Publications
* corresponding authorship
Structural mechanism for guanylate-binding proteins (GBPs) targeting by the Shigella E3 ligase IpaH9.8. Chenggong Ji, Shuo Du, Peng Li, Qinyu Zhu, Xiaoke Yang, Chunhong Long, Jin Yu, Feng Shao*, and Junyu Xiao*. PLOS Pathogens 2019 in press
Mini Review: A viral T7 RNA polymerase ratcheting along DNA with fidelity control. Chunhong Long, Chao E, Lin-Tai Da, and Jin Yu*. Computational and Structural Biotechnology 17, 638-644, 2019
Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control. Chunhong Long, Chao E, Lin-Tai Da, and Jin Yu*. Nucleic Acids Research 47(9), 4721-4735, 2019
Inspecting fluctuation and coordination around chromophore inside green fluorescent protein from water to nonpolar solvent. Liqiang Dai, Bo Zhang, Shuxun Cui*, and Jin Yu*. Proteins:Structure, Function, and Bioinformatics 87, 531-540, 2019
Novel Mechanism for Cyclic Dinucleotide Degradation Revealed by Structural Studies of Vibrio Phosphodiesterase V-cGAP3 Ming-jing Deng, Jianli Tao, Chao E, Zhao-yang Ye, Zhengfan Jiang, Jin Yu, and Xiao-dong Su*. Journal of Molecular Biology 430, 5080, 2018
How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting? Xiaobo Jing, Pavel Loskot, and Jin Yu*. Physical Biology 15(6) 066007, 2018
Base-Flipping Dynamics from an Intrahelical to an Extrahelical State Exerted by Thymine DNA Glycosylase During DNA Repair Process. Lin-Tai Da* and Jin Yu. Nucleic Acids Research 46(11) 5410-5425, 2018
Balancing Non-Equilibrium Driving with Nucleotide Selectivity at Kinetic Checkpoints in Polymerase Fidelity Control. Chunhong Long and Jin Yu*. Entropy 20(4), 306, 2018
Molecular mechanism of RNA polymerase II transcription elongation elucidated by kinetic network models. Ilona Christy Unarta, Lizhe Zhu, Camen Ka Man Tse, Peter Pak-Hang Cheung, Jin Yu, and Xuhui Huang*. Current Opinion in Structural Biology 49, 54-62, 2018
Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process. Lin-Tai Da*, Yi Shi, Guodong Ning, and Jin Yu*. Nucleic Acids Research 46(2) 569-581, 2017
Decipering intrinsic inter-subunit couplings that lead to sequential hydrolysis of F1-ATPase ring. Liqiang Dai, Holger Flechsig, and Jin Yu*. Biophysical Journal 113(7) 1440-1453, 2017
T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking. Lin-Tai Da*+,Chao E+, Yao Shuai, Shaogui Wu, Xiao-Dong Su, and Jin Yu*. Nucleic Acids Research 45(13) 7909-7921, 2017 +equal contributions as first authors
Imaging Metastable States and Transitions in Proteins by Trajectory Map. Chuanbiao Zhang, Jin Yu, and Xin Zhou*. The Journal of Physical Chemistry B, 121(18) 4678-4686, 2017
Nucleotide Selectivity at a Preinsertion Checkpoint of T7 RNA Polymerase Transcription Elongation. Chao E, Baogen Duan, and Jin Yu*. The Journal of Physical Chemistry B, 121(15) 3777-3786, 2017
Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations. Jin Yu*. Chinese Physics B, 25(1) 018706, 2016
A jump-from-cavity pyrophosphate ion release assisted by a key lysine residue in T7 RNA polymerase transcription elongation. Lin-Tai Da, Chao E, Baogen Duan, Chuanbiao Zhang, Xin Zhou, Jin Yu*. PLos Computational Biology, 11(11) e1004624, 2015
Computational modeling to elucidate molecular mechanisms of epigenetic memory. Jianhua Xing*, Jin Yu, Hang Zhang, Xiaojun Tian. Epigenetic Technological Applications In TRANSLATIONAL EPIGENETICS by Elsevier, Chapter 12, 245-264 2015
Protein denaturation at single-molecule level: the effect of nonpolar environments and its implications to the unfolding mechanism by proteases. Bo Cheng, Shaogui Wu, Shixin Liu, Piere Rodriguez, Jin Yu*, Shuxun Cui*. Nanoscale, 7, 2970, 2015
Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle. Jin Yu*, Lin-Tai Da, Xuhui Huang*. Physical Biology, 102, 016004, 2015
Efficient fidelity control by stepwise nucleotide selection in polymerase elongation. Jin Yu*. Molecular Based Mathematical Biology, 2,141-160, 2014
A critical residue selectively recruits nucleotides for T7 RNA polymerase transcription fidelity control. Baogen Duan, Shaogui Wu, Lin-Tai Da, Jin Yu*. Biophysical Journal, 107, 2130-2140, 2014
Coordination and control inside simple biomolecular machines. Jin Yu*. Advances in Experimental Medicine and Biology In Protein Conformation Dynamics by Springer 805, 2014, 353-384, Springer, 2014
Previous Publications
A small post-translocation energy bias aids nucleotide selection in T7 RNA polymerase transcription. Jin Yu*, George Oster*. Biophysical Journal, 102, 532-541, 2012
PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps.Jeehae Park, Sua Myong, Anita Niedziela-Majka, Kyung Suk Lee, Jin Yu, Timothy M. Lohman, Taekjip Ha*. Cell, 142:544-555, 2010
Coupling translocation with nucleic acid unwinding by NS3 helicase. Jin Yu*, Wei Cheng, Carlos Bustamante, and George Oster*. Journal of Molecular Biology, 404:439-455, 2010
Mechanochemistry of a viral DNA packaging motor. Jin Yu, Jeff Moffitt, Craig Hetherington, Carlos Bustamante, and George Oster*. Journal of Molecular Biology, 400:186-203, 2010
Double stranded DNA dissociates into single strands when dragged into a poor solvent. Shuxun Cui, Jin Yu, Ferdinand Kühner, Klaus Schulten, and Hermann E. Gaub*. Journal of the American Chemical Society, 129:14710-14716, 2007.
Mapping the two-dimensional reaction landscape of Holliday junction via dynamic fluorescence-force spectroscopy. Sungchul Hohng, Ruobo Zhou, Michelle K. Nahas, Jin Yu, Klaus Schulten, David M. J. Lilley, and Taekjip Ha*. Science, 318:279-283, 2007
PcrA helicase, a molecular motor studied from the electronic to the function level. Markus Dittrich, Jin Yu, and Klaus Schulten*. Atomistic Approaches in Modern Biology. Topics in Current Chemistry, 268: 319-347, Springer, 2006
How directional translocation is regulated in a DNA helicase motor. Jin Yu, Taekjip Ha, and Klaus Schulten*. Biophysical Journal, 93:3783-3797, 2007
Structure-based model of the stepping motor of PcrA helicase. Jin Yu, Taekjip Ha, and Klaus Schulten*. Biophysical Journal, 91:2097-2114, 2006
Mechanism of gating and ion conductivity of a possible tetrameric pore in Aquaporin-1. Jin Yu, Andrea J. Yool, Klaus Schulten, and Emad Tajkhorshid*. Structure, 14:1411-1423, 2006
Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. Jin Yu, Taekjip Ha, and Klaus Schulten*. Nucleic Acids Research, 32:6683-6695, 2004
The Lyapunov analysis of the highly excited bend motion of acetylene. Jin Yu and Guozhen Wu*. Chemical Physics Letters, 343: 375-382, 2001.
Classical characters of highly bend dynamics of acetylene in two coupled SU(2) coset spaces. Jin Yu and Guozhen Wu*. Journal of Chemical Physics, 113:647-652, 2000
Multifractal analysis for the eigencoefficients of the eigenstates of highly excited vibration. Jin Yu, Songtao Li and Guozhen Wu*. Chemical Physics Letters, 301:217-222, 1999
