Wenfei Li - 生物医学物理研究所

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 biomolecular self-assembly and phase transition.

2) Functioning of biomolecular machines driven by multi-scale fluctuations with MD simulations.

3) Computational study of chromatin folding and epigenetics.

4) Multi-scale theory/algorithm and applications to biomolecule systems.

5) AI for biophysics

Teaching

1) “Computational Physics” for undergraduate students in Nanjing University.

2) “Biomolecular dynamics” for graduate students in Nanjing University

Publications:

1.	Z Zhang, Y Zhang, W Ren, W Zhang, W Li, W Wang*
	Allosteric Regulation of Enzymatic Catalysis through Mechanical Force
	J. Chem. Theory Comput., 2025, doi.org/10.1021/acs.jctc.5c00250.
2.	L Chen#, X Zhou#, Y Huang#, X Wang, X Gao, Y Cao, W Li, Y Zhou
	Chirality Interplay of Peptide and Saccharide on Glycopeptide Self-Assembly
	Nano Lett. 2025, 25, 4, 1558–1566.
3.	C Li^#, Y Bian^#, Y Tang^#, L Meng, P Yin, Y Hong, J Cheng, Y Li, J Lin, C Tang, C Chen, W. Li, Z Qi*
	Deciphering the molecular mechanism underlying morphology transition in two-component DNA-protein cophase separation
	Structure, 2025, 33 (1), 62-77.e8.
4.	C Xu^#, Y Lu^#, Y Wu^#, S Yuan, J Ma, H Fu, H Wang, L Wang, H Zhang, X Yu, W Tao, C Liu, S Hu, Y Peng, W Li, Y Li, Y Lu, M Li
	Sodium Ion-Induced Structural Transition on the Surface of a DNA-Interacting Protein
	Advanced Science 2024, 11 (42), 2401838.
5.	X Guan, Y Bian, Z Guo, J Zhang, Y Cao, W Li, W Wang
	Bidirectional Allostery Mechanism in Catch-Bond Formation of CD44 Mediated Cell Adhesion
	J. Phys. Chem. Lett. 2024, 15 (43), 10786-10794.
6.	Y Bian, F Lv, H Pan, W Ren, W Zhang, Y Wang, Y Cao, W Li, W Wang
	Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein. Phase Separation
	JACS Au 2024, 4 (9), 3690-3704.
7.	X Guan, QY Tang, W Ren, M Chen, W Wang, PG Wolynes, W Li*
	Predicting protein conformational motions using energetic frustration analysis and AlphaFold2
	Proc. Natl. Acad. Sci. U. S. A. 2024, 121 (35), e2410662121.
8.	Z Xu^#, J Lu^#, D Lu, Y Li, H Lei, B Chen, W Li, B Xue, Y Cao, W Wang
	Rapidly damping hydrogels engineered through molecular friction
	Nat. Commun. 2024, 15 (1), 4895.
9.	K Wang^#, S Zhang^#, X Zhou^#, X Yang, X Li, Y Wang, P Fan, Y Xiao, W Sun, P Zhang, W Li, S Huang*
	Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by. Nanopore
	Nat. Methods 2023, 21, 92-101.
10.	X Guan, HY Huang, HQ Peng, YH Liu, WF Li, W Wang
	Machine learning in molecular simulations of biomolecules
	Acta Phys. Sin. 2023, 72 (24), 248708.
11.	Wen, W Zhang, Y Zhang, H Lei, Y Cao, W Li, W Wang
	Self-Effected Allosteric Coupling and Cooperativity in Hypoxic Response Regulation with Disordered Proteins
	J. Phys. Chem. Lett. 2022, 13 (39), 9201-9209.
12.	Y Zhang, M Chen, J Lu, W Li, PG Wolynes, W Wang*
	Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis
	J. Phys. Chem. B 2022, 126 (36), 6792–6801.
13.	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.
14.	X Guan, C Tan, W Li, W Wang, D Thirumalai*
	Role of water-bridged interactions in metal ion coupled protein allostery
	PLoS Comput. Biol. 2022, 18 (6), e1010195.
15.	C Akil, S Ali, LT Tran, J Gaillard, W Li, K Hayashida, M Hirose, T Kato, A Oshima, K Fujishima, L Blanchoin, A Narita, RC Robinson*
	Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution
	Science Advances 2022, 8 (12), eabm2225.
16.	H Lei^#, Q Ma^#, W Li^#, J Wen, H Ma, M Qin, W Wang*, Y Cao
	An ester bond underlies the mechanical strength of a pathogen surface protein
	Nat. Commun. 2021, 12 (1), 5082.
17.	T Dong, T Gong, W Li*
	Accurate Estimation of Solvent Accessible Surface Area for Coarse-Grained Biomolecular Structures with Deep Learning
	J. Phys. Chem. B, 2021,125 (33), 9490–9498.
18.	Y Wang, X Guan, S Zhang, Y Liu, S Wang, P Fan, X Du, S Yan, P Zhang, HY Chen, W Li, D Zhang, S Huang*
	Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A
	Nat. Commun, 2021, 12, 3368.
19.	J Lu, X Zhang, Y Wu, Y Sheng, W Li, W Wang
	Energy landscape remodeling mechanism of Hsp70-chaperone-accelerated protein folding
	Biophys. J. 2021, 120 (10), 1971-1983.
20.	W Zhu, J Zhang, J Wang, W Li, W Wang*
	EEnhanced sampling method with coarse graining of conformational space
	Phys. Rev. E 2021, 103 (3), 032404.
21.	W Zhang, Y Cao, W Li, W Wang
	Allostery and molecular stripping mechanism in profilin regulated actin filament growth
	New J. Phys. 2021, 23, 123010.
22.	X Xu, J Shi, J Wang, W Li*
	Long-range correlation and critical fluctuations in coevolution networks of protein sequences
	Physica A, 2021, 562, 125339.
23.	Y Guo, M Werner, W Li, JU Sommer, VA Baulin*
	Shape-Adaptive Single-Chain Nanoparticles Interacting with Lipid Membranes
	Macromolecules,2019, 52 (24), 9578-9584.
24.	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.
25.	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.
26.	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.
27.	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.
28.	R. Song, X. Wu, B. Xue, Y. Yang, W. Huang, G. Zeng, J. Wang, W. Li, Y. Cao, W. Wang, J. Lu, H. Dong*
	Principles governing catalytic activity of self-assembled short peptides
	J. Am. Chem. Soc. 2018, 141 (1), 223-231.
29.	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.
30.	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.
31.	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.
32.	Wenfei Li, Jun Wang, Jian Zhang and Wei Wang
	Molecular simulations of metal-coupled protein folding,
	Curr. Opin. Struct. Biol. 2015, 30, 25-31.
33.	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)
34.	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
35.	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.
36.	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.
37.	Chao Liu, Wenfei Li, and Wei Wang
	Correlation of Reorientational Jumps of Water Molecules in Bulk Water
	Phys. Rev. E 2013, 87, 052309.
38.	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.
39.	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.
40.	Wenhui Xi, Wenfei Li, and Wei Wang
	Template Induced Conformational Change of Amyloid-β Monomer
	J. Phys. Chem. B, 2012, 116, 7398–7405.
41.	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.
42.	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.
43.	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.
44.	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
45.	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.
46.	Wenfei Li, Hiroaki Yoshii, Naoto Hori, Tomoshi Kameda, and Shoji Takada* ,
	Multiscale methods for protein folding simulations,
	Methods 2010, 52:106-114.
47.	Wenfei Li and Shoji Takada*,
	Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously,
	J. Chem. Phys. 2009, 130: 214108.
48.	Wenfei Li, Jian Zhang, Jun Wang and Wei Wang*,
	Metal Coupled folding of Cys2His2 Zinc-finger,
	J. Am. Chem. Soc. 2008, 130, 892-900.
49.	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.
50.	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.