Research

We use X-ray crystallography as a tool to carry out the structural biology study of various biomacromolecules.​Meanwhile, we perform the biological functional study of proteins by biochemical and biophysical methods, such as Sedimentation (Analytical Ultracentrifuge), CD (Circular dichroism), FPLC (Fast Protein Liquid Chromatography), MST (MicroScale Thermophoresis) etc. ​The bioinfomatics and the three dimensional structure of target proteins are applied in structure based drug design. Our laboratory mainly focus in structural and functional studies of

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(1) Structural and functional studies of a membrane-embedded H+-translocating pyrophosphatase

(2) Structural and functional studies of chromsome partition system from Helicobacter pylori

(3) Structural and functional studies of Ubiquitin-specific-processing protease 7

​H+-translocating pyrophosphatases (H+-PPases) are active proton transporters that generate a proton gradient across the endomembrane by means of pyrophosphate (PPi) hydrolysis. H+-PPases are found primarily in the vacuolar membrane of plants and the plasma membrane of several protozoa and prokaryotes. We determined the crystal structure of a Vigna radiata H+-PPase (VrH+-PPase) in complex with a non-hydrolysable substrate analogue, imidodiphosphate (IDP), at 2.35 angstrom resolution. VrH+-PPase comprises an integral membrane domain formed by 16 transmembrane helices. A novel proton translocation pathway is created by six core transmembrane helices. We proposed a working model of the mechanism for the coupling between proton pumping and PPi hydrolysis by H+-PPases.

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Reference

1. Yu-Sung Huang, Jia-Yin Tsai, Shih-Ming Lin, Sheng-Chia Wang, Chwan-Deng Hsiao, and Yuh-Ju Sun* (2025). "Revealing the glutamate switch: insights into proton translocation in plant H+-pyrophosphatase". Biophysical Journal, 124(18), 3023–3036.

2. Jia-Yin Tsai, Kai-Zhi Tang, Kun-Mou Li, Bo-Lin Hsu, Yun-Wei Chiang, Adrian Goldman, Yuh-Ju Sun* (2019). “Roles of the hydrophobic gate and exit channel in Vigna radiata pyrophosphatase ion translocation”. Journal of Molecular Biology, 431(8), 1619-1632.

3. Kun-Mou Li, Craig Wilkinson, Juho Kellosalo, Jia-Yin Tsai, Tommi Kajander, Lars Jeuken, Yuh-Ju Sun*, and Adrian Goldman* (2016) “Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism”. Nature Communications, 7(1), 13596.

4. Jia-Yin Tsai, Juho Kellosalo, Yuh-Ju Sun* and Adrian Goldman* (2014) “Proton/sodium pumping pyrophosphatases: the last of the primary ion pumps” Current Opinion in Structural Biology, 27, 38-47.

5. Shih-Ming Lin, Jia-Yin Tsai, Chwan-Deng Hsiao, Yun-Tzu Huang, Chen-Liang Chiu, Mu-Hsuan Liu, Jung-Yu Tung, Tseng-Huang Liu, Rong-Long Pan & Yuh-Ju Sun* (2012) “Crystal Structure of a Membrane-embedded H+-translocating Pyrophosphatase”. Nature, 484(7394), 399-403.

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Spo0J (stage 0 sporulation protein J, a member of the ParB superfamily) is an essential component of the ParABS (partition system of ParA, ParB, and parS)-related bacterial chromosome partition system. ParB (partition protein B) and its regulatory protein, ParA, act cooperatively through parS (partition S) DNA to facilitate chromosome partition. ParB binds to chromosomal DNA at specific parS sites as well as the neighboring nonspecific DNA sites. Various ParB molecules can associate together and spread along the chromosomal DNA. ParB oligomer and parS DNA interact together to form a high-order nucleoprotein that is required for the loading of the structural maintenance of chromosomes proteins onto the chromosome for chromosomal DNA condensation. In our lab, we have determinned the complex structure of Spo0J with parS DNA and purposed the DNA looping model by Spo0J-mediated. Currently, the overall structural and functional studies of chromosome partition system are ongoing.

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Reference

1. Chen-Hsi Chu, Che-Ting Wu, Min-Guan Lin, Cheng-Yi Yen, Yi-Zhan Wu, Chwan-Deng Hsiao*, and Yuh-Ju Sun* (2024). "Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB" Nucleic Acids Research, 52(12), 7321-7336.

2. Chen-Hsi Chu, Cheng-Yi Yen, Bo-Wei Chen, Min-Guan Lin, Lyu-Han Wang, Kai-Zhi Tang, Chwan-Deng Hsiao*, and Yuh-Ju Sun* (2019). “Crystal structures of HpSoj–DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation” Nucleic Acids Research, 47(4), 2113-2129.

3. Bo-Wei Chen, Ming-Hsing Lin, Chen-Hsi Chu, Chia-En Hsu, and Yuh-Ju Sun* (2015) “Insights into ParB spreading from the complex structure of Spo0J and parS” Proceedings of the National Academy of Sciences, 112(21), 6613-6618.