Wenfei LI, Ph.D and Prof. | |
Institute of Biophysics and Department of Physics Nanjing University 22 Hankou Road, Nanjing 210093, P. R. China Email: wfli (at mark) nju.edu.cn Tel (o): (+86)25-83594476 |
Professional experience
2012 --- now: Professor, Department of Physics, Nanjing University
2008 --- 2010: Visiting research fellow, Department of Biophysics, Kyoto University, Japan
2006 --- 2012: Associate professor, Department of Physics, Nanjing University
2006 --- 2006: Lecturer, Department of Physics, Nanjing University
2004 --- 2006: Postdoctoral fellow, Department of Physics, Nanjing University
Education
1999 --- 2004: Ph.D., Institute of Modern Physics, Chinese Academy of Sciences
1995 --- 1999: B.Sc. Physics, Inner Mongolia University for Nationality
Research Interests
1) Computational studies of cofactor-coupled protein folding, allosteric motions, and aggregation.
2) Functioning of biomolecular machines driven by multi-scale fluctuations with MD simulations.
3) Multi-scale theory/algorithm and applications to biomolecule systems.
Teaching
1) “Computational Physics” for undergraduate students in Nanjing University.
2) “Biomolecular dynamics” for graduate students in Nanjing University
Publications:
1. | Wenfei Li*, Jun Wang, Jian Zhang, Shoji Takada*, and Wei Wang* |
Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration, | |
Phys. Rev. Lett. 2019, 122, 238102. | |
2. | H Zorgati, M Larsson, W Ren, AYL Sim, J Gettemans, JM Grimes, Wenfei Li*, R. C. Robinson*, |
The role of gelsolin domain 3 in familial amyloidosis (Finnish type) | |
Proc. Natl. Acad. Sci. U. S. A. 2019, 116, 13958-13963. | |
3. | Jianyang Kong, Jiachen Li, Jiajun Lu, Weifei Li*, Wei Wang |
Role of substrate-product frustration on enzyme functional dynamics | |
Phys. Rev. E 2019, 100, 052409 | |
4. | W. Di, X. Gao, W. Huang, Y. Sun, H. Lei, Y. Liu, W. Li, Y. Li, X. Wang, M. Qin, Z. Zhu*, Y. Cao*, W. Wang* |
Direct Measurement of Length Scale Dependence of the Hydrophobic Free Energy of a Single Collapsed Polymer Nanosphere, | |
Phys. Rev. Lett., 2019, 122: 047801. | |
5. | R. Song, X. Wu, B. Xue, Y. Yang, W. Huang, G. Zeng, J. Wang, W. Li, Y. Cao, W. Wang*, J. Lu*, H. Dong* |
J. Am. Chem. Soc. 2018, 141 (1), 223-231 | |
6. | Chao Liu, Yangyang Zhang, Jian Zhang, Jun Wang, Wenfei Li*; Wei Wang*, |
Interplay between translational diffusion and large-amplitude angular jumps of water molecules, | |
J. Chem. Phys. 2018, 148: 184502. | |
7. | Shintaroh Kubo, Wenfei Li, Shoji Takada*, |
Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations, | |
Plos Comput. Biol., 2017, 13(9): e1005748. | |
8. | Weitong Ren, Wenfei Li*; Jun Wang, Jian Zhang, Wei Wang* |
Consequences of Energetic Frustration on the Ligand-Coupled Folding/Dimerization Dynamics of Allosteric Protein S100A12 , | |
J. Phys. Chem. B, 2017 , 121(42): 9799-9806. | |
9. | Wenfei Li, Jun Wang*, Jian Zhang and Wei Wang* |
Molecular simulations of metal-coupled protein folding, | |
Curr. Opin. Struct. Biol. 2015, 30, 25-31. | |
10. | Wenfei Li*, Jian Zhang, Jun Wang, and Wei Wang* |
Multiscale theory and computational method for biomolecule simulations | |
Acta Physica Sinica, 64, 098701 (2015) (in chinese) | |
11. | Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, and Hiroo Kenzaki, |
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations, | |
Accounts of Chemical Research, 2015, 48, 3026-3035 | |
12. | Wenfei Li, Wei Wang* and Shoji Takada* |
Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains, | |
Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 10550-10555. | |
13. | Chunmei Lv#, Xiang Gao#, Wenfei Li#, Bo Xue, Meng Qin, Leslie D. Burtnick, Hao Zhou, Yi Cao*, Robert C. Robinson*, Wei Wang* |
Single-molecule force spectroscopy reveals force-enhanced binding of calcium ions by gelsolin | |
Nature Communications 2014, 5, 4623. (# contributed equally) | |
14. | Chao Liu, Wenfei Li*, and Wei Wang* |
Correlation of Reorientational Jumps of Water Molecules in Bulk Water | |
Phys. Rev. E 2013, 87, 052309. | |
15. | Cheng Tan, Wenfei Li*, and Wei Wang* |
Localized Frustration and Binding-Induced Conformational Change in Recognition of 5sRNA by TFIIIA Zinc Finger | |
J. Phys. Chem. B 2013, 117, 15917-15925 | |
16. | Wenfei Li, Tsuyoshi Terakawa, Wei Wang* and Shoji Takada* |
Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot, | |
Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 17789-17794. | |
17. | Wenhui Xi, Wenfei Li*, and Wei Wang* |
Template Induced Conformational Change of Amyloid-β Monomer | |
J. Phys. Chem. B, 2012, 116, 7398–7405 | |
18. | Wenfei Li, Peter G. Wolynes*, and Shoji Takada* |
Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins | |
Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 3504–3509. | |
19. | Wenfei Li, Meng Qin, Zuoxiu Tie, and Wei Wang* |
Effects of solvents on the intrinsic propensity of peptide backbone conformations | |
Phys. Rev. E 2011, 84, 041933. | |
20. | Hiroo Kenzaki, Nobuyasu Koga, Naoto Hori, Ryo Kanada, Wenfei Li, Kei-ichi Okazaki, Xin-Qiu Yao, and Shoji Takada |
CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work, | |
J. Chem. Theory & Comput., 2011, 7, 1979-1989. | |
21. | Guanghong Zuo, Wenfei Li*, Jian Zhang,Jin Wang, Wei Wang* |
Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics | |
J. Phys. Chem. B 2010, 114, 5835-5839 | |
22. | Wenfei Li and Shoji Takada* |
Characterizing protein energy landscape by the self-learning multiscale simulations: Application to a designed beta-hairpin | |
Biophys. J. 2010, 99, 3029-3037. | |
23. | Wenfei Li, Hiroaki Yoshii, Naoto Hori, Tomoshi Kameda, and Shoji Takada* , |
Multiscale methods for protein folding simulations, | |
Methods 2010, 52:106-114. | |
24. | Wenfei Li and Shoji Takada*, |
Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously, | |
J. Chem. Phys. 2009, 130: 214108. | |
25. | Wenfei Li, Jian Zhang, Jun Wang and Wei Wang*, |
Metal Coupled folding of Cys2His2 Zinc-finger, | |
J. Am. Chem. Soc. 2008, 130, 892-900. | |
26. | Wenfei Li, Jian Zhang, Yu Su, Jun Wang, Meng Qin, and Wei Wang |
Effects of Zinc Binding on the Conformational Distribution of the Amyloid-b Peptide Based on Molecular Dynamics Simulations, | |
J. Phys. Chem. B. 2007, 111, 13814-13821. | |
27. | Wenfei Li, Jiang Zhang, and Wei Wang |
Understanding the Folding and Stability of a Zinc Finger Based Full Sequence Design Protein with Replica Exchange Molecular Dynamics Simulations | |
Proteins 2007, 67, 338-349. |