Chemistry and Chemical Engineering
ZHANG Yuebin
Title: Associate Professor
Subject: Molecular Reaction Dynamics
Phone:
Email: zhangyb@dicp.ac.cn
Website:
Research Interests
Protein Dynamics, Molecular Dynamics Simulation, Protein Biophysics, Structural Bioinformatics and Structural Biology, Binding Thermodynamics, Biophysical Chemistry, Protein Structure, Protein Folding, Protein-Protein Interaction, Protein Purification, Protein Binding, Conformational Dynamics, Protein Modeling, Computational Biophysics, Computational Structural Biology, Protein Stability, Membrane Proteins, Protein Biochemistry, Structural Bioinformatics
Biography
1. Jul 2016 – present      Associate professor
Chinese Academy of Sciences, Dalian Institute of Chemical Physics, State Key Laboratory of Molecular Reaction Dynamics,Dalian, Liaoning, China
2. Jul 2013 – Jun 2016    Research Associate
Chinese Academy of Sciences, Dalian Institute of Chemical Physics, State Key Laboratory of Molecular Reaction Dynamics,Dalian, Liaoning, China
3. Oct 2010 – Jun 2013    Postdoctoral researcher 
The State Key Laboratory of Supramolecular Structure and Materials, Jilin University,Changchun, Jilin province, China
Honors and Awards
 
Publications
1. Wang, A.; Zhang, Y.; Chu, H.; Liao, C.; Zhang, Z.; Li, G. Higher Accuracy Achieved for Protein-Ligand Binding Pose Prediction by Elastic Network Model-Based Ensemble Docking. J. Chem. Inf. Model. 2020, 60 (6), 2939–2950. 
2. Zheng, X.; Fu, Z.; Su, D.; Zhang, Y.; Li, M.; Pan, Y.; Li, H.; Li, S.; Grassucci, R. A.; Ren, Z.; Hu, Z.; Li, X.; Zhou, M.; Li, G.; Frank, J.; Yang, J. Mechanism of Ligand Activation of a Eukaryotic Cyclic Nucleotide？gated Channel. Nat. Struct. Mol. Biol. 2020, 27 (7), 625–634. 
3. Zhou, H.; Zhang, Y.; Li, T.; Tan, H.; Li, G.; Yin, H. Distinct Interaction of Lytic Polysaccharide Monooxygenase with Cellulose Revealed by Computational and Biochemical Studies. J. Phys. Chem. Lett. 2020, 11 (10), 3987–3992. 
4. Liu, L.; Zhou, Y.; Qu, M.; Qiu, Y.; Guo, X.; Zhang, Y.; Liu, T.; Yang, J.; Yang, Q. Structural and Biochemical Insights into the Catalytic Mechanisms of Two Insect Chitin Deacetylases of the Carbohydrate Esterase 4 Family. J. Biol. Chem. 2019, 294 (15), 5774–5783. 
5. Zheng, L.; Li, Y.; Li, X.; Zhong, Q.; Li, N.; Zhang, K.; Zhang, Y.; Chu, H.; Ma, C.; Li, G.; Zhao, J.; Gao, N. Structural and Functional Insights into the Tetrameric Photosystem I from Heterocyst-Forming Cyanobacteria. Nat. Plants 2019, 5 (10), 1087–1097. 
6. Lan, P.; Tan, M.; Zhang, Y.; Niu, S.; Chen, J.; Shi, S.; Qiu, S.; Wang, X.; Peng, X.; Cai, G.; Cheng, H.; Wu, J.; Li, G.; Lei, M. Structural Insight into Precursor TRNA Processing by Yeast Ribonuclease P. Science (80-. ). 2018, 362 (6415), eaat6678. 
7. Peng, X.; Zhang, Y.; Li, Y.; Liu, Q.; Chu, H.; Zhang, D.; Li, G. Integrating Multiple Accelerated Molecular Dynamics to Improve Accuracy of Free Energy Calculations. J. Chem. Theory Comput. 2018, 14 (3), 1216–1227. 
8. Chu, H.; Peng, X.; Li, Y.; Zhang, Y.; Min, H.; Li, G. Polarizable Atomic Multipole-Based Force Field for DOPC and POPE Membrane Lipids. Mol. Phys. 2018, 116 (7–8), 1037–1050. 
9. Chu, H.; Peng, X.; Li, Y.; Zhang, Y.; Li, G. A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids. Molecules 2018, 23 (1). 
10. Pan, Y.; Zhang, Y.; Gongpan, P.; Zhang, Q.; Huang, S.; Wang, B.; Xu, B.; Shan, Y.; Xiong, W.; Li, G.; Wang, H. Single Glucose Molecule Transport Process Revealed by Force Tracing and Molecular Dynamics Simulations. Nanoscale Horizons 2018, 3 (5), 517–524. 
11. Zhang, L.; Zhang, Y.; Cheng, J.; Wang, L.; Wang, X.; Zhang, M.; Gao, Y.; Hu, J.; Zhang, X.; Lü, J.; Li, G.; Tai, R.; Fang, H. Inert Gas Deactivates Protein Activity by Aggregation. Sci. Rep. 2017, 7 (1). 
12. Zhang, Y.; Peng, X.; Ren, H.; Chu, H.; Li, Y.; Li, G. Cholesterol Modulating the Orientation of His17 in Hepatitis C Virus P7 (5a) Viroporin – A Molecular Dynamic Simulation Study. Chinese Chem. Lett. 2018, 29 (5), 719–723. 
13. Cao, L. R.; Zhang, C. Y.; Zhang, D. L.; Chu, H. Y.; Zhang, Y. Bin; Li, G. H. Recent Developments in Using Molecular Dynamics Simulation Techniques to Study Biomolecules. Acta Phys. - Chim. Sin. 2017, 33 (7), 1354–1365. 
14. Peng, X.; Zhang, Y.; Chu, H.; Li, Y.; Zhang, D.; Cao, L.; Li, G. Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections. J. Chem. Theory Comput. 2016, 12 (6), 2973–2982. 
15. Li, Y.; Han, J.; Zhang, Y.; Cao, F.; Liu, Z.; Li, S.; Wu, J.; Hu, C.; Wang, Y.; Shuai, J.; Chen, J.; Cao, L.; Li, D.; Shi, P.; Tian, C.; Zhang, J.; Dou, Y.; Li, G.; Chen, Y.; Lei, M. Structural Basis for Activity Regulation of MLL Family Methyltransferases. Nature 2016, 530 (7591), 447–452. 
16. Zhang, Y.; Feng, J.; Cui, L.; Zhang, Y.; Li, W.; Li, C.; Shi, N.; Chen, Y.; Kong, W. Investigation into Efficiency of a Novel Glycol Chitosan-Bestatin Conjugate to Protect Thymopoietin Oligopeptides from Enzymatic Degradation. J. Pharm. Sci. 2016, 105 (2), 828–837. 
17. Xu, H.; Zhang, Y.; Chen, L.; Li, Y.; Li, C.; Liu, L.; Ogura, T.; Kitagawa, T.; Li, Z. Entry of Water into the Distal Heme Pocket of Soluble Guanylate Cyclase Β1 H-NOX Domain Alters the Ligated CO Structure: A Resonance Raman and: In Silico Simulation Study. RSC Adv. 2016, 6 (49), 43707–43714.
18. Peng, X.; Zhang, Y.; Chu, H.; Li, G. Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform. J. Comput. Chem. 2016, 37 (6), 614–622.
19. Zhang, Z.; Li, W.; Li, H.; Zhang, J.; Zhang, Y.; Cao, Y.; Ma, J.; Li, Z. Construction and Characterization of Vitreoscilla Hemoglobin (VHB) with Enhanced Peroxidase Activity for Efficient Degradation of Textile Dye. J. Microbiol. Biotechnol. 2015, 25 (9), 1433–1441.
20. Zhang, Y.; Niu, H.; Li, Y.; Chu, H.; Shen, H.; Zhang, D.; Li, G. Mechanistic Insight into the Functional Transition of the Enzyme Guanylate Kinase Induced by a Single Mutation. Sci. Rep. 2015, 5, 8405. 
21. Zhang, Y.; Liu, L.; Wu, L.; Li, S.; Li, F.; Li, Z. Theoretical Investigation on the Diatomic Ligand Migration Process and Ligand Binding Properties in Non-O2-Binding H-NOX Domain. Proteins Struct. Funct. Bioinforma. 2013, 81 (8), 1363–1376. 
22. Zhang, Y. Bin; Cheng, Y. K.; Lü, M.; Zhang, H. L.; Li, Z. Q. Function of the Hydrogen-Bonding Network between the Y-S-R Motif and the Heme Propionate Groups in SGC-HNOX Domain. Chemical J. Chinese Univ. 2010, 31 (5), 1039–1044.
23. Zhang, Y.; Lu, M.; Cheng, Y.; Li, Z. H-NOX Domains Display Different Tunnel Systems for Ligand Migration. J. Mol. Graph. Model. 2010, 28 (8), 814–819.