Full publication list: Google Scholar citation
2023
51. Moises E Romero, Shannon J McElhenney and Jin Yu*. Trapping non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase
50. Carmen Al Masri, Biao Wan and Jin Yu*. Non-specific vs specific DNA binding free energetics of a transcription factor domain protein for target search and recognition. Biophysical Journal 2023, 122:4476-4487 (
49. Jin Yu*. Commentary: On the common pathways of deformation: RNA vs DNA under interrogation. Proc Natl Acad Sci USA 2023, 120 (23) e2306453120
48. Chunhong Long, Moises Ernesto Romero, Liqiang Dai, and Jin Yu*. Energetic vs entropic stabilization between Remdesivir analogue and cognate ATP upon binding and insertion into active site of SARS-CoV-2 RNA dependent RNA polymerase. Phys. Chem. Chem. Phys., 2023, 25, 13508-13520 (accepted version)
2022
47. Lingyan Wang et al. Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process. Acta Biochimica et Biophysica Sinica 2022, 54, 796-806
46. Chuan Li et al. An Interpretable Convolutional Neural Network Framework for Analyzing Molecular Dynamics Trajectories: a Case Study on Functional States for G-Protein-Coupled Receptors. J. Chem. Inf. Model. 2022, 62, 6, 1399–1410
45. Chao E✝, Liqiang Dai✝, Jiaqi Tian, Lin-Tai Da, and Jin Yu*. Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion. Video Tutorial J. Vis. Exp. (181), e63406, 2022 ✝equal contribution
44. Chao E, Liqiang Dai, and Jin Yu*. Switching Promotor Recognition of Phage RNA Polymerase in Silico Following Path along Lab Directed Evolution. Biophysical Journal 2022, 121:582-595 Interview @ Researcher
43. Biao Wan and Jin Yu*. Two-Phase Dynamics of DNA Supercoiling based on DNA Polymer Physics. Biophysical Journal 2022, 121:658-669 arXiv:2105.13594 [cond-mat.soft]
42. Jianbing Ma et al. RQC helical hairpin in Bloom’s syndrome helicase regulates DNA unwinding by dynamically intercepting nascent nucleotides. iScience, 25 (1), 103606, 2022
2020-2021
41. Moises E Romero, Chunhong Long, Daniel La Rocco, , , and Jin Yu*. Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication. (accepted version) Molecular Systems Design & Engineering, 2021, 6, 888 – 902 Feature@RSC/MSDE ( More from media (PDF)
40. Chunhong Long, Liqiang Dai, Chao E, Lin-Tai Da, and Jin Yu*. Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA in association with Cas2. Biophysical Journal 2021, 120, 3126-3137 (
39. Chunhong Long, Moises Ernesto Romero, Daniel La Rocco, and Jin Yu*. Min-review: Dissecting nucleotide selectivity in viral RNA polymerases. Computational and Structural Biotechnology Journal 19, 3339-3348, 2021
38. Liqiang Dai, Yongping Xu, Zhenwei Du, Xiao-dong Su*, and Jin Yu*. Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY Domain Protein along DNA. Proc Natl Acad Sci USA (bioRxiv 2020.02.14.950295; poster)
37. Liqiang Dai and Jin Yu*. Inchworm stepping of Myc-Max heterodimer protein diffusion along DNA. Biochemical and Biophysical Research Communication 533, 97-103, 2020 (poster)
2019
36. Chenggong Ji, Shuo Du, Peng Li, Qinyu Zhu, Xiaoke Yang, Chunhong Long, Jin Yu, Feng Shao*, and Junyu Xiao*. Structural mechanism for guanylate-binding proteins (GBPs) targeting by the Shigella E3 ligase IpaH9.8. PLOS Pathogens 15(6): e1007876, 2019
35. Chunhong Long, Chao E, Lin-Tai Da, and Jin Yu*. Mini Review: A viral T7 RNA polymerase ratcheting along DNA with fidelity control. Computational and Structural Biotechnology 17, 638-644, 2019
34. Chunhong Long, Chao E, Lin-Tai Da, and Jin Yu*. Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control. Nucleic Acids Research 47(9), 4721-4735, 2019
33. Liqiang Dai, Bo Zhang, Shuxun Cui*, and Jin Yu*. Inspecting fluctuation and coordination around chromophore inside green fluorescent protein from water to nonpolar solvent. Proteins:Structure, Function, and Bioinformatics 87, 531-540, 2019
2018
32. Min-jing Deng, Jianli Tao, Chao E, Zhao-yang Ye, Zhengfan Jiang, Jin Yu, and Xiao-dong Su*. Novel Mechanism for Cyclic di-Nucleotide Degradation Revealed by Structural Studies of Vibrio Phosphodiesterase V-cGAP3. Journal of Molecular Biology 430 (24), 5080-5093, 2018
31. Xiaobo Jing, Pavel Loskot, and Jin Yu*. How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting? Physical Biology 15 (6), 066007, 2018
30. Lin-Tai Da* and Jin Yu. Base-Flipping Dynamics from an Intrahelical to an Extrahelical State Exerted by Thymine DNA Glycosylase During DNA Repair Process. Nucleic Acids Research 46 (11), 5410-5424, 2018
29. Chunhong Long and Jin Yu*. Balancing Non-Equilibrium Driving with Nucleotide Selectivity at Kinetic Checkpoints in Polymerase Fidelity Control. Entropy 20, 306, 2018
28. Ilona Christy Unarta, Lizhe Zhu, Camen Ka Man Tse, Peter Pak-Hang Cheung, Jin Yu, and Xuhui Huang*. Molecular mechanism of RNA polymerase II transcription elongation elucidated by kinetic network models. Current Opinion in Structural Biology 49, 54-62, 2018
2017
27. Lin-Tai Da*, Yi Shi, Guodong Ning, and Jin Yu*. Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process. Nucleic Acids Research, 46(2) 569-581, 2017
26. Liqiang Dai, Holger Flechsig, and Jin Yu*. Deciphering intrinsic inter-subunit couplings that lead to sequential hydrolysis of F1-ATPase ring. Biophysical Journal 113 (7) 1440-1453, 2017
25. Lin-Tai Da✝*, Chao E✝, Yao Shuai, Shaogui Wu, Xiao-Dong Su, and Jin Yu*. T7 RNA Polymerase Translocation is Facilitated by Helix Opening on the Fingers Domain that may also Prevent Backtracking. Nucleic Acids Research 45(13) 7909-7921, 2017 ✝equal contribution
24. Chuanbiao Zhang, Jin Yu, and Xin Zhou*. Imaging Metastable States and Transitions in Proteins by Trajectory Map. The Journal of Physical Chemistry B, 121(18) 4678-4686, 2017
23. Chao E, Baogen Duan, and Jin Yu*. Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation. The Journal of Physical Chemistry B, 121(15) 3777-3786, 2017
2014- 2016
22. Jin Yu*. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations. Chinese Physics B, 25 (1) 018706, 2016
21. Lin-Tai Da, Chao E, Baogen Duan, Chuanbiao Zhang, Xin Zhou, Jin Yu*. A jump-from-cavity pyrophosphate ion release assisted by a key lysine residue in T7 RNA polymerase transcription elongation. PLoS Computational Biology, 11 (11), e1004624, 2015
20. Jianhua Xing*, Jin Yu, Hang Zhang, Xiaojun Tian. Computational modeling to elucidate molecular mechanisms of epigenetic memory. Epigenetic Technological Applications In TRANSLATIONAL EPIGENETICS by Elsevier. Chapter 12, 245-264, 2015
19. Bo Cheng, Shaogui Wu, Shixin Liu, Piere Rodriguez, Jin Yu*, Shuxun Cui*. Protein denaturation at single-molecule level: the effect of nonpolar environments and its implications to the unfolding mechanism by proteases. Nanoscale, 7, 2970 2015
18. Jin Yu*, Lin-Tai Da, Xuhui Huang*. Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle. Physical Biology, 102, 016004, 2015
17. Jin Yu*. Efficient fidelity control by stepwise nucleotide selection in polymerase elongation. Molecular Based Mathematical Biology, 2, 141-160, 2014
16. Baogen Duan, Shaogui Wu, Lin-Tai Da, Jin Yu*. A critical residue selectively recruits nucleotides for T7 RNA polymerase transcription fidelity control. Biophysical Journal, 107, 2130-2140, 2014
15. Jin Yu* Coordination and control inside simple biomolecular machines. Protein Conformational Dynamics, Advances in Experimental Medicine and Biology by Springer, 805, 353-383, 2014
14. Jin Yu＊, George Oster*. A small post-translocation energy bias aids nucleotide translocation in T7 RNA polymerase transcription. Biophysical Journal, 102, 532-541, 2012.
13. Jin Yu＊, Wei Cheng, Carlos Bustamante, and George Oster*. Coupling translocation with nucleic acid unwinding by NS3 helicase. Journal of Molecular Biology, 404:439-455, 2010.
12. Jeehae Park, Sua Myong, Anita Niedziela-Majka, Kyung Suk Lee, Jin Yu, Timothy M. Lohman, Taekjip Ha*. PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps. Cell, 142:544-555, 2010.
11. Jin Yu, Jeff Moffitt, Craig Hetherington, Carlos Bustamante, and George Oster*. Mechanochemistry of a viral DNA packaging motor. Journal of Molecular Biology, 400:186-203, 2010.
2004-2007
10. Shuxun Cui, Jin Yu, Ferdinand Kühner, Klaus Schulten, and Hermann E. Gaub*. Double stranded DNA dissociates into single strands when dragged into a poor solvent. Journal of the American Chemical Society, 129:14710-14716, 2007.
9. Sungchul Hohng, Ruobo Zhou, Michelle K. Nahas, Jin Yu, Klaus Schulten, David M. J. Lilley, and Taekjip Ha*. Mapping the two-dimensional reaction landscape of Holliday junction via dynamic fluorescence-force spectroscopy. Science, 318:279-283, 2007.
8. Markus Dittrich, Jin Yu, and Klaus Schulten*. PcrA helicase, a molecular motor studied from the electronic to the function level. Atomistic Approaches in Modern Biology. Topics in Current Chemistry, 268: 319-347, Springer, 2006.
7. Jin Yu, Taekjip Ha, and Klaus Schulten*. How directional translocation is regulated in a DNA helicase motor. Biophysical Journal, 93:3783-3797, 2007.
6. Jin Yu, Taekjip Ha, and Klaus Schulten*. Structure-based model of the stepping motor of PcrA helicase. Biophysical Journal, 91:2097-2114, 2006.
5. Jin Yu, Andrea J. Yool, Klaus Schulten, and Emad Tajkhorshid*. Mechanism of gating and ion conductivity of a possible tetrameric pore in Aquaporin-1. Structure, 14:1411-1423, 2006.
4. Jin Yu, Taekjip Ha, and Klaus Schulten*. Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. Nucleic Acids Research, 32:6683-6695, 2004.
1999-2001
3. Jin Yu and Guozhen Wu*. The Lyapunov analysis of the highly excited bend motion of acetylene. Chemical Physics Letters, 343: 375-382, 2001.
2. Jin Yu and Guozhen Wu*. Classical characters of highly bend dynamics of acetylene in two coupled SU(2) coset spaces. Journal of Chemical Physics,113:647-652, 2000.
1. Jin Yu, Songtao Li and Guozhen Wu*. Multifractal analysis for the eigencoefficients of the eigenstates of highly excited vibration. Chemical Physics Letters, 301:217-222, 1999.