- 作 者: ( "lintai da" OR "lin-tai da" )
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3D genome assisted protein–protein interaction predictionFuture Generation Computer Systems (IF 7.307) Pub Date : 2022-07-14 ,DOI:10.1016/j.future.2022.07.005Zehua Guo, Liangjie Liu, Mofan Feng, Kai Su, Runqiu Chi, Keyi Li, Qing Lu, Xianbin Su, Lintai Da, Song Cao, Mingxuan Zhang, Luming Meng, Dan Cao, Jiayi Wang, Guang He, Yi ShiProtein–protein interactions (PPIs) play key roles in the biological system, making revealing protein interactome critical. A large portion of the protein interactome however, are yet to be revealed. Dozens of computational methods have been proposed to predict PPIs, but none of the existing method considers the DNA origin the interacting proteins in the perspective of 3D genome. In this work, we project ...
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DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base FlippingJournal of Chemical Information and Modeling (IF 6.162) Pub Date : 2022-06-16 ,DOI:10.1021/acs.jcim.2c00091Lingyan Wang, Kun Xi, Lizhe Zhu, Lin-Tai DaHuman alkyladenine DNA glycosylase (AAG) is a key enzyme that corrects a broad range of alkylated and deaminated nucleobases to maintain genomic integrity. When encountering the lesions, AAG adopts a base-flipping strategy to extrude the target base from the DNA duplex to its active site, thereby cleaving the glycosidic bond. Despite its functional importance, the detailed mechanism of such base extrusion ...
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Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process.Acta Biochimica et Biophysica Sinica (IF 3.511) Pub Date : 2022-05-25 ,DOI:10.3724/abbs.2022050Lingyan Wang,Kaiyuan Song,Jin Yu,Lin-Tai DaDNA glycosylase, as one member of DNA repair machineries, plays an essential role in correcting mismatched/damaged DNA nucleotides by cleaving the N-glycosidic bond between the sugar and target nucleobase through the base excision repair (BER) pathways. Efficient corrections of these DNA lesions are critical for maintaining genome integrity and preventing premature aging and cancers. The target-site ...
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Dynamics of peptide loading into major histocompatibility complex class I molecules chaperoned by TAPBPRPhysical Chemistry Chemical Physics (IF 3.945) Pub Date : 2022-05-11 ,DOI:10.1039/d2cp00423bHonglin Xu, Kaiyuan Song, Lin-Tai DaKey Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.Major histocompatibility complex class I (MHC-I) molecules display antigenic peptides on the cell surface for T cell receptor scanning, thereby activating the immune response. Peptide loading into MHC-I molecules is thus a critical step during the antigen presentation process. Chaperone TAP-binding protein related (TAPBPR) plays a critical role in promoting high-affinity peptide loading into MHC-I ...
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion.Journal of Visualized Experiments Pub Date : 2022-03-01 ,DOI:10.3791/63406Chao E,Liqiang Dai,Jiaqi Tian,Lin-Tai Da,Jin YuOne-dimensional (1-D) sliding of transcription factor (TF) protein along DNA is essential for facilitated diffusion of the TF to locate target DNA site for genetic regulation. Detecting base-pair (bp) resolution of the TF sliding or stepping on the DNA is still experimentally challenging. We have recently performed all-atom molecular dynamics (MD) simulations capturing spontaneous 1-bp stepping of ...
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Early aggregation mechanism of Aβ16−22 revealed by Markov state modelsInternational Journal of Biological Macromolecules (IF 8.025) Pub Date : 2022-02-05 ,DOI:10.1016/j.ijbiomac.2022.02.001Mueed Ur Rahman, Kaiyuan Song, Lin-Tai Da, Hai-Feng ChenAβ16–22 is believed to have critical role in early aggregation of full length amyloids that are associated with the Alzheimer's disease and can aggregate to form amyloid fibrils. However, the early aggregation mechanism is still unsolved. Here, multiple long-term molecular dynamics simulations combining with Markov state model were used to probe the early oligomerization mechanism of Aβ16−22 peptides ...
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RQC helical hairpin in Bloom's syndrome helicase regulates DNA unwinding by dynamically intercepting nascent nucleotidesiScience (IF 6.107) Pub Date : 2021-12-10 ,DOI:10.1016/j.isci.2021.103606Jianbing Ma, Chunhua Xu, Jinghua Li, Xi-Miao Hou, Lin-Tai Da, Qi Jia, Xingyuan Huang, Jin Yu, Xuguang Xi, Ying Lu, Ming Li
The RecQ family of helicases are important for maintenance of genomic integrity. Although functions of constructive subdomains of this family of helicases have been extensively studied, the helical hairpin (HH) in the RecQ-C-terminal domain (RQC) has been underappreciated and remains poorly understood. Here by using single-molecule fluorescence resonance energy transfer, we found that HH in the human
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Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2Biophysical Journal (IF 3.699) Pub Date : 2021-06-29 ,DOI:10.1016/j.bpj.2021.06.007Chunhong Long, Liqiang Dai, Chao E, Lin-Tai Da, Jin Yu
Cas1 and Cas2 are highly conserved proteins across clustered-regularly-interspaced-short-palindromic-repeat-Cas systems and play a significant role in protospacer acquisition. Based on crystal structure of twofold symmetric Cas1-Cas2 in complex with dual-forked protospacer DNA (psDNA), we conducted all-atom molecular dynamics simulations to study the psDNA binding, recognition, and response to cleavage
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Altered O-glycosylation Level of SARS-CoV-2 Spike Protein by Host O-glycosyltransferase Strengthens Its Trimeric StructurebioRxiv - Biochemistry Pub Date : 2021-04-06 ,DOI:10.1101/2021.04.06.438614Zhijue Xu, Xin Ku, Jiaqi Tian, Han Zhang, Jingli Hou, Can Zhang, Jingjing Shi, Yang Li, Hiroyuki Kaji, Sheng-ce Tao, Atsushi Kuno, Wei Yan, Lin-Tai Da, Yan Zhang
The trimeric spike protein (S) mediates host-cell entry and membrane fusion of SARS-CoV-2. S protein is highly glycosylated, whereas its O-glycosylation is still poorly understood. Herein, we site-specifically examine the O-glycosylation of S protein through a mass spectrometric approach with HCD-triggered-ETD model. We identify 15 high-confidence O-glycosites and at least 10 distinct O-glycan structures
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Mechanism of REST/NRSF regulation of clustered protocadherin α genesNucleic Acids Research (IF 19.16) Pub Date : 2021-03-26 ,DOI:10.1093/nar/gkab248Yuanxiao Tang, Zhilian Jia, Honglin Xu, Lin-tai Da, Qiang WuCenter for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF
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Mechanism of REST/NRSF Regulation of Clustered Protocadherin Alpha GenesbioRxiv - Molecular Biology Pub Date : 2021-03-07 ,DOI:10.1101/2021.03.06.434230Yuanxiao Tang, Zhilian Jia, Honglin Xu, Lin-Tai Da, Qiang Wu
Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF
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Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA in association with Cas2bioRxiv - Biophysics Pub Date : 2020-10-30 ,DOI:10.1101/2020.10.30.361584Chunhong Long, Liqiang Dai, Chao E, Lin-Tai Da, Jin Yu
Cas1 and Cas2 are highly conserved proteins across CRISPR-Cas systems and play a significant role in protospacer acquisition. Here we study the protospacer (or ps) DNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence or PAMc by Cas1-Cas2, implementing all-atom molecular dynamics simulations. First, we noticed that two active sites of Cas1&1′ bind
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DeepAntigen: A Novel Method for Neoantigen Prioritization via 3D Genome and Deep Sparse Learning.Bioinformatics (IF 6.931) Pub Date : 2020-09-11 ,DOI:10.1093/bioinformatics/btaa596Yi 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,Lintai Da,Guang He,Ze-Guang HanThe mutations of cancers can encode the seeds of their own destruction, in the form of T-cell recognizable immunogenic peptides, also known as neoantigens. It is computationally challenging, however, to accurately prioritize the potential neoantigen candidates according to their ability of activating the T-cell immunoresponse, especially when the somatic mutations are abundant. Although a few neoantigen ...
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A novel neoantigen discovery approach based on chromatin high order conformation.BMC Medical Genomics (IF 3.622) Pub Date : 2020-08-27 ,DOI:10.1186/s12920-020-0708-zYi Shi,Mingxuan Zhang,Luming Meng,Xianbin Su,Xueying Shang,Zehua Guo,Qingjiao Li,Mengna Lin,Xin Zou,Qing Luo,Yaoliang Yu,Yanting Wu,Lintai Da,Tom Weidong Cai,Guang He,Ze-Guang Han
High-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify potential neoantigens that stimulate the immune response of the T cell. However, when the somatic mutations are abundant, it is computationally challenging to efficiently prioritize the identified
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Designed peptides as potential fusion inhibitors against SARA-CoV-2 coronavirus infectionbioRxiv - Microbiology Pub Date : 2020-06-10 ,DOI:10.1101/2020.06.09.142315Ke Chen, Shihao Bai, Xin Zou, Jie Hao, Lin-tai Da, Ze-Guang Han
Inspired by fusion-inhibitory peptides from heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains from human immuno-deficiency virus type 1 (HIV-1) envelope glycoprotein gp41 and severe acute respiratory syndrome-coronavirus (SARS-CoV) based on viral fusogenic mechanism in the present work, we provided a similar approach to design the synthesized peptides against the entry into host cells of SARA-CoV-2
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A single dose SARS-CoV-2 simulating particle vaccine induces potent neutralizing activitiesbioRxiv - Bioengineering Pub Date : 2020-05-15 ,DOI:10.1101/2020.05.14.093054Di Yin, Sikai Ling, Xiaolong Tian, Yang Li, Zhijue Xu, Hewei Jiang, Xue Zhang, Xiaoyuan Wang, Yi Shi, Yan Zhang, Lintai Da, Sheng-ce Tao, Quanjun Wang, Jianjiang Xu, Tianlei Ying, Jiaxu Hong, Yujia Cai
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for which a vaccine is urgently needed to control its spreading. To facilitate the representation of a native-like immunogen without being infectious, here, we reported a SARS-CoV-2 vaccine candidate (designated ShaCoVacc) by incorporating spike-encoding mRNA inside and decorating spike protein
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Key structural motifs in Thymine DNA glycosylase responsible for recognizing certain DNA bent conformation revealed by atomic simulations.Biochemical and Biophysical Research Communications (IF 3.322) Pub Date : 2020-04-11 ,DOI:10.1016/j.bbrc.2020.03.173Shuang Li,Lin-Tai DaKey Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.Knowledge of how DNA bending facilitates the target-base searching by Thymine DNA glycosylase (TDG) is of major importance for unraveling the recognition mechanism between DNA and TDG in DNA repair process. An atomic-level understanding of the initial encounter between TDG and DNA before base-flipping, however, is still elusive. Here, we employ all-atom molecular dynamics (MD) simulations with an integrated ...
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Ikarugamycin inhibits pancreatic cancer cell glycolysis by targeting hexokinase 2The FASEB Journal (IF 5.834) Pub Date : 2020-01-16 ,DOI:10.1096/fj.201901237rShu‐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 XuMangrove‐derived actinobacteria strains are well‐known for producing novel secondary metabolites. The polycyclic tetramate macrolactam (PTM), ikarugamycin (IKA) isolated from Streptomyces xiamenensis 318, exhibits antiproliferative activities against pancreatic ductal adenocarcinoma (PDAC) in vitro. However, the protein target for bioactive IKA is unclear. In this study, whole transcriptome‐based profiling ...
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Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry.Journal of Chemical Information and Modeling (IF 6.162) Pub Date : 2019-12-31 ,DOI:10.1021/acs.jcim.9b00746Mengna Lin,Lin-Tai DaKey Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China.The HIV-1 infection is triggered by the binding of the viral envelope glycoprotein (Env) gp120-gp41 trimer to host-cell receptor CD4 and co-receptor CCR5/CXCR4, which leads to substantial conformational changes of Env, that is, structural transition of gp120 from a closed to an open state followed by gp41 refolding from pre-fusion to post-fusion states. The latter finally promotes membrane fusion, ...
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Rational engineering of amide synthetase enables bioconversion to diverse xiamenmycin derivatives.Chemical Communications (IF 6.065) Pub Date : 2019-11-18 ,DOI:10.1039/c9cc07826fJing-Yi Weng,Xu-Liang Bu,Bei-Bei He,Zhuo Cheng,Jun Xu,Lin-Tai Da,Min-Juan XuKey Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.XimA is a unique amide synthetase that belongs to the ANL superfamily of adenylating enzymes, but with a special structural fold. In order to improve the enzyme promiscuity, we engineered XimA by site-directed mutagenesis at a specific position based on our theoretical model of XimA. Thus, we were able to produce diverse benzopyran derivatives with up to 15 different L-form and D-form amino acid substitutions ...
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Opening dynamics of HIV-1 gp120 upon receptor binding is dictated by a key hydrophobic core.Physical Chemistry Chemical Physics (IF 3.945) Pub Date : 2019-11-11 ,DOI:10.1039/c9cp04613eLin-Tai Da,Mengna LinKey Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.HIV-1 entry is mediated firstly by the molecular recognition between the viral glycoprotein gp120 and its receptor CD4 on host T-cells. As a key antigen that can be targeted by neutralizing antibodies, gp120 has been a focus for extensive studies with efforts to understand its structural properties and conformational dynamics upon receptor binding. An atomistic-level revelation of gp120 opening dynamics ...
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Regulatory Role of One Critical Catalytic Loop of Polypeptide N-Acetyl-Galactosaminyltransferase-2 in Substrate Binding and Catalysis during Mucin-Type O-GlycosylationACS Catalysis (IF 13.7) Pub Date : 2019-10-23 ,DOI:10.1021/acscatal.9b03782Jiaqi Tian,Feng Liu,Zhijue Xu,Jingjing Shi,Tao Liang,Yan Zhang,Lin-Tai DaKey Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, ChinaOne of the dominant post-translational modifications in mammals is mucin-type (GalNAc-type) O-glycosylation initiated by polypeptide N-acetyl-galactosaminyltransferases (ppGalNAc-Ts), which is closely associated with many physiological and pathological conditions. An atomic-level understanding of the structural dynamics of one critical catalytic loop in ppGalNAc-Ts from an open to a closed state upon ...
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Characterization and Nonenzymatic Transformation of Three Types of Alkaloids from Streptomyces albogriseolus MGR072 and Discovery of Inhibitors of Indoleamine 2,3-Dioxygenase.Organic Letters (IF 6.072) Pub Date : 2019-10-15 ,DOI:10.1021/acs.orglett.9b03149Du Gao,Ting Zhou,Lin-Tai Da,Torsten Bruhn,Li-Li Guo,Yu-Hang Chen,Jun Xu,Min-Juan XuThe known benzonaphthyridine alkaloid, albogrisin A (1), and six new compounds, including two pyrazinone stereoisomers, albogrisin B (2)/B′ (2′), together with four 4H-pyrroloquinolinones, two diastereoisomers, albogrisin C (3)/C′ (3′), and their methyl esters, albogrisin D (4)/D′ (4′), were isolated from mangrove-derived Streptomyces albogriseolus MGR072. 2 and 2′ are converted into 1 in acidic aqueous ...
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Inhibition of polypeptide N-acetyl-α-galactosaminyltransferases is an underlying mechanism of dietary polyphenols preventing colorectal tumorigenesis.Bioorganic & Medicinal Chemistry (IF 3.461) Pub Date : 2019-06-11 ,DOI:10.1016/j.bmc.2019.06.020Feng Liu,Yalu Cui,Fang Yang,Zhijue Xu,Lin-Tai Da,Yan ZhangKey Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.Ellagitannin-derived ellagic acid (EA) and colonic metabolite urolithins are functional dietary ingredients for cancer prevention, but the underlying mechanism need elucidation. Mucin-type O-glycosylation, initiated by polypeptide N-acetyl-α-galactosaminyltransferases (ppGalNAc-Ts), fine-tunes multiple biological processes and is closely associated with cancer progression. Herein, we aim to explore ...
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pH-Induced Misfolding Mechanism of Prion Protein: Insights from Microsecond-Accelerated Molecular Dynamics Simulations.ACS Chemical Neuroscience (IF 5.78) Pub Date : 2019-05-22 ,DOI:10.1021/acschemneuro.8b00582Shuangyan Zhou,Danfeng Shi,Xuewei Liu,Xiaojun Yao,Lin-Tai Da,Huanxiang LiuThe conformational transition of prion protein (PrP) from a native form PrPC to a pathological isoform PrPSc is the main cause of a number of prion diseases in human and animals. Thus, understanding the molecular basis of conformational transition of PrP will be valuable for unveiling the etiology of PrP-related diseases. Here, to explore the potential misfolding mechanism of PrP under the acidic condition ...
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Understanding the molecular mechanism of umami recognition by T1R1-T1R3 using molecular dynamics simulations.Biochemical and Biophysical Research Communications (IF 3.322) Pub Date : 2019-05-12 ,DOI:10.1016/j.bbrc.2019.05.066Hai Liu,Lin-Tai Da,Yuan Liu
Taste receptor T1R1-T1R3 can be activated by binding to several natural ligands, e.g., l-glutamate and 5'-ribonucleotides etc., thereby stimulating the umami taste. The molecular mechanism of umami recognition at atomic details, however, remains elusive. Here, using homology modeling, molecular docking and molecular dynamics (MD) simulations, we investigate the effects of five natural umami ligands
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A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control.Computational and Structural Biotechnology Journal (IF 6.155) Pub Date : 2019-05-09 ,DOI:10.1016/j.csbj.2019.05.001Chunhong Long,Chao E,Lin-Tai Da,Jin Yu
RNA polymerase (RNAP) from bacteriophage T7 is a representative single-subunit viral RNAP that can transcribe with high promoter activities without assistances from transcription factors. We accordingly studied this small transcription machine computationally as a model system to understand underlying mechanisms of mechano-chemical coupling and fidelity control in the RNAP transcription elongation
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Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity controlNucleic Acids Research (IF 19.16) Pub Date : 2019-03-27 ,DOI:10.1093/nar/gkz213Chunhong Long,Chao E,Lin-Tai Da,Jin Yu
An elongation cycle of a transcribing RNA polymerase (RNAP) usually consists of multiple kinetics steps, so there exist multiple kinetic checkpoints where non-cognate nucleotides can be selected against. We conducted comprehensive free energy calculations on various nucleotide insertions for viral T7 RNAP employing all-atom molecular dynamics simulations. By comparing insertion free energy profiles
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Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair processNucleic Acids Research (IF 19.16) Pub Date : 2018-05-14 ,DOI:10.1093/nar/gky386Lin-Tai Da,Jin Yu
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby
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