Molecular Biochemistry Lab

                       PI: Huang, Cheng-Yang  Ph.D.

            Professor, Chung Shan Medical University

      This PI has been selected as "World's Top 2% Scientists 2022"

              Int. J. Mol. Sci. (Editorial board member)

              Plants (Lead Editor of the Special Issue)

             Adv. Biol. (Editor)

             BioMed Research International (Lead Editor of the Special Issue)

             Bioinorg. Chem. Appl. (Lead Editor of the Special Issue)

                 

                   

　

 

　

 

　

　

　

　

　

　

E-mail: cyhuang@csmu.edu.tw  　

Experience

2008.02-present    Professor/Associate Professor/Assistant Professor, Chung Shan Medical University, Taiwan

2007.08-2008.01  Adjunct Assistant Professor, Department of Nature Sciences, Taipei Municipal University of Education, Taiwan

2003.09-2008.01  Postdoctoral Fellow, Institute of Molecular Biology, Academia Sinica, Taiwan

1999.09-2003.09  Ph.D., Department of Biological Science and Technology, National Chiao Tung University, Taiwan

                   

Research Field

Enzymology, Protein engineering, Molecular and Structural Biology, Structure-Based Drug Design, Biosynthesis

　

Activity

As a reviewer (2013-2017): Molecular Biology and Evolution; Biochimie; BMC Biochemistry; BBA; PLOS ONE; Sensors; Biocatalysis and Biotransformation; Biomedical J.; Journal of Cellular Physiology; Nucleic Acids Res; Oncotarget; Journal of Cellular Biochemistry

As an editor (2013-2016): Advances in Biology

As a lead editor of the Special Issue (2013-2014): BioMed Research International (IF: 2.47)

As a lead editor of the Special Issue (2017-2018): Bioinorg. Chem. Appl. (IF: 2.583)

　

Refereed Papers

  1. Chen, C.B., Wang, C.W., Lu, C.W., Chen, W.T., Zhou, B.R., Chu, C.Y., Hsu, S.F., Yang, C.T., Wen-Cheng Chang, J., Yang, C.K., Wang, C.L., Fang, Y.F., Hsu, P.C., Hua, C.C., Wu, C.E., Ko, H.W., Chen, K.C., Yang, Y.C., Tseng, H.C., Cheng, A.Y., Tseng, L.C., Shih, F.Y., Hung, S.I., Huang, C.Y.*, Chung, W.H.* (2024) Class I HLA Alleles are associated with an increased risk of osimertinib-induced hypersensitivity. J. Allergy Clin. Immunol. Pract., accepted and in press. (SCI)

  2. Huang, Y.H., Huang, C.Y.* (2024) Anti-skin aging and cytotoxic effects of methanol-extracted Solanum betaceum red fruit seed extract on Ca9-22 gingival carcinoma cells. Plants, 13, 2215. (SCI)

  3. Huang, Y.H., Huang, C.Y.* (2024) Anti-skin aging potential, antibacterial activity, inhibition of single-stranded DNA-binding protein, and cytotoxic effects of acetone-extracted Passiflora edulis (Tainung No. 1) rind extract on oral carcinoma cells. Plants, 13, 2194. (SCI)

  4. Su, H.H., Lin, E. S., Huang, Y.H., Lien, Y., Huang, C.Y.* (2024) Inhibition of SARS-CoV-2 Nsp9 ssDNA-binding activity and cytotoxic effects on H838, H1975, and A549 human non-small cell lung cancer cells: Exploring the potential of Nepenthes miranda leaf extract for pulmonary disease treatment. Int. J. Mol. Sci., 25, 6120. (SCI)

  5. Lin, E.S., Huang, C.Y.* (2024) Binding pattern and structural interactome of the anticancer drug 5-fluorouracil: A critical review. Int. J. Mol. Sci., 25, 3404. (SCI)

  6. Lee, C.Y., Chen, Y.C., Huang, Y.H., Lien, Y., Huang, C.Y.* (2024) Cytotoxicity and multi-enzyme inhibition of Nepenthes miranda stem extract on H838 human non-small cell lung cancer cells and RPA32, elastase, tyrosinase, and hyaluronidase proteins. Plants, 13, 797. (SCI)

  7. Wu, S.W., Chen, Y.J., Chang, Y.W., Huang, C.Y., Liu, B.H., Yu, F.Y.* (2024) Novel enzyme‑linked aptamer‑antibody sandwich assay and hybrid lateral flow strip for SARS‑CoV‑2 detection. J. Nanobiotechnology, 22, 5. (SCI)

  8. Huang, Y.H., Huang, C.Y.* (2024) The complexed crystal structure of dihydropyrimidinase reveals a potential interactive link with the neurotransmitter γ-aminobutyric acid (GABA). Biochem. Biophys. Res. Commun., 692, 149351. (SCI)

  9. Su, H.H., Huang, Y.H., Lien, Y., Yang, P.C., Huang, C.Y.* (2023) Crystal structure of DNA replication protein SsbA complexed with the anticancer drug 5-fluorouracil. Int. J. Mol. Sci., 24, 14899. (SCI)

  10. Lin, E.S., Huang, C.Y.* (2023) The inhibition activities of the fruit extract of Plinia cauliflora against melanoma cells and the single-stranded DNA-binding protein (SSB) from Klebsiella pneumoniae. Appl. Sci., 13, 11061. (SCI)

  11. Lin, E.S., Huang, Y.H., Chung, J.C., Su, H.H., Huang, C.Y.* (2023) The inhibitory effects and cytotoxic activities of the stem extract of Nepenthes miranda against single-stranded DNA-binding protein and oral carcinoma cells. Plants, 12, 2188. (SCI)

  12. Chen, P.J., Lin, E.S., Su, H.H., Huang, C.Y.* (2023) Cytotoxic, antibacterial, and antioxidant activities of the leaf extract of Sinningia bullata. Plants, 12, 859. (SCI)

  13. Huang, Y.H., Yang, P.C., Lin, E.S., Ho.Y.Y., Peng, W.F., Lu, H.P., Huang, C.C., Huang, C.Y.* (2023) Crystal structure of allantoinase from Escherichia coli BL21: a molecular insight into a role of the active site loops in catalysis. Molecules, 28, 827. (SCI)

  14. Lin, E.S., Huang, Y.H., Yang, P.C., Peng, W.F., Huang, C.Y.* (2023) Complexed crystal structure of the dihydroorotase domain of human CAD protein with the anticancer drug 5-fluorouracil. Biomolecules, 13, 149. (SCI)

  15. Liu, H.W., Chiang, W.Y., Huang, Y.H., Huang, C.Y.* (2022) The inhibitory effects and cytotoxic activities of the stem extract of Sarracenia purpurea against melanoma cells and the SsbA protein. Plants, 11, 3164. (SCI)

  16. Lin, E.S., Huang, C.Y.* (2022) Cytotoxic activities and the allantoinase inhibitory effect of the leaf extract of the carnivorous pitcher plant Nepenthes miranda. Plants, 11, 2265. (SCI)

  17. Huang, Y.H., Chiang, W.Y., Chen, P.J., Lin, E.S., Huang, C.Y.* (2022) Anticancer and antioxidant activities of the root extract of the carnivorous pitcher plant Sarracenia purpurea. Plants, 11, 1668. (SCI)

  18. Lin, E.S., Huang, Y.H., Luo, R.H., Basharat, Z., Huang, C.Y.* (2022) Crystal structure of an SSB protein from Salmonella enterica and its inhibition by flavanonol taxifolin. Int. J. Mol. Sci., 23, 4399. (SCI)

  19. Lin, E.S., Luo, R.H., Yang, Y.C., Huang, C.Y.* (2022) Molecular insights into how the dimetal center in dihydropyrimidinase can bind the thymine antagonist 5-aminouracil: A different binding mode from the anticancer drug 5-fluorouracil. Bioinorg. Chem. Appl., 2022, 1817745. (SCI)

  20. Lin, E.S., Luo, R.H., Huang, C.Y.* (2022) A complexed crystal structure of a single-stranded DNA-binding protein with quercetin and the structural basis of flavonol inhibition specificity. Int. J. Mol. Sci., 23, 588. (SCI).

  21. Guan, H.H., Huang, Y.H., Lin, E.S., Chen, C.J., Huang, C.Y.* (2021) Structural analysis of Saccharomyces cerevisiae dihydroorotase reveals molecular insights into the tetramerization mechanism. Molecules, 26, 7249. (SCI)

  22. Lin, E.S., Huang, Y.H., Huang, C.Y.* (2021) Characterization of the chimeric PriB-SSBc protein. Int. J. Mol. Sci., 22, 10854. (SCI)

  23. Guan, H.H., Huang, Y.H., Lin, E.S., Chen, C.J., Huang, C.Y.* (2021) Complexed crystal structure of Saccharomyces cerevisiae dihydroorotase with inhibitor 5-fluoroorotate reveals a new binding mode. Bioinorg. Chem. Appl., 2021, 2572844. (SCI)

  24. Guan, H.H., Huang, Y.H., Lin, E.S., Chen, C.J., Huang, C.Y.* (2021) Plumbagin, a natural product with potent anticancer activities, binds to and inhibits dihydroorotase, a key enzyme in pyrimidine biosynthesis. Int. J. Mol. Sci., 22, 6861. (SCI)

  25. Guan, H.H., Huang, Y.H., Lin, E.S., Chen, C.J., Huang, C.Y.* (2021) Structural basis for the interaction modes of dihydroorotase with the anticancer drugs 5-fluorouracil and 5-aminouracil. Biochem. Biophys. Res. Commun., 551, 33-37. (SCI)

  26. Lin, E.S., Huang, C.Y.* (2021) Crystal structure of the single-stranded DNA-binding protein SsbB in complex with the anticancer drug 5-fluorouracil: Extension of the 5-fluorouracil interactome to include the oligonucleotide/oligosaccharide-binding fold protein. Biochem. Biophys. Res. Commun., 534, 41-46. (SCI)

  27. Wang CW, Tassaneeyakul W, Chen CB, Chen WT, Teng YC, Huang CY, Sukasem C, Lu CW, Lee YS, Choon SE, Nakkam N, Chung-Yee Hui R, Huang YH, Chang YC, Yu-Wei Lin Y, Chang CJ, Chiu TM, Chantratita W, Konyoung P, Lee CN, Klaewsongkram J, Rerkpattanapipat T, Amornpinyo W, Saksit N, Rerknimitr P, Huei HY, Lin SH, Hsu CK, Fan WL, Chan CC, Lin YJ, Hung SI, Chung WH (2021) Whole genome sequencing identifies genetic variants associated with co-trimoxazole hypersensitivity in Asians. J. Allergy Clin. Immunol., 147, 1402-1412. (SCI)

  28. Huang, Y.H., Huang, C.Y.* (2021) Comparing SSB-PriA functional and physical interactions in Gram-positive and -negative bacteria. Methods Mol. Biol., 2281, 67-80.

  29. Huang, C.Y.* (2020) Structure, catalytic mechanism, posttranslational lysine carbamylation, and inhibition of dihydropyrimidinases. Adv. Protein Chem. Struct. Biol. (Elsevier), 122,  63-96. (SCI)

  30. Huang, Y.H., Lien, Y., Chen, J.H., Lin, E.S., Huang, C.Y.* (2020) Identification and characterization of dihydropyrimidinase inhibited by plumbagin isolated from Nepenthes miranda extract. Biochimie, 171-172, 124-135. (SCI)

  31. Huang, Y.H., Chen, I.C., Huang, C.Y.* (2019) Characterization of an SSB–dT25 complex: structural insights into the S-shaped ssDNA binding conformation. RSC Adv., 9, 40388-40396. (SCI)

  32. Huang, Y.H., Lin, E.S., Huang, C.Y.* (2019) Complexed crystal structure of SSB reveals a novel single-stranded DNA binding mode (SSB)3:1: Phe60 is not crucial for defining binding paths. Biochem. Biophys. Res. Commun., 520, 353-358. (SCI)

  33. Huang, Y.H., Ning, Z.J., Huang, C.Y.* (2019) Crystal structure of dihydropyrimidinase in complex with anticancer drug 5-fluorouracil. Biochem. Biophys. Res. Commun., 519, 160-165. (SCI)

  34. Chen, K.L., Huang, Y.H., Liao, J.F., Lee, W.C., Huang, C.Y.* (2019) Crystal structure of the C-terminal domain of the primosomal DnaT protein: Insights into a new oligomerization mechanism. Biochem. Biophys. Res. Commun., 511, 1-6. (SCI)

  35. Huang, Y.H., Huang, C.Y.* (2018) The glycine-rich flexible region in SSB is crucial for PriA stimulation. RSC Adv., 8, 35280-35288. (SCI)

  36. Cheng, J.H., Huang, Y.H., Lin, J.J., Huang, C.Y.* (2018) Crystal structures of monometallic dihydropyrimidinase and the human dihydroorotase domain K1556A mutant reveal no lysine carbamylation within the active site. Biochem. Biophys. Res. Commun., 505, 439-444. (SCI)

  37. Huang, C.Y.* (2018) Crystal structure of SSB complexed with inhibitor myricetin. Biochem. Biophys. Res. Commun., 504, 704-708. (SCI)

  38. Chen, K.L., Cheng, J.H., Lin, C.Y., Huang, Y.H., Huang, C.Y.* (2018) Characterization of single-stranded DNA-binding protein SsbB from Staphylococcus aureus: SsbB cannot stimulate PriA helicase. RSC Adv., 8, 28367-28375. (SCI)

  39. Cheng, J.H., Huang, C.C., Huang, Y.H., Huang, C.Y.* (2018) Structural basis for pH-dependent oligomerization of dihydropyrimidinase from Pseudomonas aeruginosa PAO1. Bioinorg. Chem. Appl., 2018, 9564391. (SCI)

  40. Huang, Y.H., Huang, C.Y.* (2018) SAAV2152 is a single-stranded DNA binding protein: the third SSB in Staphylococcus aureus. Oncotarget, 9, 20239-20254. (SCI) 

  41. Huang, Y.H., Guan, H.H., Chen, C.J., Huang, C.Y.* (2017) Staphylococcus aureus single-stranded DNA-binding protein SsbA can bind but cannot stimulate PriA helicase. PLoS One, 12, e0182060. (SCI)

  42. Tzeng, C.T., Huang, Y.H., Huang, C.Y.* (2016) Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1: Insights into the molecular basis of formation of a dimer. Biochem. Biophys. Res. Commun., 478, 1449-1455. (SCI)

  43. Ko, T.P., Huang, C.Y., Hsieh, T.J., Chen, S.C., Chen, Y.R., Yang, C.S., Kuo, H.C., Wang, W.L., Hsiao, T.H., Lin, C.H., Chen, Y.* (2016) Crystal structures of Staphylococcal SaeR reveal possible DNA-binding modes. Biochem. Biophys. Res. Commun., 474, 686-690. (SCI)

  44. Huang, C.C., Huang, C.Y.* (2016) DnaT is a PriC-binding protein. Biochem. Biophys. Res. Commun., 477, 988-992. (SCI)

  45. Huang, Y.H., Lien, Y., Huang, C.C., Huang, C.Y.* (2016) Characterization of Staphylococcus aureus primosomal DnaD protein: Highly conserved C-terminal region is crucial for ssDNA and PriA helicase binding but not for DnaA protein-binding and self-tetramerization. PLoS One, 11, e0157593. (SCI)

  46. Huang, C.Y.* (2015) Inhibition of a putative dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by flavonoids and substrates of cyclic amidohydrolases. PLoS One, 10, e0127634. (SCI)

  47. Huang, C.Y.*, Abe Y., Ding, H., Chung, IF. (2015) Helicase and its interacting factors: regulation mechanism, characterization, structure, and application for drug design. Biomed Res. Int., 2015, 909047. (SCI)

  48. Huang, Y.H., Huang, C.C., Chen, C.C., Yang, K.J., Huang, C.Y.* (2015) Inhibition of Staphylococcus aureus PriA helicase by flavonol kaempferol. Protein J., 34, 169-172.(SCI)

  49. Huang, Y.H., Huang, C.Y.* (2015) Creation of a putative third metal binding site in type II dihydroorotases significantly enhances enzyme activity. Protein Pept. Lett., 22, 1117-1122. (SCI)

  50. Huang, Y.H., Huang, C.Y.* (2014) Structural insight into the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT. Review article. Biomed Res. Int., 2014, 195162. (SCI)

  51. Huang, Y.H., Huang, C.Y.* (2014) C-terminal domain swapping of SSB changes the size of the ssDNA binding site. Biomed Res. Int., 2014, 573936. (SCI)

  52. Peng, W.F., Huang, C.Y.* (2014) Allantoinase and dihydroorotase binding and inhibition by flavonols and the substrates of cyclic amidohydrolases. Biochimie, 101, 113-122. (SCI)

  53. Huang, Y.H., Lin, M.J., Huang, C.Y.* (2013) DnaT is a single-stranded DNA binding protein. Genes Cells, 18, 1007-1019. (SCI)

  54. Huang, Y.H., Huang, C.Y.* (2013) The N-terminal domain of DnaT, a primosomal DNA replication protein, is crucial for PriB binding and self-trimerization. Biochem. Biophys. Res. Commun., 442, 147-152. (SCI)

  55. Ho, Y.Y., Huang, Y.H., Huang, C.Y.* (2013) Chemical rescue of the post-translationally carboxylated lysine mutant of allantoinase and dihydroorotase by metal ions and short-chain carboxylic acids. Amino Acids, 44, 1181-1191. (SCI)

  56. Huang, Y.H., Lin, M.J., Huang, C.Y.* (2013) Yeast two-hybrid analysis of PriB-interacting proteins in replication restart primosome: a proposed PriB-SSB interaction model. Protein J., 32, 477-483. (SCI)

  57. Huang, Y.H., Lo, Y.H., Huang, W., Huang, C.Y.* (2012) Crystal structure and DNA-binding mode of Klebsiella pneumoniae primosomal PriB protein. Genes Cells, 17, 837-849. (SCI); this article was also selected in World Biomedical Frontiers (2013) Infection and Immunity, 11, 17 (ISSN 2328-0166). 

  58. Lin, H.H., Huang, C.Y.* (2012) Characterization of flavonol inhibition of DnaB helicase: real-time monitoring, structural modeling, and proposed mechanism. J. Biomed. Biotechnol., 2012, 735368. (SCI)

  59. Huang, Y.H., Huang, C.Y.* (2012) Characterization of a single-stranded DNA binding protein from Klebsiella pneumoniae: mutation at either Arg73 or Ser76 causes a less cooperative complex on DNA. Genes Cells, 17, 146-157. (SCI)

  60. Huang, Y.H., Lin, H.H., Huang, C.Y.* (2012) A single residue determines the cooperative binding property of a primosomal DNA replication protein, PriB, to single-stranded DNA. Biosci. Biotechnol. Biochem., 76, 1110-1115. (SCI)

  61. Huang, C.Y.* (2012) Determination of the binding site-size of the protein-DNA complex by use of the electrophoretic mobility shift assay, an invited review in a book chapter: Stoichiometry and Research - The Importance of Quantity in Biomedicine (ISBN 978-953-51-0198-7), Chapter 10, pp. 235-242, edited by Innocenti, A., InTech Press Inc.

  62. Ho, Y.Y., Hsieh, H.C., Huang, C.Y.* (2011) Biochemical characterization of allantoinase from Escherichia coli BL21. Protein J., 30, 384-394. (SCI)

  63. Huang, Y.H., Lee, Y.L., Huang, C.Y.* (2011) Characterization of a single-stranded DNA binding protein from Salmonella enterica serovar Typhimurium LT2. Protein J., 30, 102-108. (SCI)

  64. Hsieh, H.C., Huang, C.Y.* (2011) Identification of a novel protein, PriB, in Klebsiella pneumoniae. Biochem. Biophys. Res. Commun., 404, 546-551. (SCI)

  65. Chen, C.C., Huang, C.Y.* (2011) Inhibition of Klebsiella pneumoniae DnaB helicase by the flavonol galangin. Protein J., 30, 59-65. (SCI)

  66. Jan, H.C., Lee, Y.L., Huang, C.Y.* (2011) Characterization of a single-stranded DNA-binding protein from Pseudomonas aeruginosa PAO1. Protein J., 30, 20-26. (SCI)

  67. Wang, C.C., Tsau, H.W., Chen, W.T., Huang, C.Y.* (2010) Identification and characterization of a putative dihydroorotase, KPN01074, from Klebsiella pneumoniae. Protein J., 29, 445-452. (SCI)

  68. Lo, Y.H., Tsai, K.L., Sun, Y.J., Chen, W.T., Huang, C.Y., Hsiao, C.D. (2009) The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA. Nucleic Acids Res., 37, 804-814. (SCI).

  69. Huang, C.Y., Hsu, C.C., Chen, M.C., Yang, Y.S. (2009) Effect of metal binding and posttranslational lysine carboxylation on the activity of recombinant hydantoinase. J. Biol. Inorg. Chem., 14, 111-121. (SCI)

  70. Huang, C.Y.*, Chang, Y.W., Chen, W.T. (2008) Crystal structure of the N-terminal domain of Geobacillus kaustophilus HTA426 DnaD protein. Biochem. Biophys. Res. Commun., 375, 220-224. (SCI)

  71. Tsai, K.L., Sun, Y.J., Huang, C.Y., Yang, J.Y., Hung, M.C., Hsiao, C.D. (2007) Crystal structure of the human FOXO3a-DBD/DNA complex suggests the effects of post-translational modification. Nucleic Acids Res., 35, 6984-6994. (SCI)

  72. Huang, C.Y., Hsu, C.H., Sun, Y.J., Wu, H.N., Hsiao, C.D. (2006) Complexed crystal structure of replication restart primosome protein PriB reveals a novel single-stranded DNA binding mode. Nucleic Acids Res., 34, 3878-3886. (SCI)

  73. Tsai, K.L., Huang, C.Y., Chang, C.H., Sun, Y.J., Chuang, W.J., Hsiao, C.D. (2006) Crystal structure of the human FOXK1a/DNA complex and its implications on the diverse binding specificity of winged helix/forkhead proteins. J. Biol. Chem., 281, 17400-17409. (SCI)

  74. Huang, C.Y., Yang, Y.S. (2005) Discovery of a novel N-iminylamidase activity: substrate specificity, chemicoselectivity and catalytic mechanism. Protein Expr. Purif. 40, 203-11. (SCI)

  75. Liu, J.H., Chang, T.W., Huang, C.Y., Chen, S.U., Wu, H.N., Chang, M.C., Hsiao, C.D. (2004) Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli. J. Biol. Chem. 279, 50465-71. (SCI)

  76. Huang, C.Y., Chao, Y.P., Yang, Y.S. (2003) Purification of industrial hydantoinase in one chromatographic step without affinity tag. Protein Expr. Purif. 30, 134-139. (SCI)

  77. Huang, C.Y., Chiang, S.K., Yang, Y.S., Sun, Y.J. (2003) Crystallization and preliminary X-ray diffraction analysis of thermophilic imidase from pig liver. Acta Crystallogr. D. Biol. Crystallogr. 59, 943-945. (SCI)

  78. Huang, C.Y., Yang, Y.S. (2003) A novel cold-adapted imidase from fish Oreochromis niloticus that catalyzes hydrolysis of maleimide. Biochem. Biophys. Res. Commun. 312, 467-472. (SCI)

  79. Huang, C.Y., Yang, Y.S. (2002) The role of metal on imide hydrolysis: metal content and pH profiles of metal ion-replaced mammalian imidase. Biochem. Biophys. Res. Commun. 297, 1027-1032. (SCI)