國立中興大學基因體暨生物資訊學研究所

　　

　　 　　

　　　　　　　

　　　　　　　

　　　　　　　

基因體暨生物資訊學研究所

Graduate Institute of Genomics and Bioinformatics

Chinese
English

興大首頁

National Chung Hsing University

醫科博班

Doctoral Program in Medical Biotechnology

生命科學院

College of Life Sciences

Liu, Jyung-Hurng

Lab: Structural Bioinformatics Lab

Honors:

Time Title
2006/07 “Glycosphingolipid-facilitated membrane insertion and internalization of cobra cardiotoxin: crystal structure of the cardiotoxin/sulfatide complex.”
中央研究院分子生物研究所 學生/助理/博士後申請出席國際學術會議獎助
2004/10 “Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli.”
國家同步輻射研究中心第十屆用戶年會暨研討會 學生口頭報告比賽第二名與壁報比賽佳作
2004/05 “Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli.”
第九屆生物物理新知研討會青年學子壁報論文獎第二名

Experience

Title Department Period
Joint Assistant Professor Graduate Institute of Biotechnology, NCHU 2008/08 – now
Assistant Professor Institute of Genomics and Bioinformatics 2009/02 – now
Assistant Professor Biophysics Society of R.O.C. 2007/05 –
Adjunct Assistant Professor Graduate Institute of Biotechnology, NCHU 2007/02 –
Joint Assistant Professor Department of Life Sciences, NCHU 2007/02 -now
Assistant Professor Biotechnology Center, NCHU 2008/08 -now
Postdoctoral Fellow Institute of Molecular Biology, Academia Sinica 2006/01 – 2007/01
Ph.D. Graduate Institute of Life Science, National Defense Medical Center and Academia Sinica 2001/08 – 2005/12
M.S. Institute of Genetics, National Yang Ming University 1995/09 to 1997/06
B.P. School of Pharmacy, Taipei Medical College 1991/09 to 1995/06

Professional

Content
  1. 美國結晶學會暑期訓練課程「Summer course in crystallography」蛋白質結構與功能(Structure and function of proteins) 美國喬治亞大學 (University of Georgia)(2001/06)

Speech

Content
  1. “Glycosphingolipid-facilitated membrane insertion and internalization of cobra cardiotoxin: crystal structure of the cardiotoxin/sulfatide complex.”美國結晶學會 2006 年年會「環太平洋地區X光與中子設施的科學研究」議程 (2006/07)

Lectures

Course [download course materials]
  • [Undergraduate courses] Biochemistry
  • [Undergraduate courses] Biotechnology
  • [Graduate courses] Seminar
  • [Graduate courses] Advanced Biochemistry
  • [Graduate courses] Applied Genomics and Bioinformatics: Lecture and Experiment
  • [Graduate courses] Protein Engineering
  • [Graduate courses] Protein Molecular Simulation & Rational Drug Design
  • [Grad. Inst. Biotech] Special Topics in Biochemistry
  • [Grad. Inst. Biotech] Special Topics in Biotechnology
  • [General education Lecture] Life Sciences & Life
  • [Summer Core Credit Course] Application and Experiment of Bioinformatics in Life Science
  • [Summer Core Credit Course] Functional Proteomics and Experiment
  • [Summer Core Credit Course] Genomics

 

Expertise
  1. Protein Structure Analyze
  2. Structural Bioinformatics
  3. X-ray Biomolecular Crystallography

Research

Lab research [details]

Research Interests:

 

My research interests are in the structure and function of a wide range of important biological macromolecules, including:

I. Chromatin structure remodeling mechanism in yeast

The eukaryotic genome is packaged into chromatin, which can inhibit the accessibility of certain DNA binding factors to their cognate sites in vivo. However, changes in chromatin structure play an important role in processes such as transcription, replication, DNA damage repair, and recombination. Two such ATP-dependent chromatin remodeling complexes in yeast Saccharomyces cerevisiae include the SWI/SNF complex and the RSC complex (Remodels the Structure of Chromatin). Of the two, only RSC is essential for viability, serving an important function in cell cycle progression from G2 to M. RSC is an abundant complex of at least 16 subunits, which was purified on the basis of homology of several of its subunits to those of the SWI/SNF complex.

 

II. JAK/STAT signaling pathway in fruitfly

The signal transduction pathway conducted by JAK (Janus Activated Kinases) and STAT(Signal Transducers and Activators of Transcription) plays a critical role in hematopoiesis and immune response, and mis-regulation of the pathways is associated with a wide range of immunologic diseases and to leukemia in humans. However, the structure/function relationship of the interaction between cytokine receptors, JAKs and STATs still remains largely elusive duo to the lack of structural information. In vertebrates, there are many ligands, receptors, JAKs and STATs making this signaling pathway very complex to be analyzed. By contrast, the JAK/STAT pathway in the fruitfly Drosophila melanogaster is less redundant offering a simpler model to study.

 

III. The telomere system of the Streptomyces linear plasmid SCP1

Linear plasmids and chromosomes of Streptomyces carry terminal proteins (TPs) covalently attached to the 5′ ends of the DNA. Most known telomeres are conserved in primary sequence and in the potential secondary structures formed during replication. The TP that caps these telomeres is also highly conserved and its coding gene, tpg, is present in most Streptomyces chromosomes and some linear plasmids. However, linear plasmid SCP1 of Streptomyces coelicolor contains atypical telomere sequences and no tpg homologue, and can replicate in the absence of tpg, suggesting that it carries a novel TP gene. A gene on SCP1 (designated tpc) encodes the TP that caps the SCP1 telomeres. The Tpc protein sequence does not resemble the Tpg proteins. A gene (designated tac) upstream of tpc was also required for replication of the SCP1 telomeres. These findings indicate that the Tac-Tpc system of SCP1 represents a novel telomere-capping system of Streptomyces linear replicons.

Publications

Journal (*Corresponding author)
  1. Liu, J.-H.*, Yang, J.-Y., Hsu, D.-W., Lai, Y.-H., Li, Y.-P., Tsai, Y.-R. and Hou, M.-H. (2019, Oct.) Crystal structure-based exploration of arginine-containing peptide binding in the ADP-ribosyltransferase domain of the type III effector XopAI protein(2019)
  2. Fang, Y.-T., Lai, W.-S., Liu, J.-H.*, Liu, Y.-C.*: Enhanced cecropin B2 production via chitin-binding domain and intein self-cleavage system. Biotechnology And Applied Biochemistry(2018)
  3. Shen, W.-F., Galula, J.U., Liu, J.-H., Liao, M.-Y., Huang, C.-H., Wang, Y.-C., Wu, H.-C., Liang, J.-J., Lin, Y.-L., Whitney, M.-T., Chang, G.-J., Chen, S.-R., Wu, S.-R., Chao, D.-Y.: Epitope resurfacing on dengue virus-like particle vaccine preparation to induce broad neutralizing antibody. Elife(2018)
  4. Chiu, H.-C., Huang, W.-R., Liao, T.-L., Chi, P.-I., Nielsen, B.L., Liu, J.-H., Liu, H.-J.: Mechanistic insights into avian reovirus p17-modulated suppression of cell cycle CDK-cyclin complexes and enhancement of p53 and cyclin H interaction. Journal Of Biological Chemistry(2018)
  5. Lee, C.-Y., Lin, C.-C., Liu, Y.-L., Liu, G.-Y.*, Liu, J.-H.*, Hung, H.-C.*: Molecular interplay between the dimer interface and the substrate-binding site of human peptidylarginine deiminase 4. Scientific Report(2017)
  6. Li, C., Bai, X., Meng, R., Shaozhou, W., Zhang, Q., Hua, R., Liu, J.-H., Liu, M., Zhang, Y.*: Identification of a new broadly cross-reactive epitope within domain III of the duck Tembusu virus E protein. Scientific Reports(2016)
  7. Li, C., Liu, J., Shaozhou, W., Bai, X., Zhang, Q., Hua, R., Liu, J.-H.*, Liu, M.*, Zhang, Y.*: Epitope identification and application for diagnosis of duck Tembusu virus infections in ducks. VIRUSES-BASEL(2016)
  8. Kuo, T.-C., Li, L.-W., Pan, S.-H.*, Fang, J.-M.*, Liu, J.-H., Cheng, T.-J., Wang, C.-J., Hung, P.-F., Chen, H.-Y., Hong, T.-M., Hsu, Y.-L., Wong, C.-H., Yang, P.-C.: Purine-type compounds induce microtubule fragmentation and lung cancer cell death through interaction with katanin. Journal of Medicinal Chemistry(2016)
  9. Chen, J.-C., Liu, J.-H., Hsu, D.-W., Shu, J.-C., Chen C.-Y., Chen, C.-C.*: Methylatable signaling helix coordinated inhibitory receiver domain in sensor kinase modulates environmental stress response in Bacillus cereus. PLoS One(2015)
  10. Hsieh, J.-Y., Li, S.-Y., Tsai, W.-C., Liu, J.-H., Lin, C.-L., Liu, G.-Y.*, Hung, H.-C.*: A small-molecule inhibitor suppresses the tumor-associated mitochondrial NAD(P)+-dependent malic enzyme (ME2) and induces cellular senescence. Oncotarget(2015)
  11. Lin, H.-Y., Liu, J.-H., Cheng, K.-L., Lin, J.-Y., Liu, N.-R., Meng, M.-H.*: A novel binding of GTP stabilizes the structure and modulates the activities of human phosphoglucose isomerase/autocrine motility factor. Biochemistry and Biophysics Reports(2015)
  12. Hsieh, J.-Y., Li, S.-Y., Chen, M.-C., Yang, P.-C., Chen, H.-Y., Chan, N.-L.*, Liu, J.-H.*, Hung, H.-C.*: Structural characteristics of the nonallosteric human cytosolic malic enzyme. BIOCHIMICA ET BIOPHYSICA ACTAPROTEINS AND PROTEOMICS(2014)
  13. Hsieh, J.-Y., Liu, J.-H., Yang, P.-C., Lin, C.-L., Liu, G.-Y.*, Hung, H.-C.* (2014, Jun). :Fumarate analogs act as allosteric inhibitors of the human mitochondrial NAD(P)+-dependent malic enzyme.PLoS One
  14. 1. Chepyshko, H., Lai, C.-P., Huang, L.-M., Liu, J.-H., and Shaw, J.-F. (2012, Jul.) Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. BMC Genomics 13, 309 doi:10.1186/1471-2164-13-309 (SCI, IF2011=4.073 Times cited :8)
  15. Hsieh, J.-Y., Liu, J.-H., Fang, Y.-W., Hung, H.-C. (2009, May.) Dual roles of Lys57 at the dimer interface of human mitochondrial NAD(P)+-dependent malic enzyme. Biochem. J. 402, 201-9. (SCI, IF2007=4.009 Times cited :0)
  16. Li, T.-N., Chin, K.-H., Liu, J.-H., Wang, A H.-J., Chou, S.-H. (2009, May.) XC1028 from Xanthomonas campestris adopts a PilZ domain-like structure without a c-di-GMP switch. Proteins. 75, 282-8. (SCI, IF2007=3.354 Times cited :0)
  17. Chou, C.-C., Chang, C.-W., Liu, J.-H., Chen, L.-F., Hsiao, C.-D., Chen, H.-W. (2007, Sep.) Small Ubiquitin-like Modifier Modification Regulates the DNA Binding Activity of Glial Cell Missing Drosophila Homolog a. J. Biol. Chem. 282, 27239-49. (SCI, IF2006=5.808 Times cited :3)
  18. Wang, C.-H.*, Liu, J.-H.*, Lee, S.-C., Wu, W.-g., and Hsiao, C.-D. (2006, Jan.) Glycosphingolipid-facilitated membrane insertion and internalization of cobra cardiotoxin: the sulfatide/cardiotoxin complex structure in a membrane-like environment suggests a lipid-dependent cell-penetrating mechanism for membrane binding polypeptides. J. Biol. Chem. 281, 656-77.(SCI, IF 2006=5.808; Times cited: 15) *These authors contributed equally to this work.
  19. Liu, J.-H., Chang, T.-W., Huang, C.-Y., Chen, S.-U., Wu, H.-N., Chang, M.-C., Hsiao, C.-D. (2004, Nov.) Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli. J. Biol. Chem. 279, 50465-71. (SCI, IF2006=5.808 Times cited : 5)
  20. Forouhar, F., Huang, W.-N., Liu, J.-H., Chien, K.-Y., Wu, W.-g. and Hsiao, C.-D. (2003, Jun.) Structural basis of the membrane-induced cardiotoxin A3 oligomerization. J. Biol. Chem. 278, 21980-8. (SCI, IF2006=5.808 Times cited :21)[PDB]
  21. Liu, J. H., Liao, Y. D., Sun Y. J. (2001, Nov.) Crystallization and preliminary X-ray diffraction analysis of cytotoxic ribonucleases from bullfrog Rana catesbeiana. Acta Crystallogr. D57, 1697-9. (SCI, IF2006=1.687 Times cited :0)

 

Conference (*Invited speaker)
  1. Liu, J.-H., Lee, Y.-P., Yang, J.-Y.: The Crystal Structure of the N-terminally Deleted Type III Effector protein XopAI. The 23th Biophysics Conference.
  2. Liu, J.-H., Lee, C.-Y., Lin, C.-C., Liu, Y.-L., Liu, G.-Y., Hung, H.-C.: Molecular Dynamics Study on the Interaction between Dimer Interface and Substrate-Binding Site of Human Peptidylarginine Deiminase 4. The 22th Biophysics Conference.
  3. Liu, J.-H.: Replica exchange molecular dynamics method for Trp-cage folding simulation in implicit solvent. The 20th Biophysics Conference.
  4. Peng, L.-W., Chen, Y.-T., and Liu, J.-H.: Crystallization of Dps protein from Klebsiella oxytoca The 20th NSRRC Users’ Meeting.
  5. Lin, C.-W., Hung, H.-C., and Liu, J.-H.: Crystallization of human cytosolic NADP+-dependent malic enzyme complexed with cofactor and substrates. The 20th NSRRC Users’ Meeting.
  6. Chen, C.-W., Shen, G.-H., Chen, J.-H., and Liu, J.-H.(2013, Nov) Virtual screening and experimental verification to identify potential inhibitors of the Erm(41) methyltransferase responsible for bacterial resistance against macrolide antibiotics. 台灣生物化學及分子生物學學會2013年冬令營. (Poster)
  7. Peng, L.-W., Chen, Y.-T. and Liu, J.-H.. (2013, Sep) Crystallization of β-lactamase like protein from Klebsiella oxytoca E718. The 19th NSRRC Users’ Meeting. (Poster)
  8. Liu, J.-H., Chen, C. K.-M., Chang, S.-W., Shaw, J.-F., Wang, A. H.-J., and Liu, J.-H. (2012, Oct.) Preliminary X-ray crystallographic analysis of trehalose synthase from Deinococcus radiodurans. The 18th NSRRC Users’ Meeting. (Poster)
  9. Chen, J.-W., Nien, C.-Y., Chen, C. K.-M., Chang, S.-W., Shaw, J.-F., Wang, A. H.-J., and Liu, J.-H.(2012, Oct.) Preliminary X-ray crystallographic analysis of trehalose synthase from Picrophilus torridus. The 18th NSRRC Users’ Meeting. (Poster)
  10. Nien, C.-Y., Cheng, C.-Y., Liu, J.-H., Shaw, J.-F., and Chen, Y.-T. (2012, May.) Crystal structure of glutaredoxin from Chlorella sorokiniana T-89. The 17th Biophysics Conference. (Poster)
  11. Hung, S.-J. and Liu, J.-H. (2012, May.) Design of an accurate predictor for the thermostable protein design in PERT server. The 17th Biophysics Conference. (Poster)
  12. Wu, J.-E., Chiu, S.-W., Yang, J.-Y., and Liu, J.-H. (2012, Mar.) Crystal structure of XopAI from Xanthomonas axonopodis pv. citri. 2012 International Conference on c-di-GMP and Xanthomonads. (Poster)
  13. Hung, S.-J. andLiu, J.-H. (2011, Dec.) PERT: an integrated informatics platform for thermostable protein design. 2011 Taiwan Enzyme Mechanism Conference. (Poster)
  14. Nien, C.-Y., Cheng, C.-Y., Shaw, J.-F., Chen, Y.-T., and Liu, J.-H. (2011, Oct.) Crystallization and preliminary X-ray crystallographic analysis of Chlorella glutaredoxin. The 17th NSRRC Users’ Meeting. (Poster)
  15. Wu, J.-E., Chiu, S.-W., Yang, J.-Y., and Liu, J.-H. (2010, Oct.) Crystallization and preliminary X-ray crystallographic analysis of XopAI from Xanthomonas axonopodis pv. citri. The 16th NSRRC Users’ Meeting. (Poster)
  16. Liu, J.-H., Hong, C.-S., Chang, S.-W., and Shaw, J.-F. (2009, Nov.) Investigation of the structural basis for thermostability of trehalose synthase from Picrophilus torridus. The 5th International Symposium on Biocatalysis and Biotechnology. (Poster)
  17. Hsu, Y.-J. and Liu, J.-H. (2009, Oct.) Effects of trimethylamine-N-oxide (TMAO) on the interactions of lysozyme in crystal. The 15th NSRRC Users’ Meeting. (Poster)