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Ph.D., Biochemistry, 2001
Iowa State University

M.S., Bioinformatics and Computational Biology, 2003
Iowa State University

The overall research interest of Dr. Xu is to understand protein function and structure relation. Dr. Xu’s lab is focused on developing a new computational algorithm, Triangular Spatial Relationship (TSR)-based, for protein 3D structure comparison, motif discovery, and protein – protein and drug – protein interactions. Dr. Xu is also interested in understanding the mechanisms underlying early fast processes of solar energy conversion into chemical energy.

Opportunities for Student Research/Collaboration:

Dr. Xu is  looking for Ph.D. students who are interested in bioinformatics or biochemistry.

• Titli Sarkar, Camille R Reaux, Jianxiong Li, Vijay Raghavan and Wu Xu. The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2. Data in Brief 45, 2022
• Jinlong Wang, Xiahe Huang, Haitao Ge, Yan Wang, Weiyang Chen, Limin Zheng, Chengcheng Huang, Haomeng Yang, Lingyu Li, Na Sui, Yu Wang, Yuanya Zhang, Dandan Lu, Longfa Fang, Wu Xu, Yuqiang Jiang, Fang Huang, and Yingchun Wang. The quantitative proteome atlas of a model cyanobacterium. Journal of Genetics and Genomics 49(2):96-108, 2022
• Sarika Kondra, Feng Chen, Yixin Chen, Yuwu Chen, Caleb J Collette, and Wu Xu. A study of a hierarchical structure of proteins and ligand binding sites of receptors using the TSR-based structure comparison method and development of a size-filtering feature designed for comparing different sizes of protein structures. Proteins: Structure, Function and Bioinformatics 90(1), 2022
• Vasily Kurashov, George Milanovsky, Lujun Luo, Antoine Martin, Alexey Yu. Semenov, Sergei Savikhin, Dmitry A. Cherepanov, John H. Golbeck, and Wu Xu. Conserved Residue PsaB-Trp673 is Essential for High Efficiency Electron Transfer Between the Phylloquinones and the Iron-Sulfur Clusters in Photosystem I. Photosynthesis Research 148(3):161-180, 2021
• Titli Sarkar, Vijay V. Raghavan, Feng Chen, Andrew Riley, Sophia Zhou, and Wu Xu. Exploring the effectiveness of the TSR-based protein 3-D structural comparison method for protein clustering, and structural motif identification and discovery of protein kinases, hydrolases, and SARS-CoV-2’s protein via the application of amino acid grouping. Computational Biology and Chemistry 92(101479), 2021
• Dmitry A. Cherepanov, Ivan V. Shelaev, Fedor E. Gostev, Anastasia Petrova, Arseniy V. Aybush, Victor A. Nadtochenko, Wu Xu, John H. Golbeck, and Alexey Yu. Semenov. Primary Charge Separation in Photosystem I: Ultrafast Optical Studies of Variants Near the Accessory Chlorophylls in the A- and B-Branches of Electron Transfer Cofactors. Physical Chemistry Chemical Physics 217(112154), 2021
• Sarika Kondra, Titli Sarkar, Vijay Raghavan, and Wu Xu. Development of a TSR-based method for protein 3-D structural comparison with its applications to protein classification and motif discovery. Frontiers in Chemistry-Theoretical and Computational Chemistry 8(602291), 2021
• Wu Xu, Lawryn H. Kasper, Stephanie Lerach, Trushar Jeevan and Paul K. Brindle. CREB-target genes dictate usage of at least three distinct cAMP-responsive coactivation mechanisms. EMBO Journal 26:2890-2903, 2007
• Wu Xu, Tomofusa Fukuyama, Paul Ney, Demin Wang, Jerold Rehg, Kelli Boyd, Jan M.A. van Deursen, and Paul K. Brindle. Global transcriptional coactivators CREB-binding protein and p300 are essential for mouse B-cells in vivo. Blood 107(11):4407-4416, 2006
• Seung-Hoi Koo, Lawrence Flechner, Ling Qi, Xinmin Zhang, Robert A. Screaton, Shawn Jeffries, Susan Hedrick, Wu Xu, Fayçal Boussouar, Paul Brindle, Hiroshi Takemori, and Marc Montminy. The CREB coactivator TORC2 is a key regulator of fasting glucose metabolism. Nature 437:1109-1114, 2005
• Wu Xu, Parag R. Chitnis, Alfia Valieva, Art van der Est, Klaus Brettel, Mariana Guergova-Kuras, Yulia N. Pushkar, Stephan G. Zech, Dietmar Stehlik, Gaozhong Shen, Boris Zybailov, and John H. Golbeck. Electron Transfer in Cyanobacterial Photosystem I: II. Determination of Forward Electron Transfer Rates of Site-directed Mutants in a Putative Electron Transfer Pathway from A0 through A1 to FX. J Biol Chem 278:27876-27887, 2003
• Wu Xu, Parag Chitnis, Alfia Valieva, Art van der Est, Yulia N. Pushkar, Maciej Krzystyniak, Christian Teutloff, Stephan G. Zech, Robert Bittl, Dietmar Stehlik, Boris Zybailov, Gaozhong Shen, and John H. Golbeck. Electron Transfer in Cyanobacterial Photosystem I: I. Physiological and Spectroscopic Characterization of Site-directed Mutants in a Putative Electron Transfer Pathway from A0 through A1 to FX. J Biol Chem 278:27864-27875, 2003

PI: Wu Xu 
Source of Support: NIH NIGMS (1R15GM144944-01)
Title: Development of a new computational method for predicting drug - target interactions using a TSR-based representation of 3-D structures
Project Period Covered: September 15, 2021 – August 31, 2024
Award Amount: $420,456
Location: 51¹ú²úÊÓƵ