Full publication list: Google Scholar citation
2023-2024
53. Chunhong Long et al. Dissecting the CRISPR Cas1-Cas2 Protospacer Binding and Selection Mechanism by Using Molecular Dynamics Simulations. J. Phys. Chem. B 2024, 128, 15, 3563–3574
52. Jianfang Chen et al. Computational insights into diverse binding modes of the allosteric modulator and their regulation on dopamine D1 receptor Computers in Biology and Medicine 2024, 173, 108283
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.