After joining SJTU

Structural Insights into the Substrate Recognition Mechanism of an ATP-Grasp Peptide-Ligase Producing Diverse Dipeptides Containing Unnatural Amino Acids. Ya-Qian Yan, Si-Yuan Li, Xiao-Na Wu, Ting Zhou, Jia-Xin Li, Shu-Xin Huang, Jian-Ting Zheng, Jun Xu, Lin-Tai Da*, and Min-Juan Xu*, ACS Catal. 2025, 15: 2550–2560

High hydrostatic pressure promotes gene transcription via a cystathionine-β-synthase domain-containing protein in the hyperthermophilic archaeon Pyrococcus yayanosii. Cong Li, Siyuan Li, Qinghao Song, Lin-Tai Da*, and Jun Xu*, Nucleic Acids Research 2025, 53: gkae1289.

Comprehensive Investigations of MUC1 O Glycosylation Process Reveal Initial Site Preference by the Polypeptide GalNAc Transferases. Han Zhang, Kaiyuan Song, Yihan Liu, Fang Yang, Congcong Lu, Rumeng Wei, Zhijue Xu, Xia Zou, Liang Lin, Ting Shi, Lin-Tai Da*, and Yan Zhang*, ACS Catal. 2024, 14: 18365-18377.

Investigating TCR-pMHC interactions for TCRs without identified epitopes by constructing a computational pipeline. Kaiyuan Song, Honglin Xu, Yi Shi, Xin Zou*, Lin-Tai Da*, Jie Hao*, Int. J. Biol. Macromol. 2024, 282: 136502.

Sequence-encoded bioactive protein-multiblock polymer conjugates via quantitative one-pot iterative living polymerization. Ziying Li, Kaiyuan Song, Yu Chen, Qijing Huang, Lujia You, Li Yu, Baiyang Chen, Zihang Yuan, Yaqin Xu, Yue Su, Lin-Tai Da*, Xinyuan Zhu & Ruijiao Dong*, Nat. Commun. 2024, 15: 6729.

Structural and mechanistic investigations on C-C bond forming α-oxoamine synthase allowing L-glutamate as substrate. Dai-Ke Zhang, Kai-Yuan Song, Ya-Qian Yan, Jian-Ting Zheng, Jun Xu, Lin-Tai Da*, Min-Juan Xu*, Int. J. Biol. Macromol. 2024, 268: 131696.

Kinetic Model Reveals the Critical Gating Motifs for Donor-Substrate Loading into Actinobacillus pleuropneumoniae N-glycosyltransferase. Zhiqiang Hao, Qiang Guo, Wenjie Peng* and Lin-Tai Da*, Phys. Chem. Chem. Phys. 2024, 26: 13441-13451.

SSRI antidepressant citalopram reverses the Warburg effect to inhibit hepatocellular carcinoma by directly targeting GLUT1. Fangyuan Dong, Kang He, Shan Zhang, Kaiyuan Song, Luju Jiang, Li-Peng Hu, Qing Li, Xue-Li Zhang, Naiqi Zhang, Bo-Tai Li, Li-Li Zhu, Jun Li, Mingxuan Feng, Yunchen Gao, Jie Chen, Xiaona Hu, Jiaofeng Wang, Chongyi Jiang, Cun Wang, Helen He Zhu, Lin-Tai Da, Jianguang Ji*, Zhi-Gang Zhang*, Zhijun Bao*, and Shu-Heng Jiang*, Cell Reports, 2024, 43: 114818.

Cryo-EM structures of a mycobacterial ABC transporter that mediates rifampicin resistance. Yinan Wang, Shan Gao, Fangyu Wu, Yicheng Gong, Nengjiang Mu, Chuancun Wei, Chengyao Wu, Jun Wang, Ning Yan, Huifang Yang, Yifan Zhang, Jiayi Liu, Zeyu Wang, Xiuna Yang, Sin Man Lam, Guanghou Shui, Siyuan Li, Lin-Tai Da, Luke W. Guddat, Zihe Rao*, and Lu Zhang*, PNAS 2024, 121: e2403421121.

TMEFF1 is a neuron-specific restriction factor for herpes simplex virus. Yao Dai, Manja Idorn, Manutea C. Serrero, Xiaoyong Pan, Emil A. Thomsen, Ryo Narita, Muyesier Maimaitili, Xiaoqing Qian, Marie B. Iversen, Line S. Reinert, Rasmus K. Flygaard, Muwan Chen, Xiangning Ding, Bao-cun Zhang, Madalina E. Carter-Timofte, Qing Lu, Zhuofan Jiang, Yiye Zhong, Shuhui Zhang, Lin-Tai Da, Jinwei Zhu, Mark Denham, Poul Nissen, Trine H. Mogensen, Jacob Giehm Mikkelsen, Shen-Ying Zhang, Jean-Laurent Casanova, Yujia Cai* & Søren R. Paludan*, Nature 2024, 632: 383–389.

Allele-Specific Suppression of Variant MHC With High-Precision RNA Nuclease CRISPR-Cas13d Prevents Hypertrophic Cardiomyopathy. Ping Yang, Yingmei Lou, Zilong Geng, Zhizhao Guo, Shuo Wu, Yige Li , Kaiyuan Song, Ting Shi, Shasha Zhang, Junhao Xiong, Alex F. Chen, Dali Li, William T. Pu, Lin-Tai Da, Yan Zhang*, Kun Sun*, Bing Zhang*, Circulation. 2024, 150: 283–298.

Antifouling Asymmetric Block Copolymer Nanofilms via Freestanding Interfacial Polymerization for Efficient and Sustainable Water Purification. Yu Chen, Kaiyuan Song, Ziying Li, Yue Su, Li Yu, Baiyang Chen, Qijing Huang, Lin-Tai Da, Zeguang Han, Yongfeng Zhou, Xinyuan Zhu, Jia Xu*, and Ruijiao Dong*, Angew. Chem. Int. Ed. 2024, 63: e202408345.

Dendritic-cell-targeting virus-like particles as potent mRNA vaccine carriers. Di Yin, Yiye Zhong, Sikai Ling, Sicong Lu, Xiaoyuan Wang, Zhuofan Jiang, Jie Wang, Yao Dai, Xiaolong Tian, Qijing Huang, Xingbo Wang, Junsong Chen, Ziying Li, Yang Li, Zhijue Xu, Hewei Jiang, Yuqing Wu, Yi Shi, Quanjun Wang, Jianjiang Xu, Wei Hong, Heng Xue, Hang Yang, Yan Zhang, Lin-Tai Da, Ze-guang Han, Sheng-ce Tao, Ruijiao Dong, Tianlei Ying, Jiaxu Hong* & Yujia Cai*, Nat. Biomed. Eng. 2024, s41551-024-01208-4.

Dynamic Phosphorylation of G9a Regulates its Repressive Activity on Chromatin Accessibility and Mitotic Progression. Qizhi Geng, Yue-Yu Kong, Weizhe Li, Jianhao Zhang, Haoli Ma, Yuhang Zhang, Lin-Tai Da, Yan Zhao*, Hai-Ning Du*, Adv Sci (Weinh). 2023 Sep 3:e2303224.

Investigation of the Catalytic Mechanism of a Soluble N-glycosyltransferase Allows Synthesis of N-glycans at Noncanonical Sequons. Zhiqiang Hao, Qiang Guo, Yuanyuan Feng, Zihan Zhang, Tiantian Li, Zhixin Tian, Jianting Zheng, Lin-Tai Da*, Wenjie Peng*,JACS Au. 2023 Aug 7;Volume 3(8), Pages 2144-2155.

Structure of the priming arabinosyltransferase AftA required for AG biosynthesis of Mycobacterium tuberculosis Yicheng Gong, Chuancun Wei, Jun Wang, Nengjiang Mu, Qinhong Lu, Chengyao Wu, Ning Yan, Huifang Yang, Yao Zhao, Xiuna Yang, Sudagar S Gurcha, Natacha Veerapen, Sarah M Batt, Zhiqiang Hao, Lin-tai Da, Gurdyal S Besra*, Zihe Rao, Lu Zhangi*, Proc Natl Acad Sci U S A. 2023 Jun 6, Volume 120(23):e2302858120.

Discovery and Engineering of the L Threonine Aldolase from Neptunomonas marine for the Efficient Synthesis of β-Hydroxy-α-amino Acids via C-C Formation. Yuanzhi He, Siyuan Li, Jun Wang, Xinrui Yang, Jiawei Zhu, Qi Zhang, Li Cui, Zaigao Tan, Wupeng Yan, Yong Zhang, Luyao Tang, Lin-Tai Da*, and Yan Feng*, ACS Catal. 2023 May 12, Volume 13, Pages 7210–7220

Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation. Yanyan Wang, Senxin Zhang, Xinrui Yang, Joyce K Hwang, Chuanzong Zhan, Chaoyang Lian, Chong Wang, Tuantuan Gui, Binbin Wang, Xia Xie, Pengfei Dai, Lu Zhang, Ying Tian, Huizhi Zhang, Chong Han, Yanni Cai, Qian Hao, Xiaofei Ye, Xiaojing Liu, Jiaquan Liu, Zhiwei Cao, Shaohui Huang, Jie Song, Qiang Pan-Hammarström, Yaofeng Zhao, Frederick W Alt, Xiaoqi Zheng, Lin-Tai Da, Leng-Siew Yeap*, Fei-Long Meng*, Cell. 2023 May 11, Volume 186(10), Pages 2193-2207.e19.

Loading dynamics of one SARS-CoV-2-derived peptide into MHC-II revealed by kinetic models. Kaiyuan Song, Honglin Xu, and Lin-Tai Da*, Biophys J. 2023 May 2; Volume 122(9), Pages 1665-1677.

Legumain inhibitor prevents breast cancer bone metastasis by attenuating osteoclast differentiation and function. Junsong Chen, Wenke Xu, Kaiyuan Song, Lin-Tai Da, Xin Zhang, Mengyao Lin, Xiaowu Hong, Sheng Zhang*, Fang Guo*. Bone. 2023 Jan 24, Volume 169,

3D genome assisted protein–protein interaction prediction. Zehua Guo, Liangjie Liu, Mofan Feng, Kai Su, Runqiu Chi, Keyi Li, Qing Lu, Xianbin Su, Lin-tai Da, Song Cao, Mingxuan Zhang, Luming Meng, Dan Cao, Jiayi Wang, Guang He*, Yi Shi*, Future Gener Comp Sy. 14 July 2022, Volume 137, Pages 87-96

DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base Flipping. Lingyan Wang, Kun Xi, Lizhe Zhu*,Lin-Tai Da* J Chem Inf Model. 2022 Jul 11;62(13):3213-3226.

Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process. Lingyan Wang, Kaiyuan Song, Lin-Tai Da* Acta Biochim Biophys Sin (Shanghai). 2022 May 25.

Dynamics of peptide loading into major histocompatibility complex class I molecules chaperoned by TAPBPR. Honglin Xu, Kaiyuan Song, Lin-Tai Da* Phys Chem Chem Phys. 2022 May 25;24(20):12397-12409.

Structure-Based simulation and sampling of transcription factor protein movements along DNA from atomic-scale stepping to coarse-grained diffusion. Chao E, Liqiang Dai, Jiaqi Tian, Lin-Tai Da, Jin Yu*. J Vis Exp. 2022 Mar 1. (181)

Early aggregation mechanism of Aβ16-22 revealed by Markov state models. Mueed Ur Rahman, Kaiyuan Song, Lin-Tai Da, Hai-Feng Chen*. Int J Biol Macromol. 2022 Apr 15. 204:606-616.

RQC helical hairpin in Bloom's syndrome helicase regulates DNA unwinding by dynamically intercepting nascent nucleotides. Jianbing Ma, Chunhua Xu, Jinghua Li, Xi-Miao Hou, Lin-Tai Da, Qi Jia, Xingyuan Huang, Jin Yu, Xuguang Xi*, Ying Lu*, Ming Li. iScience. 2022 Jan 21. 25(1), 103606.

Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2. Chunhong Long, Liqiang Dai, Chao E, Lin-tai Da, Jin Yu*. Biophys J. 2021;120(15):3126-3137.

Antigenic Peptide Loading into Major Histocompatibility Complex Class I Is Driven by the Substrate N-Terminus. Mengna Lin, Honglin Xu, Yi Shi*, Lin-tai Da*. CCS Chem. 2021, 3, 979-994

Mechanism of REST/NRSF regulation of clustered protocadherin α genes. Yuanxiao Tang, Zhilian Jia, Honglin Xu, Lin-tai Da, Qiang Wu*. Nucleic Acids Res. 2021 Apr 13:gkab248.

Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition. Jiaqi Tian, Lingyan Wang, Lin-tai Da*. Nucleic Acids Res. 2021 Feb 22;49(3):1278-1293.

A novel neoantigen discovery approach based on chromatin high order conformation. Yi Shi*, Mingxuan Zhang, Luming Meng*, Xianbin Su, Xueying Shang, Zehua Guo, Qingjiao Li, Mengna Lin, Xin Zou, Qing Luo, Yaoliang Yu, Yanting Wu, Lin-tai Da*, Tom Weidong Cai*, Guang He* & Ze-Guang Han*. BMC Med Genomics. 2020 Aug 27;13(Suppl 6):62.

DeepAntigen: A Novel Method for Neoantigen Prioritization via 3D Genome and Deep Sparse Learning. Yi Shi*, Zehua Guo, Xianbin Su, Luming Meng*, Mingxuan Zhang, Jing Sun, Chao Wu, Minhua Zheng, Xueyin Shang, Xin Zou, Wangqiu Cheng, Yaoliang Yu, Yujia Cai, Chaoyi Zhang, Weidong Cai, Lin-tai Da*, Guang He*, Ze-Guang Han*. Bioinformatics. 2020, btaa596

Key Structural Motifs in Thymine DNA Glycosylase Responsible for Recognizing Certain DNA Bent Conformation Revealed by Atomic Simulations, Biochemical and Biophysical Research Communications. Shuang Li, Lin-Tai Da*. Biochemical and Biophysical Research Communications. 2020. 526:953-959

Ikarugamycin inhibits pancreatic cancer cell glycolysis by targeting hexokinase 2. Shu-Heng Jiang; Fang-Yuan Dong; Lin-Tai Da; Xiao-Mei Yang, Xiao-Xue Wang, Jing-Yi Weng, Lei Feng, Li-Li Zhu, Yan-Li Zhang, Zhi-Gang Zhang, Yong-Wei Sun, Jun Li, Min-Juan Xu*. The FASEB Journal. 2020. 34: 3943-3955

Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States During HIV-1 Entry. Mengna Lin, Lin-Tai Da*. Journal of Chemical Information and Modeling. 2020. 60: 162-174

Opening dynamics of HIV-1 gp120 upon receptor binding is dictated by a key hydrophobic core. Lin-Tai Da*, Mengna Lin. Physical Chemistry Chemical Physics. 2019. 21: 26003-26016

Rational Engineering of Amide Synthetase Enables Bioconversion to Diverse Xiamenmycin Derivatives. Jingyi Weng, Xuliang Bu, Beibei He, Zhuo Cheng, Jun Xu, Lin-Tai Da*, Minjuan Xu*. Chemical Communications. 2019. 55: 14840-14843

Characterization and Nonenzymatic Transformation of Three Types of Alkaloids from Streptomyces albogriseolus MGR072 and Discovery of Inhibitors of Indoleamine 2,3-Dioxygenase. Du Gao, Ting Zhou, Lin-Tai Da, Torsten Bruhn, Li-Li Guo, Yu-Hang Chen, Jun Xu, Min-Juan Xu*. Organic letters. 2019. 21(21):8577-8581

Regulatory Role of One Critical Catalytic Loop of Polypeptide N-Acetyl-Galactosaminyltransferase-2 in Substrate Binding and Catalysis during Mucin-Type O-Glycosylation. Jiaqi Tian, Feng Liu, Zhijue Xu, Jingjing Shi, Tao Liang, Yan Zhang*, Lin-Tai Da*. ACS Catalysis 2019. 9(11):10536-10550

Inhibition of polypeptide N-acetyl-α-galactosaminyltransferases is an underlying mechanism of dietary polyphenols preventing colorectal tumorigenesis. Feng Liu, Yalu Cui, Fang Yang, Zhijue Xu, Lin-Tai Da, Yan Zhang*. Bioorganic & Medicinal Chemistry. 2019. 27(15): 3372-3382

pH-Induced Misfolding Mechanism of Prion Protein: Insights from Microsecond-Accelerated Molecular Dynamics Simulations. Shuangyan Zhou, Danfeng Shi, Xuewei Liu, Xiaojun Yao, Lin-Tai Da*, Huanxiang Liu*. ACS Chem. Neurosci. 2019. 10: 2718-2729

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, Jin Yu*. Nucleic Acids Res. 2019. 47(9): 4721-4735

Understanding the molecular mechanism of umami recognition by T1R1-T1R3 using molecular dynamics simulations. Hai Liu, Lin-Tai Da*, Yuan Liu*. Biochemical and Biophysical Research Communications. 2019. 514(3): 967-973

A viral T7 RNA polymerase ratcheting along DNA with fidelity control. Chunhong Long, Chao E, Lin-Tai Da, Jin Yu*. Computational and Structural Biotechnology Journal. 2019. 17: 638-644

Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process. Lin-Tai Da*, Jin Yu. Nucleic Acids Res. 2018 46(11): 5410-5425

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 Res. 2018 46(2): 568-581

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, Jin Yu*. Nucleic Acids Res. 2017 45(13): 7909-7921

Before joining SJTU

Bridge Helix Bending Promotes RNA Polymerase II Backtracking Through a Critical Threonine Residue. Lin-Tai Da, Fátima Pardo-Avila, Liang Xu, Daniel-Adriano Silva, Lu Zhang, Xin Gao, Dong Wang, Xuhui Huang. Nat. Commun. 2016 DOI: 10.1038/ncomms11244

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

Application of Markov State Models to Simulate Long Timescale Dynamics of Biological Macromolecules. Lin-Tai Da, Sheong, F.K., Silva, D., Huang, X.Book Chapter, Protein Conformational Dynamics, Advances in Experimental Medicine and Biology. 805, 29-66, Springer, (2014)

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

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

Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis. Xu, L., Lin-Tai Da, Plouffe, S.W., Chong, J., Kool, E., Wang, D. DNA Repair. 2014 19 71-83.

Molecular dynamics simulation study for the conformation of TFIIS and the insertion of the catalytic domain of TFIIS into RNA Polymerase II. Changsun Eun, Juan Manuel Ortiz-Sánchez, Lin-Tai Da, Dong Wang, J Andrew McCammon.PLoS One. 2014, 9(5): e97975.

Millisecond Dynamics of RNA Polymerase II Translocation at Atomic Resolution. Daniel-Adriano Silva, Dahlia Weiss, Fátima Pardo-Avila, Lin-Tai Da, Michael Levitt, Dong Wang, and Xuhui Huang. PNAS 2014 111(21): 7665-7670.

Theoretical Investigations on Elucidating Fundamental mechanisms of catalysis and dynamics involved in transcription by RNA polymerase. Pardo-Avila, Fátima, Lin-Tai Da, Ying Wang, and Xuhui Huang. J. Theor. Comput. Chem. 2013 12(8): 1341005.

A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase. Lin-Tai Da, Pardo-Avila, Fátima, Dong Wang, and Xuhui Huang. PLoS. Comp. Bio. 2013 9(4): e1003020.

Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Tip Motion from Closed to Open State in RNA Polymerase II. Lin-Tai Da, Dong Wang, and Xuhui Huang. J. Am. Chem. Soc. 2012 134, 2399−2406.

Monitoring and Inhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission Characteristics. Yuning Hong, Luming Meng, Sijie Chen, Chris Wai Tung Leung, Lin-Tai Da, Mahtab Faisal, Daniel-Adriano Silva, Jianzhao Liu, Jacky Wing Yip Lam, Xuhui Huang, and Ben Zhong Tang. J. Am. Chem. Soc. 2012 134, 1680-1689.

Theoretical Studies on the Interactions and Interferences of HIV-1 Glycoprotein gp120 and Its Coreceptor CCR5. Lin-Tai Da, and Yun-Dong Wu. J. Chem. Inf. Model. 2011 51, 359–369.

Understanding the Binding Mode and Function of BMS-488043 Against HIV-1 Viral Entry. Lin-Tai Da, Jun-Min Quan and Yun-Dong Wu. Proteins. 2011 79, 1810–1819.

Understanding of the Bridging Sheet Formation of HIV-1 Glycoprotein gp120. Lin-Tai Da, Jun-Min Quan and Yun-Dong Wu. J. Phys. Chem. B. 2009 113, 14536–14543.