A229E), TER94(R188Q), and TER94(R152H)). Of all the proteins identified, a significant fraction of proteins altered in TER94(A229E) and TER94(R188Q) mutants belong to the same functional categories, i.e. apoptosis and metabolism. Among these, Drosophila transferrin is observed to be significantly up-regulated in mutant flies expressing TER94(A229E). A knock-down experiment suggests that fly transferrin might be a potential modifier in IBMPFD disease. The molecular analysis of IBMPFD disease may benefit from the proteomics approach which combines the advantages of high throughput analysis and the focus on protein levels.
Collapse
Affiliation(s)
- Hsin-Tzu Chan
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | | | | | | | | | | | | |
Collapse
|
38
|
Chou HC, Lu YC, Cheng CS, Chen YW, Lyu PC, Lin CW, Timms JF, Chan HL. Proteomic and redox-proteomic analysis of berberine-induced cytotoxicity in breast cancer cells. J Proteomics 2012; 75:3158-76. [PMID: 22522123 DOI: 10.1016/j.jprot.2012.03.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/30/2012] [Accepted: 03/08/2012] [Indexed: 01/06/2023]
Abstract
Berberine is a natural product isolated from herbal plants such as Rhizoma coptidis which has been shown to have anti-neoplastic properties. However, the effects of berberine on the behavior of breast cancers are largely unknown. To determine if berberine might be useful in the treatment of breast cancer and its cytotoxic mechanism, we analyzed the impact of berberine treatment on differential protein expression and redox regulation in human breast cancer cell line MCF-7 using lysine- and cysteine-labeling two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry (MS). This study demonstrated that 96 and 22 protein features were significantly changed in protein expression and thiol reactivity, respectively and revealed that berberine-induced cytotoxicity in breast cancer cells involves dysregulation of protein folding, proteolysis, redox regulation, protein trafficking, cell signaling, electron transport, metabolism and centrosomal structure. Our work shows that this combined proteomic strategy provides a rapid method to study the molecular mechanisms of berberine-induced cytotoxicity in breast cancer cells. The identified targets may be useful for further evaluation as potential targets in breast cancer therapy.
Collapse
Affiliation(s)
- Hsiu-Chuan Chou
- Department of Applied Science, National Hsinchu University of Education, Hsinchu, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Stephen P, Tseng KL, Liu YN, Lyu PC. Circular permutation of the starch-binding domain: inversion of ligand selectivity with increased affinity. Chem Commun (Camb) 2012; 48:2612-4. [PMID: 22294161 DOI: 10.1039/c2cc17376j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Proteins containing starch-binding domains (SBDs) are used in a variety of scientific and technological applications. A circularly permutated SBD (CP90) with improved affinity and selectivity toward longer-chain carbohydrates was synthesized, suggesting that a new starch-binding protein may be developed for specific scientific and industrial applications.
Collapse
Affiliation(s)
- Preyesh Stephen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan ROC
| | | | | | | |
Collapse
|
40
|
Abstract
BACKGROUND Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain. METHODS In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database--nsLTPDB--which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/. RESULTS Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prosite-styled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC × G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L, F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs. CONCLUSIONS Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.
Collapse
Affiliation(s)
- Nai-Jyuan Wang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Ching Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Wei-Cheng Lo
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ya-Fen Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Nan Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
- Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan
| |
Collapse
|
41
|
Tseng HC, Kao HW, Ho MR, Chen YR, Lin TW, Lyu PC, Lin WC. Cytoskeleton network and cellular migration modulated by nuclear-localized receptor tyrosine kinase ROR1. Anticancer Res 2011; 31:4239-4249. [PMID: 22199287] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
UNLABELLED Biological functions of receptor tyrosine kinase-like orphan receptor 1 (ROR1) remain to be elucidated due to the lack of identified genuine ligands. Previously, transiently expressed ROR1 was unexpectedly found to exhibit nuclear localization, the functions of which are unknown. MATERIALS AND METHODS We constructed nuclear-homing peptidyl-prolyl cis-trans isomerases (FKBP) domain fusion ROR1-expressing cells and used a synthetic dimerizer to specifically activate FKBP-fused ROR1 proteins for subsequent functional characterization. RESULTS Activation of nuclear-homing ROR1 by treating cells with AP20187 dimerizer led to significant increase in actin stress fibers and increased cellular migration. Following gene expression microarray analysis, we demonstrated that activated ROR1 affects several genes involved in the regulation of the actin cytoskeleton (radixin (RDX), ezrin (EZR), son of sevenless homolog 2 (SOS2) and caldesmon 1 (CALD1)). CONCLUSION Our data indicate that nuclear-localized ROR1 may play an important role in cell migration and cytoskeleton remodeling. This might explain the critical roles of ROR1 in neuron development.
Collapse
Affiliation(s)
- Hsiao-Chun Tseng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | | | | | | | | | | | | |
Collapse
|
42
|
Huang PJ, Lin WC, Chen SC, Lin YH, Sun CH, Lyu PC, Tang P. Identification of putative miRNAs from the deep-branching unicellular flagellates. Genomics 2011; 99:101-7. [PMID: 22120185 DOI: 10.1016/j.ygeno.2011.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 11/28/2022]
Abstract
MicroRNAs (miRNAs) are a class of extensively studied RNAi-associated small RNAs that play a critical role in eukaryotic gene regulation. However, knowledge on the miRNA and its regulation in unicellular eukaryotes is very limited. In order to obtain a better understanding on the origin of miRNA regulation system, we used deep-sequencing technology to investigate the miRNA expression pattern in four deep-branching unicellular flagellates: Giardia lamblia, Trichomonas vaginalis, Tritrichomonas foetus, and Pentatrichomonas hominis. In addition to the known miRNAs that have been described in G. lamblia and T. vaginalis, we identified 14 ancient animal miRNA families and 13 plant-specific families. Bioinformatics analysis also identified four novel miRNA candidates with reliable precursor structures derived from mature tRNAs. Our results indicated that miRNAs are likely to be a general feature for gene regulation throughout unicellular and multicellular eukaryotes and some of them may derive from unconventional ncRNAs such as snoRNA and tRNA.
Collapse
Affiliation(s)
- Po-Jung Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | | | | | | | | | | |
Collapse
|
43
|
Chen YW, Liu JY, Lin ST, Li JM, Huang SH, Chen JY, Wu JY, Kuo CC, Wu CL, Lu YC, Chen YH, Fan CY, Huang PC, Law CH, Lyu PC, Chou HC, Chan HL. Proteomic analysis of gemcitabine-induced drug resistance in pancreatic cancer cells. Mol Biosyst 2011; 7:3065-74. [PMID: 21894339 DOI: 10.1039/c1mb05125c] [Citation(s) in RCA: 35] [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] [Indexed: 01/12/2023]
Abstract
Currently, the most effective agent against pancreatic cancer is gemcitabine (GEM), which inhibits tumor growth by interfering with DNA replication and blocking DNA synthesis. However, GEM-induced drug resistance in pancreatic cancer compromises the therapeutic efficacy of GEM. To investigate the molecular mechanisms associated with GEM-induced resistance, 2D-DIGE and MALDI-TOF mass spectrometry were performed to compare the proteomic alterations of a panel of differential GEM-resistant PANC-1 cells with GEM-sensitive pancreatic cells. The proteomic results demonstrated that 33 proteins were differentially expressed between GEM-sensitive and GEM-resistant pancreatic cells. Of these, 22 proteins were shown to be resistance-specific and dose-dependent in the regulation of GEM. Proteomic analysis also revealed that proteins involved in biosynthesis and detoxification are significantly over-expressed in GEM-resistant PANC-1 cells. In contrast, proteins involved in vascular transport, bimolecular decomposition, and calcium-dependent signal regulation are significantly over-expressed in GEM-sensitive PANC-1 cells. Notably, both protein-protein interaction of the identified proteins with bioinformatic analysis and immunoblotting results showed that the GEM-induced pancreatic cell resistance might interplay with tumor suppressor protein p53. Our approach has been shown here to be useful for confidently detecting pancreatic proteins with differential resistance to GEM. Such proteins may be functionally involved in the mechanism of chemotherapy-induced resistance.
Collapse
Affiliation(s)
- Yi-Wen Chen
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Cheng CS, Chen CH, Luo YC, Chen WT, Chang SY, Lyu PC, Kao MC, Yin HS. Crystal structure and biophysical characterisation of Helicobacter pylori phosphopantetheine adenylyltransferase. Biochem Biophys Res Commun 2011; 408:356-61. [PMID: 21527250 DOI: 10.1016/j.bbrc.2011.04.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 04/12/2011] [Indexed: 12/11/2022]
Abstract
Helicobacter pylori is a bacterium that causes chronic active gastritis and peptic ulcers. Drugs targeting H. pylori phosphopantetheine adenylyltransferase (HpPPAT), which is involved in CoA biosynthesis, may be useful. Herein, we report the expression in Escherichia coli and purification of recombinant HpPPAT and describe a crystal structure for an HpPPAT/CoA complex. As is the case for E. coli PPAT (EcPPAT), HpPPAT is hexameric in solution and as a crystal. Each protomer has a well-packed dinucleotide-binding fold in which CoA binds. Structural characterisation demonstrated that CoA derived from the E. coli expression system bound tightly to HpPPAT, presumably to initiate feedback inhibition. However, the interactions between the active-site residues of HpPPAT and CoA are not identical to those of other PPATs. Finally, CoA binding affects HpPPAT thermal denaturation.
Collapse
Affiliation(s)
- Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
Abstract
Collapse
Affiliation(s)
- Che-Wei Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Taiwan.
| | | | | |
Collapse
|
46
|
Lee TS, Pan CC, Peng CC, Kou YR, Chen CY, Ching LC, Tsai TH, Chen SF, Lyu PC, Shyue SK. Anti-atherogenic effect of berberine on LXRalpha-ABCA1-dependent cholesterol efflux in macrophages. J Cell Biochem 2011; 111:104-10. [PMID: 20506155 DOI: 10.1002/jcb.22667] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Berberine, a botanical alkaloid purified from Cortidis rhizoma, has effects in cardiovascular diseases, yet the mechanism is not fully understood. Foam cells play a critical role in the progression of atherosclerosis. This study aimed to investigate the effect of berberine on the formation of foam cells by macrophages and the underlying mechanism. Treatment with berberine markedly suppressed oxidized low-density lipoprotein (oxLDL)-mediated lipid accumulation, which was due to an increase in cholesterol efflux. Berberine enhanced the mRNA and protein expression of ATP-binding membrane cassette transport protein A1 (ABCA1) but did not alter the protein level of ABCG1 or other scavenger receptors. Additionally, functional inhibition of ABCA1 with a pharmacological inhibitor or neutralizing antibody abrogated the effects of berberine on cholesterol efflux and lipid accumulation. Moreover, berberine induced the nuclear translocation and activation of liver X receptor alpha (LXRalpha) but not its protein expression. Knockdown of LXRalpha mRNA expression by small interfering RNA abolished the berberine-mediated protective effects on ABCA1 protein expression and oxLDL-induced lipid accumulation in macrophages. These data suggest that berberine abrogates the formation of foam cells by macrophages by enhancing LXRalpha-ABCA1-dependent cholesterol efflux.
Collapse
Affiliation(s)
- Tzong-Shyuan Lee
- Institute of Physiology, National Yang-Ming University, Taipei 11221, Taiwan, ROC.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Cheng CS, Chen WT, Lee LH, Chen YW, Chang SY, Lyu PC, Yin HS. Structural and functional comparison of cytokine interleukin-1 beta from chicken and human. Mol Immunol 2011; 48:947-55. [PMID: 21288573 DOI: 10.1016/j.molimm.2011.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/04/2011] [Accepted: 01/04/2011] [Indexed: 01/12/2023]
Abstract
Interleukin-1 beta (IL-1β) is an important cytokine in the immune system. The properties of avian IL-1βs are less well understood than the mammalian IL-1βs, and there is no available structure of avian IL-1βs in the Protein Data Bank. Here, we report the crystal structures of wild-type and Y157F mutant IL-1βs from chicken. Both the wild-type and mutant IL-1βs share a beta-trefoil conformation similar to that of human IL-1β and also have an internal hydrophobic cavity. However, the cavity sizes clearly differ from that of human IL-1β due to the packing of hydrophobic residues. Our studies also reveal that the relative thermal stability of IL-1βs does not correlate with cavity size but rather is dependent on the amino acid residues present around the cavity. This cavity serves as a scaffold for maintaining the structure of the IL-1β core region but does not have a biological function per se. Moreover, we found that human IL-1β cannot induce chemokine expression in chicken fibroblasts or elevate plasma cortisol levels in chickens, implying a lack of cross-species bioactivity. Close examination reveals that significant structural and sequence differences occur in the terminal and some loop regions between human and chicken IL-1βs. These variable regions have been shown to be critical for receptor binding, thus resulting in a lack of species cross-reactivity between human and chicken IL-1β.
Collapse
Affiliation(s)
- Chao-Sheng Cheng
- Institute of Bioinformatics and Structural Biology, and College of Life Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | | | | | | | | | | | | |
Collapse
|
48
|
Hung PH, Chen YW, Cheng KC, Chou HC, Lyu PC, Lu YC, Lee YR, Wu CT, Chan HL. Plasma proteomic analysis of the critical limb ischemia markers in diabetic patients with hemodialysis. Mol BioSyst 2011; 7:1990-8. [DOI: 10.1039/c1mb05055a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
49
|
Chu CH, Lo WC, Wang HW, Hsu YC, Hwang JK, Lyu PC, Pai TW, Tang CY. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PLoS One 2010; 5:e13361. [PMID: 20976204 PMCID: PMC2955075 DOI: 10.1371/journal.pone.0013361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [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: 07/10/2010] [Accepted: 09/13/2010] [Indexed: 11/18/2022] Open
Abstract
This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications.
Collapse
Affiliation(s)
- Chia-Han Chu
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Wei-Cheng Lo
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Hsin-Wei Wang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan, Republic of China
| | - Yen-Chu Hsu
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan, Republic of China
| | - Jenn-Kang Hwang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan, Republic of China
- * E-mail: (T-WP); (CYT)
| | - Chuan Yi Tang
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan, Republic of China
- * E-mail: (T-WP); (CYT)
| |
Collapse
|
50
|
Peng YH, Coumar MS, Leou JS, Wu JS, Shiao HY, Lin CH, Lin WH, Lien TW, Chen X, Hsu JTA, Chao YS, Huang CF, Lyu PC, Hsieh HP, Wu SY. Structural Basis for the Improved Potency of Peroxisome Proliferator-Activated Receptor (PPAR) Agonists. ChemMedChem 2010; 5:1707-16. [DOI: 10.1002/cmdc.201000194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|