top of page

Yi-Sheng Cheng Professor

Ph.D. Graduate institute of life sciences, National Defense Medical Center, Taiwan

Specialty: Structural Biology, Structural Bioinformatics

E-mail: chengys@ntu.edu.tw

Laboratory: Life Science Building R1121

Telephone: 886-2-3366-2951

Current Research Interests

ys_edited.jpg

  1. Bioenergy: Structural and functional analyses of cellulose synthases from Bambusa oldhamii (BoCesAs)

  2. Epigenetics regulatory proteins: Biochemical and biophysical study of plant histone deacetylases (HDAs)

  3. Drug design and development: Structure based inhibitors development of MutT Homolog 1 (MTH1)

Brief of Researches

  • Fin219-FIP1 complex structure and function analysis

FIN219 (Far-red insensitive 219), also known as JAR1 (Jasmonate Resistant 1), is a protein composed of 575 amino acids, belonging to the Arabidopsis thaliana GH3 protein family. This protein in plants regulates the constancy of hormones in plants by combining plant hormones and amino acids such as indole-3-acetic acid (IAA) and jasmonic acid (JA) , Which in turn affects the growth and development of plants and the ability to resist pests and diseases. The functions of FIN219 can be divided into the following two directions:

(i) Related to Photomorphogenesis Photomorphogenesis is jointly regulated by photosensitizers that absorb red and far-red light and cryptochromes that absorb UV-A and blue light. Under far-red light irradiation, the fin219 mutant seedlings of Arabidopsis thaliana have an elongated hypocotyl phenotype and act as an extragenic suppressor of cop1 (Hsieh et al., 2000). In addition, the GST (glutathione S-transferases) protein gene fip1 (FIN219-interacting protein 1), the protein produced by it has been confirmed to interact with the C-terminus of FIN219 (Hsieh et al., 2007)

 

(ii) Regarding the regulation of plant hormones Jasmonic acid plays an important message transmission role in plants, which involves the transmission pathways of growth and development, resistance to diseases and insect pests and plant injuries. However, the understanding of jasmonic acid at the molecular level is very limited. At present, it is known that there are many small molecules that connect jasmonic acid and amino acid in plants, such as JA-Leu, JA-Val and JA-Phe, which are derived from JAR1. Catalyzes the joining of jasmonic acid and amino acids, of which JA and Ile have the highest affinity. Taking the Arabidopsis mutant strain jar1-1 of JAR1, adding JA-Ile in the medium can inhibit the elongation of the hypocotyl of seedlings, which is consistent with the wild type of JAR1. The JAZ (jasmonate ZIM-domain) protein family is considered to be an important key to regulating the transmission of jasmonate. JAZ1 can usually inhibit the transcription of jasmonate-responsive genes, but after treatment with jasmonate, it will cause the Degradation in the nucleus promotes the expression of genes related to the jasmonic acid reaction. The degradation mechanism is through SCFCOI1 (Skp/Cullin/F-box complex), a ubiquitin ligase (E3 ubiquitin ligase), which completes the interaction between proteins . The small molecule JA-Ile that promotes the interaction between Col1 and JAZ1 is the small molecule JA-Ile, which shows that JAR1 may be an important hub in regulating the delivery of jasmonic acid and the quality of related proteins. The results of this research were published in Proc. Natl. Acad. Sci. USA 114:E1815-E1824. Epub Feb 21, 2017

Previously completed research topics

Protein structure and function is an area that is highly valued in the post-genome era. Structural and functional analysis provides a three-dimensional view of the molecular level.
We use the technology of protein crystallography to analyze the three-dimensional structure of biological macromolecules (including DNA, RNA and protein), and to explore the structure, function, molecular evolution and related biological information.
Our current research directions are:

1. Biomass energy:
Analysis of protein structure and function of green bamboo cellulose synthase The plant cell wall is mainly composed of cellulose, hemicellulose, pectin, and secondary metabolites. Cellulose accounts for more than 50% of the cell wall composition and is the most abundant biomass on earth. The enzyme responsible for the production of cellulose in plant cells is the cellulose synthase complex (CSC), of which cellulose synthase (CesA) is the catalytic core and serves as the synthesis of long-chain sugars for the cellulose synthase complex Produce microfibril (microfibril), and further form plant cell wall. Bamboo is the fastest growing plant, with an average daily growth of up to 25 cm, indicating that its cellulose synthesis also needs to match its growth rate. This study analyzes the protein structure and biophysical properties of green bamboo cellulose synthases (Bambusa oldhamii Cellulose synthases, BoCesAs). There are 10 types of green bamboo cellulose synthase (BoCesA1~10). Currently, yeast expression system, fermented enzymes, has been used. The tank mass cultivation and rapid protein purification instrument successfully expressed BoCesA1, 2, 3, 4, 5 and 7 proteins, and subsequent development of enzyme activity analysis methods, protein crystal structure analysis and related biophysical research will be carried out successively. The ultimate goal is to analyze the structure of the green bamboo cellulose synthase complex to explore the molecular mechanism of plant cellulose synthesis.

2. Research on epigenetic regulatory proteins:
Biochemical and Biophysical Research on Plant Deacetylases HDAs Histone deacetylases (HDAs) are involved in the regulation of plant growth, development and the gene expression required for plant response to stress. The enzymatic activity of HDAs is to remove the acetyl group on histones and promote the formation of tight binding between histones and DNA. As a result, the chromatin will be concentrated and the genes located in this region cannot be expressed. There are 18 HDAs in Arabidopsis thaliana, which can be divided into three families: RPD3/HDA1-like family, HD2 family and Sirtuin family. Among them, RPD3/HDA1-like family has the most members and can be subdivided into three groups. This study is mainly aimed at The second group of HDA5, HDA15 and HDA18 were studied. Other HDAs will also continue to be studied. At present, we have constructed the active regions of the second group of deacetylases respectively, and performed activity analysis and comparison and protein structure analysis. Among them, the activity and polymerization form of HDA15 are affected by its N-terminal and C-terminal, which helps to understand its The molecular mechanism of action. Since epigenetic research has been very popular in recent years, and there are many proteins that interact with each other, this research topic will not only explore the structure of HDAs, but also focus on the binding proteins of related HDAs, such as transcription factors and post-translational modification proteins, etc. , To explore the ways of co-regulating gene expression. If the structure of these interacting proteins and HDAs can be resolved, it will be a major breakthrough for epigenetic research.

3. Drug design and development: MTH1 inhibitor structure and its inhibitory efficiency analysis
MutT Homolog 1 (MTH1) has been confirmed to have hydrolyzed and oxidized nucleotide triphosphates (dNTPs) to prevent the wrong nucleotide triphosphates (dNTPs) from being incorporated into DNA replication and causing gene mutations. In cancer cells, high levels of peroxide are easily produced, causing DNA damage. MTH1 can remove oxidized dNTPs to prevent cancer cells from entering the process of apoptosis. MTH1 is expressed in a small amount in normal cells, but in a large amount in cancer cells. Therefore, inhibiting the activity of MTH1 may be used as a drug to inhibit cancer cells and promote cancer cells to enter apoptosis. This study was developed in cooperation with the Department of Pharmacy. At the initial stage, more than 2,300 fragment based compound libraries were jointly screened. Using the ultra high throughput drug system of the Academia Sinica, 4 compounds were found to have MTH1 inhibitory ability. We analyzed The IC50 and enzyme kinetics of these four compounds, and the protein structure of three of them and MTH1 are solved. Based on the structure of these three compounds, new compounds will be further designed to analyze the inhibitory efficiency of MTH1 and the growth of cancer cells. The impact of these results will provide valuable drug design and development, and test the effectiveness of experiments in animal systems.

pnas-1609980114fig06.jpg

  • Ipomoelin-a sugar-binding protein induced by trauma and Jasmonate in sweet potato leaves

Lectin is a superfamily of a group of sugar-binding proteins in plants. When plants are subjected to biological adversity, such as herbivores gnawing and causing trauma, they will express this type of protein in large quantities. Therefore, they are regarded as plants suffering from animal taking. One of the defensive proteins produced during eating. Ipomoelin (IPO) is derived from sweet potato, and is abundantly expressed in leaves when sweet potato is infested by insects. After analysis, it can be classified as a group of glyco-binding proteins called Jacalin-related Lectins. This group is structurally composed of a single protein folded into a beta-prism monomer, and then further composed of four Tetramer. At present, it is known that this group of Jacalin-related Lectins have the characteristics of structural diversity, which means that this group of proteins consists of similar triangular-shaped monomers, which can form different forms of dimers, tetramers, and hexamers. (hexamer) and octomer, etc.
After analyzing the structure of IPO, it was found that it has an additional N-terminal structure that can form a tighter tetrad, which is not the same as the current tetrad formed in the Jacalin group, although they are all beta-triangular. It is composed of monomers, but the combination is very variable. This variability can provide useful information about protein-protein interaction. In addition, we also co-crystallized sugars such as methyl-alpha-D-mannose, methyl-alpha-D-glucose, and (sialic acid) sialic acid with IPO to obtain a complex structure. After comparing the binding modes of these sugars, we can Providing the specificity of IPO for carbohydrate binding will help the application of this type of carbohydrate binding protein in glycoprotein analysis. PLoS ONE (2012) 7: e40618. Epub on Jul 11, 2012

ipo-tetramer-20101118.jpg

  • Structural analysis of plant anti-insect and antibacterial protein-cysteine ​​protease inhibitor​​​

Tarocystatin is a kind of cysteine ​​protease inhibitor, a protease inhibitor that is expressed in large quantities in taro. The current research on this type of protease inhibitor mainly lies in the analysis of the inhibitory activity of its corresponding protease (such as papain). Since fungi, nematodes, and insects ingest plants, they need the action of cysteine ​​proteases. Therefore, plants use a large number of protease inhibitors to reduce or avoid the invasion of these organisms. We co-crystallized Tarocystatin and papain, and analyzed the structure of this complex by X-ray crystal diffraction technology, and established that its protease inhibition mode is similar to the binding mode in animals, showing that this type of cysteine ​​protease inhibits during the evolution process. The agent is based on a similar structure to achieve the purpose of plant insect resistance. In addition, we also completed the analysis of the inhibitory ability of tarocystatin by the analysis of inhibitory activity, and then we will target the C-terminal structure.

Tarocystatin is a family of plant cysteine ​​protease inhibitors (Phytocystatins). This family can be divided into three groups according to molecular weight: the first group has the smallest molecular weight, about 100 amino acids have a single CY domain, represented by rice OC-1. Its protein structure was solved by NMR method in 2000 and published in Biochemistry by Nagata et al. The second group has a larger molecular weight, about 205-250 amino acids, represented by tarocystatin, which can be divided into two domains, one The N-terminus, which is similar to the first group sequence, is the main inhibitory region. The other C-terminus extension region may have a structure similar to CY domain without inhibitory function. The third group is a protease inhibitor composed of repeated CY domains, with about 750 amino acids and 6 to 8 CY domains, represented by Potato PMC. Its structure was published by Nissen et al. in this year's Plant cell ( 2009).

Here our research focuses on the second group of tarocystatin. This feature is that this protein has a C-terminal CY-like domain and does not have the function of an inhibitor. Therefore, we tried to co-crystallize tarocystatin and papain, hoping to solve the problem. The full-length crystal structure of Tarocystatin and papain will be developed. This will be the first complex structure of Phytocystatins and papain, and it will also provide important molecular evolution information. Due to the difficulty of co-crystallization with active papain, according to previous literature, under many conditions, only the structure of papain can be resolved. Even so, we still try to test its composite structure.

After two years of continuous protein expression, purification, and co-crystallization conditions, the complex crystals were finally grown under a specific crystallization condition for one month. After synchrotron radiation diffraction analysis, a complex structure with a resolution of 2.03 Å was obtained. Interestingly, only the N-terminal CY domain is combined with papain in a 1:1 manner, and the C-terminal structure cannot be observed. This phenomenon seems to mean that the C-terminal may be combined with papain first to increase its N Inhibition ability at the end. In addition, we also designed different fragments, such as full length, N-terminal and C-terminal and GST binding or not, and tested the binding ability of N-terminal and C-terminal. The analysis by Glutaraldehyde cross-linking and yeast two hybrid test showed that the majority of Tarycystatin N-terminal and C-terminal are separated; a small part can form intramolecular binding; in addition, some can form homodimer through the combination of N-terminal and N-terminal. Finally, we also tested the difference in its inhibitory ability. The results found that GST-FL has the best ability to inhibit papain, followed by GST-Nt and FL. Nt inhibition is the weakest here. In addition, GST-Ct can promote papaya. Enzyme activity capacity. This result indicates that the appearance of Ct is very important for improving the suppression ability. Planta. (2011) 234(2):243-54. Epub on Mar 17, 2011

fp200_orig.png

  • Analysis of the structure and function of the stress-resistant protein TLP 18.3, which is abundantly expressed in chloroplasts, when plants are subjected to non-biological (water shortage) stress

There are very few research reports on TLP 18.3. In the knock out experiment, no obvious external phenotype appeared, indicating that it may have similar proteins in the chloroplast at the same time, performing similar effects, showing its importance. It is speculated that TLP18.3 may be involved in the photorepair of photosynthetic system II (PSII). Because the photosynthetic system is under long-term action, its D1 protein is easily damaged by light. At this time, peripheral proteins are needed to help remove damaged proteins. At that time, TLP 18.3 may perform this important task, but its molecular function is not clear! Therefore, this study is to use the correlation between structure and function, try to use X-ray crystal diffraction to study its structure, and use the structure Compare and find out its possible molecular functions.
Since TLP18.3 protein does not have methionine, many tests have been conducted for the expression, purification, and site-directed mutagenesis of this protein in the first two years, and the native TLP18.3 high-resolution diffraction data (resolution of 1.52Å) were obtained. , And use the TLP18.3 mutant (resolution 2.6Å) to obtain the phase angle by the single-wavelength unusual scattering method (SAD), and then use the modeling software and correction program to complete the protein structure analysis. After structural comparison, several similar structures have acid phospholytic enzyme activity. Therefore, it is speculated that this protein may have similar phospholytic enzyme activity. The activity analysis is further designed to perform sequence enzyme concentration, pH value, and temperature with substrate pNPP. , The experiment of removing bound ions shows that it does have the function of phospholytic enzyme activity. TLP18.3 has only a single Domain, belonging to the unknown family DUF477 (pfam). It has similar proteins in photosynthetic bacteria, algae, plants and prokaryotes. It is expected that this highly resolved protein structure will provide important information for this family. Structure and function information. Plant Physiol. (2011) 157(3):1015-25 Epub on Sep 9, 2011

tlp200.png

There are other different protein related research and biological information analysis-Homology Modeling, Protein-Protein Docking, Molecular Dynamics and Simulation, etc. Welcome to the university department for protein expression, purification, crystallization, X-ray diffraction, structural analysis and protein function research , Master and PhD students join the research room and travel together in the three-dimensional world of giant molecules.
For more relevant research information, please refer to the laboratory's webpage.

Selected Publications

(A) Academic Published Paper

  1. Hung, F.Y., Feng, Y.R., Hsin, K.T., Shih, Y.H., Chang, C.H., Zhong, W., Lai, Y.C., Xu, Y., Yang, S., Sugimoto, K., Cheng, Y.S., Wu, K.* (2023) Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2. Commun. Biol., 6:219.

  2. Hsin, K.T., Kuo, H.C., Kokubugata, G., Möller, M., Wang, C.N.*, Cheng, Y.S.* (2022) Allopatric Lineage Divergence of the East Asian Endemic Herb Conandron ramondioides Inferred from Low-Copy Nuclear and Plastid Markers. Int. J. Mol. Sci. 23:14932.

  3. Hsin, KT, Yang, TJ, Lee, YH and Cheng, YS* (2021) Phylogenetic and Structural Analysis of NIN-Like Proteins With a Type I/II PB1 Domain That Regulates Oligomerization for Nitrate Response. Front. Plant Sci. 12: 672035. doi: 10.3389/fpls.2021.672035.

  4. Li, L., Li, W., Gong, J., Xu, Y., Wu, Z., Jiang, Z., Cheng, YS , Li, Q., Ni, H.* (2021) An effective computational -screening strategy for simultaneously improving both catalytic activity and thermostability of α-L-rhamnosidase. Biotechnol Bioeng. 2021 Mar 20. doi: 10.1002/bit.27758.

  5. Peng C., Li, YH, Yu, CW, Cheng, ZH, Liu, JR, Hsu, JL, Hsin, LW, Huang, CT, Juan, HF, Chern, JW, Cheng, YS* (2021) Inhibitor development of MTH1 via high-throughput screening with fragment based library and MTH1 substrate binding cavity. Bioorg Chem. 2021 Mar 10;110:104813. doi: 10.1016/j.bioorg.2021.104813.

  6. He, MY, Lin, YJ, Kao, YL, Kuo, P., Grauffel, C., Lim, C., Cheng, YS , Chou, HD* (2021) Sensitive and Specific Cadmium Biosensor Developed by Reconfiguring Metal Transport and Leveraging Natural Gene Repositories. ACS Sens. 6:995-1002. doi: 10.1021/acssensors.0c02204.

  7. Chen, CY, Tu, YT, Hsu, JC, Hung, HC, Liu, TC, Lee, YH, Chou, CC, Cheng, YS * and Wu, K.* (2020). Structure of Arabidopsis HISTONE DEACETYLASE15. Plant Physiol . 184:1585-1600.

  8. Chen, CY, Lin, PH, Chen, KH and Cheng, YS * (2020) Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box. Plant Mol. Biol., 104:483-498.

  9. Li, LJ, Tan, WS, Li, WJ, Zhu, YB, Cheng, YS and Ni, H.* (2019). Citrus Taste Modification Potentials by Genetic Engineering. Int. J. Mol. Sci., 20(24) , 6194.

  10. Huang, HY and Cheng, YS * (2019). Heterologous overexpression, purification and functional analysis of plant cellulose synthase from green bamboo. Plant Methods, 15:80.

  11. Li, L., Gong, J., Wang, S., Li, G., Gao, T., Jiang, Z., Cheng, YS , Ni, H.*, and Li, Q. (2019). Heterologous Expression and Characterization of a New Clade of Aspergillus α-L-Rhamnosidase Suitable for Citrus Juice Processing. J. Agr. Food. Chem., 67(10), 2926-2935.

  12. Yu, CW, Hung, PY, Yang, HT, Ho, YH, Lai, HY, Cheng, YS *, and Chern, JW* (2019). Quinazolin-2,4-dione-Based Hydroxamic Acids as Selective Histone Deacetylase- 6 Inhibitors for Treatment of Non-Small-Cell Lung Cancer. J. Med. Chem., 62(2):857-874.

  13. Hsieh, HC and Cheng, YS * (2018). Structural and thermondynamics analysis of Ipomoelin with metal ions show the metal-binding ability in Jacalin-related lectin. J. Nat. Taiwan Museum, 71:35-52.

  14. Ho, YH, Wang, KJ, Hung, PY, Cheng, YS , Liu, JR, Fung, ST, Liang, PH, Chern, JW* and Yu, CW* (2018). A highly HDAC6-selective inhibitor acts as a fluorescent probe. Org. Biomol. Chem., 16, 7820-7832.

  15. Yu, CW, Tai, R., Wang, SC, Yang, P., Luo, M., Yang, S., Cheng, K., Wang, WC Cheng YS , Wu, K.* (2017) HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing. Plant Cell. 29: 1970-1983 Epub on Aug 4, 2017

  16. Chen, CY, Ho, SS, Kuo, TY, Hsieh, HL, Cheng YS * (2017) Structural basis of jasmonate-amido synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation. Proc. Natl. Acad. Sci. USA 114:E1815-E1824. Epub Feb 21, 2017

  17. Chen, HY, Cheng YS , Shih, HH* (2015) Expression patterns and structural modelling of Hsp70 and Hsp90 in a fish-borne zoonotic nematode Anisakis pegreffii. Vet Parasitol. 212:281-91. Epub on Jul 9, 2015.

  18. Chen, HY, Cheng YS , Grabner, DS, Chang SH and Shih, HH* (2014) Effect of different temperatures on the expression of the newly characterized heat shock protein 90 (Hsp90) in L3 of Anisakis spp. isolated from Scomber australasicus. Vet Parasitol. 205:540-550. Epub on Sep 13, 2014.

  19. Wu HY and Cheng YS * (2014) Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion. Acta Crystallogr F Struct Biol Commun. 70:378-83. Epub on Fed 19, 2014.

  20. Yang, WC; Lin, YM, Cheng, YS and Cheng, CP* (2013) Ralstonia solanacearum RSc0411 (lptC) is a determinant for full virulence and has a strain-specific essential function in the T3SS activity. Microbiology. 159:1136- 48. Epub on Mar 21, 2013.

  21. Chang, WC, Liu, KL, Hsu, FC, Jeng, ST and Cheng, YS * (2012) Ipomoelin, a Jacalin-related lectin with a compact tetrameric association and versatile carbohydrate binding properties regulated by its N terminus. PLoS ONE 7: e40618. Epub on Jul 11, 2012

  22. Wu, HY, Liu, MS, Lin, TP and Cheng, YS * (2011) Structural and functional assays of AtTLP18.3 Identify its novel acid phosphatase activity in thylakoid lumen. Plant Physiol. 157(3):1015-25 Epub on Sep 9, 2011

  23. Chu, MH, Liu, KL, Wu, HY, Yeh, KW and Cheng, YS * (2011) Crystal structure of tarocystatin-papain complex: implications for the inhibition property of group-2 phytocystatins. Planta. 234(2):243 -54.Epub on Mar 17, 2011

  24. Chu, WY, Huang YF, Huang CC, Cheng, YS , Huang CK and Oyang YJ (2009) ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. Nucl. Acids Res. 37 (Web Server issue):W396-401.Epub on May 29, 2009

  25. Wang, KM, Rajendran, SK, Cheng, YS , Venkatagiri, S, Yang, AH, Yeh, KW (2008) Characterization of inhibitory mechanism and antifungal activity between group-1 and group-2 phytocystatin from taro (Colocasia esculenta) FEBS J . 275(20):4980-9.Epub on Sep 10, 2008

  26. Lai, CK, Jeng, KS, Machida, K., Cheng, YS , and Lai, MM (2008) Hepatitis C virus NS3/4A protein interacts with ATM, impairs DNA repair and enhances sensitivity to ionizing radiation. Virology. 2008 Jan 20 ;370(2):295-309. Epub on Oct 10, 2007

  27. Shen, ST, Cheng, YS , Shen, TY, and Yu, JYL (2006) Molecular cloning of follicle-stimulating hormone beta-subunit cDNA from duck pituitary. Gen. Comp. Endocrinol. 148:388-94.

  28. Cheng, YS , Doudeva, LG, Yang, WZ, Hsia, KC, Shi, Z., Chak KF and Yuan, HS (2006) High-resolution crystal structure of ColE7 translocation domain: Implications for transport across membranes. J. Mol. Biol. 356:22-31

  29. Doudeva, LG, Huang, HC, Hsia, KC, Shi, ZG, Li, CL, Shen, YL, Cheng, YS and Yuan HS (2006) How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor. Protein Science 15:269-280

  30. Tsai, LC, Shyur LF, Cheng, YS and Lee, SH(2005) Crystal Structure of Truncated Fibrobacter succinogenes 1,3-1,4-β-D-Glucanase in Complex with β-1,3-1,4-Cellotriose . J. Mol. Biol., 354:642-651

  31. Liu, H., Peng, HH, Cheng, YS , Yuan, HS and Yang-Yen HF (2005) Stabilization and Enhancement of the anti-apoptotic activity of Mcl1 by TCTP. Mol. Cell. Biol. 25:3117-3126

  32. Hsia, KC, Chak, KF, Liang, PH, Cheng, YS , Ku, WY and Yuan, HS (2004) DNA binding and degradation by the HNH protein ColE7. Structure, 12:205-214.

  33. Cheng, YS , Hsia, KC, Doudeva, LG and Yuan, HS (2002) The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the HNH endonucleases. J. Mol. Biol. 324 :227-236.

  34. Cheng, YS , Yang, WZ, Johnson, RS and Yuan, HS (2000) Structural Analysis of the Transcriptional Activation Region on Fis: Crystal Structures of Six Fis Mutants with Different Activation Properties. J. Mol. Biol. 302:1139-1151 .

  35. Cheng, YS , Tang, TK and Hwang, MJ (1999) Amino acid conservation and clinical severity of human glucose-6-phosphate dehydrogenase mutations. J. Biomed. Sci. 6:106-114

  36. Cheng, YS ; Lin, CH and Chen, LJ (1997) Transcription and processing of the gene for spinach chloroplast threonine tRNA in a homologous in vitro system. Biochem. Biophys. Res Commun. 233:380-385

 

(B) Conference Paper

  1. Yen-Hua Chang, Yi-Sheng Cheng (2022, Nov) Heterogeneous Expression, Purification and Inhibitor Development of Histone Deacetylase 10. 2022 TSBMB Autumn Camp, The frontiers of biochemistry in Biomedical Science. 麻布山林，新竹縣北埔鄉

  2. Jian-sheng Chen, Yi-Sheng Cheng (2022, Oct) Interplay between WRYKY63 and HDA15 in regulation of gene expression of stress responses. 2022 post-pandemic era for frontier plant science and sustainable agriculture conference, 惠蓀林場，南投

  3. Kuan-Ting Hsin, Hao-Chih Kuo, Goro Kokubugata, Michael Möller, Chun-Neng Wang, Yi-Sheng Cheng (2022, Oct) Allopatric lineage divergence of an East Asia endemic herb Conandron ramondioides inferred from low copy nuclear and plastid markers. 2022 post-pandemic era for frontier plant science and sustainable agriculture conference, 惠蓀林場，南投

  4. Ting-Yi Yu, Yi-Sheng Cheng, Hsin-Hung Yeh (2022, Jun) Functional analysis between AtSAP5 and AtTrx3 in the reduced salicylic acid immunity pathway. ABA, APPA and TBS Joint Congress, National Cheng Kung University, International Conference Center.

  5. Yi-Sheng Cheng (2019). Heterologous overexpression, purification and functional analysis of cellulose synthases from green bamboo. The 7th Cross-Strait Symposium on Plant Science and Agricultural Biotechnology and the 2019 Annual Meeting of the Guangdong Society of Plant Physiology, Maoming, Guangdong.

  6. Chia-Yang Chen, Yi-Tsung Tu, Yi-Sheng Cheng , and Keqiang Wu (2019). The structure and activity of Arabidopsis histone heacetylase 15 are regulated by oligomerization and phosphorylation. 2019 TSPB Annual meeting & Symposium, International Conference Hall, Academica Sinica, Taipei, Taiwan.

  7. Yi-Sheng Cheng (2019). Structural and functional analyses reveal Histone Deacetylase 15 regulated by oligomerization and phosphorylation in Arabidopsis. Japan-Taiwan Plant Biology 2019, Nagoya University, Japan.

  8. Yi-Sheng Cheng (2018). Structural and functional analyses reveal Histone Deacetylase 15 regulated by oligomerization and phosphorylation in Arabidopsis. 2018 International Symposium on Plant and Environment Interaction, Conference room R332, Life Science Building, NTU.

  9. Yi-Sheng Cheng (2018). Structural basis of jasmonate-amido synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation. NTU-CUHK Plant Science Seminar, National Taiwan University School of Management Hall 1.

  10. Hsuan-Yu Huang and Yi-Sheng Cheng * (2018). Heterologous overexpression, purification and functional analysis of cellulose synthases from green bamboo. The 23rd Biophysics Symposium, International Conference Hall, 7th Floor, National Chung Hsing University Library.

  11. Ting-Chun Liu and Yi-Sheng Cheng * (2018). Development of Ipomoelin as an affinity tag in recombinant protein expression and purification. The 23rd Biophysics Symposium, International Conference Hall, 7th Floor, National Chung Hsing University Library.

  12. Yu-Hsuan Lee and Yi-Sheng Cheng * (2018). Structure based drug development for MutT homolog 1. The 23rd Biophysics Symposium, International Conference Hall, 7th Floor, National Chung Hsing University Library.

  13. Yi-Sheng Cheng (2018). Structural basis of Jasmonate-amido Synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation. School of Food and Bioengineering, Jimei University, Xiamen, Jimei University, Xiamen.

  14. Yi-Sheng Cheng (2018). Structural basis of Jasmonate-amido Synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation. Small seminar on crystallography, Conference Room B281, Department of Chemistry, National Taiwan University.

  15. Yi-Sheng Cheng (2017) Dissecting molecular function of Arabidopsis Histone Deacetylase 15. Invited Speaker, 2017Taiwan-Japan Plant Biology2017. Humanities and Social Sciences Building, Academia Sinica. Nov. 3-6.

  16. Cheng Peng and Yi-Sheng Cheng (2017) Structure based inhibitor development for MutT Homolog 1. The 22nd Biophysics Symposium, International Lecture Hall, 10th Floor, Administration Building, Yishou University. May, 17-19 *This article was awarded the 22nd Biophysics Second place in the seminar poster contest

  17. Pei-Wen Liao, Heng-Chen Hung and Yi-Sheng Cheng (2017) Enzymatic Activity and Oligomerization of Histone Deacetylase 15 Regulated by Phosphorylation. The 22nd Biophysics Symposium, International Lecture Hall, 10th Floor, Yishou University Administration Building. May, 17 -19; The Institute of Plant Sciences 105 Scientific Paper Poster Contest

  18. Min-Che Hsieh and Yi-Sheng Cheng (2016) The Mechanisms of Arabidopsis WRKY54 DNA binding Domain to W boxes. The 21st Biophysics Symposium, Department of Life Sciences, National Tsinghua University. May, 19-21; Institute of Plant Sciences 104 academic year Scientific Paper Poster Contest, June, 3

  19. Kun-Hong Chen and Yi-Sheng Cheng (2016) Structural and functional analyses of ERF19 in response to biotic stresses. The 21st Biophysics Symposium, Department of Life Sciences, National Tsinghua University. May, 19-21;; Institute of Plant Sciences 104 Academic Year Science Paper Poster Contest, June, 3

  20. Jhe-Cheng Hsu and Yi-Sheng Cheng (2016) Characterization of Arabidopsis histone deacetylase 15. The 21st Biophysics Symposium, Department of Life Sciences, National Tsinghua University. May, 19-21;; Institute of Plant Sciences 104th Academic Year Scientific Paper Poster Contest Choice Award, June, 3

  21. Hsuan-Yu Huang and Yi-Sheng Cheng (2016) Heterologous overexpression and purification of plant celluloase synthase from Bambusa oldhamii. 21st Biophysics Symposium, Department of Life Sciences, National Tsinghua University. May, 19-21;; Institute of Plant Science 104 Academic Year Science Paper Poster Contest, June, 3

  22. Yi-Sheng Cheng (2015) Structural and biochemical analyses of Arabidopsis HDA5 reveal the regulation of histone deacetylase activity. Invited Speaker, The 6th Cross-Strait Plant Science and Agricultural Biotechnology Symposium Guangdong, Guangzhou Dec, 3-7

  23. Yi-Sheng Cheng (2015) Biochemical Assays and EM Structure of the Class II of AtHDA5. Invited Speaker, The 12th Cross-Strait Electron Microscopy Symposium, Sichuan, Daocheng Sep, 6-11

  24. Yi-Sheng Cheng (2015) Structure insights into FIN219-FIP1 complex. Invited Speaker, Workshop of Zentrum für Molekularbiologie der Pflanzen (ZMBP), Tübigen University, Germany. July, 13-15

  25. Yi-Jui Chen, Ready Tai, Keqiang Wu, and Yi-Sheng Cheng (2015) Structural and Biochemical Assays of ClassII AtHDA5. 26th International Conference on Arabidopsis Research (ICAR), Paris, French. July, 5-9

  26. Han-Chen Hsieh and Yi-Sheng Cheng (2015) Structural and thermodynamic analysis of Ipomoelin in complex with metals reveal its metal binding properties. Excellent Prize in the 103rd Academic Year Scientific Paper Poster Contest of the Institute of Plant Sciences. Jun 5.

  27. Wei Chen and Yi-Sheng Cheng (2015) Study on bHLH domain from Arabidopsis PIF3 binding to G-Box DNA. The 20th Biophysics Symposium, Institute of Biochemistry, Academia Sinica. May, 11-13; Institute of Plant Sciences 103 Excellent Prize of Academic Year Scientific Paper Poster Contest Jun 5.

  28. Pei-Husan Lin and Yi-Sheng Cheng (2015) DNA Binding Assays of ERF96 with GCC boxes. The 20th Biophysics Symposium, Institute of Biochemistry, Academia Sinica. May, 11-13; Institute of Plant Sciences 103 academic year scientific papers The best poster contest Jun 5.

  29. Chun-Yen Chen, Hsu-Liang Hsieh and Yi-Sheng Cheng (2015) Mechanistic insights into structure of FIN219-FIP1 complex. The 20th Biophysics Symposium, Institute of Biochemistry, Academia Sinica. May, 11-13

  30. Tzu-Jing Yang and Yi-Sheng Cheng (2015) Molecular basis for oligomerization of nitrate response regulator AtNLP7. The 20th Biophysics Symposium, Institute of Biochemistry, Academia Sinica. May, 11-13; Institute of Plant Sciences 103 Academic Year Science Excellent Prize of thesis Poster Contest Jun 5.

  31. Yi-Sheng Cheng (2014) Molecular structure and function of Ipomoelin in oligomerization for its antibacterial and insecticidal ability. The Southern Research Center of Academia Sinica invited to speak Yang Xiangfa Lecture Hall. Oct, 22

  32. Yi-Sheng Cheng (2014) Exploring the Polymer Form of Arabidopsis Histone Deacetylase 6 by Electron Microscopy to Reveal Its Composition. The 34th Symposium of the Microscopy Society of Taiwan and the 11th Cross-Strait Electron Microscopy Symposium, National Taiwan University International Conference Hall of Applied Mechanics Hall. Jun, 23-24

  33. Yi-Sheng Cheng (2014) Insect-resistant and anti-bacterial phytohemagglutinin, the reversal way of survival of plants. Biological Research, Jianguo Middle School, Taipei City, May, 20.

  34. Hsing-Yi Lai and Yi-Sheng Cheng (2014) Study on the binding modes between hHDAC6 and its inhibitors. The 19th Biophysics Conference, Multifunctional Hall and International Conference Hall, Student Activity Center, Guangfu Campus, National Cheng Kung University May, 7-10

  35. Yi-Jui Chen, Ready Tai, Keqiang Wu, and Yi-Sheng Cheng (2014) Plant HDA5 shows a large polysome with histone deacetylase activity. The 19th Biophysics Conference, Multifunctional Hall and International Conference, Student Activity Center, Guangfu Campus, National Cheng Kung University Hall May, 7-10

  36. Han-Chen Hsieh, Rong-Huay Juang and Yi-Sheng Cheng (2014) Oligomeric states of AtPCS1 by biophysical analyses show its nonspecific association. The 19th Biophysics Conference, Multifunctional Hall and International Conference Hall, Student Activity Center, Guangfu Campus, National Cheng Kung University May, 7-10

  37. Wen-Jiun Wang and Yi-Sheng Cheng (2014) Structural and Functional Studies For Arabidopsis Histone Deacetylase 6. The 19th Biophysics Conference, Multifunctional Hall and International Conference Hall, Student Activity Center, Guangfu Campus, National Cheng Kung University May, 7-10

  38. Chia-Yu Chien and Yi-Sheng Cheng (2014) Structural and Biophysical Analyses of Arabidopsis PIF3 basic helix-loop-helix Domain binding to e-box DNA. For Arabidopsis Histone Deacetylase 6. The 19th Biophysics Conference, National Cheng Kung University Guangfu Campus Student Activity Center Multi-function Hall and International Conference Hall May, 7-10

  39. Yi-Sheng Cheng (2013) Molecular structure and function of Ipomoelin in oligomerization for its antibacterial and insecticidal ability. "Institute of Cell and Individual Biology, Academia Sinica", National Taiwan University, Department of Life Sciences Academic Review Conference, National Taiwan University Health Sciences Building 3rd floor lecture Hall, Oct, 8-9.

  40. Hsin-Yi Wu, Tsan-Piao Lin, and Yi-Sheng Cheng (2013) Structural and Functional Assay of AtTLP18. Gymnasium, Jun, 7.

  41. Yung-Chi Huang, Shih-Tong Jeng, Yi-Sheng Cheng (2013) Molecular Function of Ipomoelin in Oligomerization for Their Antibacterial and Insecticidal Ability. Excellent Prize in the 101st Academic Year Scientific Paper Poster Contest, National Taiwan University Gymnasium, Jun, 7.

  42. Yi-Sheng Cheng (2012) Expression and purification strategies of recombinant proteins for further related applications. Institute of Preventive Medicine, National Defense Medical College, Three Gorges, Nov, 30.

  43. Yi-Sheng Cheng (2012) Protein structures of Epigenetic regulating proteins. Tsinghua University and National Taiwan University Cooperation and Exchange Seminar, Conference Room 143, New Life Science Building, Tsinghua University, June, 26.

  44. Kai-Wen Fan, Kai-Wun Yeh, Yi-Sheng Cheng (2012) Monomeric and Dimeric Form of Tarocystatin Showed Different Binding Property to Papain. The 17th Biophysics Conference, Institute of BioMedical Sciences, Academia Sinica; 100 academic year scientific papers of the Institute of Plant Sciences Poster contest

  45. Chun-Yen Chen, Yi-Sheng Cheng (2012) Determination of protein interaction and enzymatic kinetics between FIN219/JAR1 and Glutathione S-Transferases using Quartz Crystal Microbalance. The 17th Biophysics Conference, Institute of BioMedical Sciences, Academia Sinica

  46. Wei-Chieh Chang, Kai-Lun Liu, Shih-Tong Jeng, Fang-Ciao Hsu and Yi-Sheng Cheng (2011) Ipomoelin, a member of Jacalin-related Lectin with a different tetrameric association and versatile carbohydrate binding properties regulating by its N terminus. The 2nd Cross-Strait Symposium on Plant Science and Agricultural Biotechnology, Sun Yat-sen University, Guangzhou

  47. Wei-Chieh Chang, Shih-Tong Jeng and Yi-Sheng Cheng (2011) Quaternary structure and energetic analysis of ipomoelin in complex with various carbohydrates for exploring its binding diversity. The 16th Biophysics conference, College of Sciences and Engineering, National Dong Hwa University , Taiwan

  48. Ming-Hung Chu, Kai-Lun Liu, Kai-Wun Yeh and Yi-Sheng Cheng (2009) Complex structure of tarocystatin-papain and characterization of tarocystatin proposed the roles of C-terminal extension in phytocystatins. Joint Conference of the Asian Crystallographic Association & Chinese Crystallography Society (AsCA'09) Beijing, China

  49. Hsin-Yi Wu, Mao-Sen Liu, Tsan-Piao Lin, and Yi-Sheng Cheng (2009) High-Resolution Crystal Structure and Functional Analysis of a Truncated Thylakoid Lumen Protein AtTLP18.3 Reveal its Novel Phosphatase Activity. Joint Conference of the Asian Crystallographic Association & Chinese Crystallography Society (AsCA'09) Beijing, China

  50. Kai-Lun Liu, Shih-Tong Jeng, and Yi-Sheng Cheng (2009) Crystal structures of Ipomoelin in complex with various carbohydrates, MMP, MGP and Sialic acid NSRRC Fifteenth User' Meeting, Hsinchu, Taiwan

  51. Hsin-Yi Wu, Mao-Sen Liu, Tsan-Piao Lin, and Yi-Sheng Cheng (2009) High-Resolution Crystal Structure and Functional Assay of a Truncated Thylakoid Lumen Protein AtTLP18.3 Reveal its Novel Phosphatase Activity. Joint International Conference of Biophysics and 14th Annual Conference of the Biophysical Society of ROC, NCKU, Tainan

  52. Ming-Hung Chu, Kai-Wun Yeh and Yi-Sheng Cheng (2009) Domain analysis of tarocystatin revealed the inhibitory property of group II phytocystatin. Joint International Conference of Biophysics and 14th Annual Conference of the Biophysical Society of ROC, NCKU, Tainan

  53. Sih-Syun Ho, Zhi-Gong Wang, Hsu-Liang Hsieh, and Yi-Sheng Cheng (2009) Purification and crystallization of FIN219-FIP1 complex and biochemical assay of FIN219. Joint International Conference of Biophysics and 14th Annual Conference of the Biophysical Society of ROC, NCKU, Tainan

  54. Yi-Sheng Cheng , Hsin-Yi Wu, Ming-Hung Chu, Kai-Wun Yeh (2008)Structural model for group-2 phytocystatin revealed the protein folds resembling to human latexin. 19th International Conference on Genome Informatics 2008, GIW2008, Australia

  55. Yi-Sheng Cheng (2008) Structural analysis of IL2-inducible T-cell kinase (ITK) in pedigree 135 mice. Symposium of the national research program for genomic medicine.

  56. Ke-Ming Wang, Shripathi Venkatagiri, Ai-Hwa Yang, Yi-Sheng Cheng * and Kai-Wun Yeh (2007) Structural model and inhibitory characteristics for group-2 phytocystatin from taro. Symposium on Frontiers of Plant Science. *Invited Speaker

  57. Kuo-Chiang Hsia, Kin-Fu Chak, Po-Huang Liang, Yi-Sheng Cheng , Wen-Yen Ku, and Hanna S. Yuan (2004) DNA Binding and Degradation by the HNH Protein ColE7. The 9th Symposium on Recent Advances in Biophysics.

  58. Nancy Yu, Yi-Sheng Cheng (2004) Codon Usage Enhancer (CUE): A JAVA-based Freeware for Manipulating Codon Usage. The 9th Symposium on Recent Advances in Biophysics.

  59. Kuo-Chiang Hsia, Kin-Fu Chak, Po-Huang Liang, Yi-Sheng Cheng , Wen-Yen Ku, and Hanna S. Yuan (2003) DNA Binding and Degradation by the HNH Protein ColE7. The 4th East Asia Biophysics Symposium meeting

  60. Cai Lizhu, Li Shuhua, Zheng Yisheng, Xu Lifen (2003) The crystal structure of glucanohydrolase and trisaccharide complex. The 92nd Annual Meeting of the Chinese Chemical Society

  61. Yi-Sheng Cheng , Wen-Yen Ku, Meng-Jiun Sui, Kuo-Chiang Hsia, Li-Chu Tsai, Jia-Lueng Li, Wei-Zeng Yang, Lyudmila G. Doudeva and Hanna S. Yuan (2002) Bacterial offense and defense mechanisms using nucleases. The 8th Symposium on Recent Advances in Biophysics.

  62. Yi-Sheng Cheng , Kuo-Chiang Hsia, Lyudmila G. Doudeva, and Hanna S. Yuan (2002) The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the HNH endonucleases. The 8th Symposium on Recent Advances in Biophysics.

  63. Meng-Jiun Sui, Li-Chu Tsai, Yi-Sheng Cheng , Ludmila Doudeva and Hanna S. Yuan (2001) The zinc ion in the HNH motif of colicin E7 plays a catalytic role. The 8th Symposium on Recent Advances in Biophysics.

  64. Yi-Sheng Cheng , Hanna S. Yuan (2000) Structural Analysis of the Transcriptional Activation Region on Fis: Crystal Structures of Six Fis Mutants with Different Activation Properties. The 6th Symposium on Recent Advances in Biophysics.

  65. Yi-Sheng Cheng , Ming-Jing Hwang (1998) Sequence Conservation in Three-dimensional Structure of Human G6PD and Its Mutants. The 6th Symposium on New Knowledge in Cell and Molecular Biology

  66. Yi-Sheng Cheng , Ming-Jing Hwang (1998) A scheme for visualizing amino acid conservation and its structural context. XVIII international conference on magnetic resonance in biological systems.

  67. Yi-Sheng Cheng , Ming-Jing Hwang (1997) Computer modeling the substrate binding of glucose-6-phosphate dehydrogenase. The 3th Symposium on Recent Advances in Biophysics.

(C) Book Essay

  1. Chen HY, Cheng YS ., Shih HH* (2018) Heat Shock Proteins: Role, Functions and Structure in Parasitic Helminths. Chapter 12 in Heat Shock Proteins in Veterinary Science, Heat Shock Proteins Book Series, ed. by AA Asea and P. Kaur, Springer International Publishers.

  2. Zheng Yisheng , Cai Lizhu, Yang Weiren, Yuan Xiaoxuan (2003) Chapter 7 X-ray crystal diffraction and structural biology Biotechnology in the post-genome era pp81-90

Courses Taught

  • B01 101B0 General Biology B

  • B01 106B1 General Biology experiment B

  • B01 10300 Plant Biology

  • B01 49100 Undergraduate Seminar

  • P05 U2020 Biotechnology core experiment

  • B43 U1250 Genomics

  • LS 1028 Introduction to Genetic Engineering

  • B42 U1240 Proteomics

  • LS 7037 Structure Biology Seminar

bottom of page