检索结果-南通市图书馆

Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination,revealed by multi-scale molecular dynamics simulations

在线全文

学校读者我要写书评

暂无评论

Science China(Life Sciences) 2023年第2期66卷 313-323页

作者： Jixue Sun Fei Liu Longxiao Yuan Ning-Ning Pang Bing Zhu Na Yang State Key Laboratory of Medicinal Chemical Biology College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of TianjinNankai UniversityTianjin 300353China National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China

DNMT1 is a DNA methyltransferase that catalyzes and maintains methylation in CpG *** blocks the entrance of DNA into the catalytic pocket via the replication foci targeting sequence(RFTS)*** studies have shown that an H3-tail-conjugated two-mono-ubiquitin mark(H3Ub2)activates DNMT1 by binding to the RFTS ***,the activation mechanism of DNMT1 remains *** this work,we combine various sampling methods of extensive simulations,including conventional molecular dynamics,Gaussian-accelerated molecular dynamics,and coarse-grained molecular dynamics,to elucidate the activation mechanism of *** and energy analyses show that binding of H3Ub2 to the RFTS domain of DNMT1 results in the bending of theα4-helix in the RFTS domain at approximately 30°–35°,and the RFTS domain rotates~20°anti-clockwise and moves~3?away from the target recognition domain(TRD).The hydrogen-bonding network at the RFTSTRD interface is significantly disrupted,implying that the RFTS domain is dissociated from the catalytic core,which contributes to activating the auto-inhibited conformation of *** results provide structural and dynamic evidence for the role of H3Ub2 in regulating the catalytic activity of DNMT1.

关键词： DNA methyltransferase conformational change molecular dynamics simulation activation molecular mechanism

E-selectin ligand complexes adopt an extended high-affinity conformation

在线全文

学校读者我要写书评

暂无评论

分子细胞生物学报:英文版 2016年第1期8卷 62-72页

作者： Roland C.Preston Roman P.Jakob Florian P.C.Binder Christoph P.Sager Beat Ernst Timm Maier Institute of Molecular Pharmacy Universitat Basel4056 BaselSwitzerland Biozentrum Universitat Basel4056 BaselSwitzerland

E-selectin is a cell-adhesion molecule of the vascular endothelium that promotes essential leukocyte rolling in the early inflammatory response by binding to glycoproteins containing the tetrasaccharide sialyl Lewisx(sLex).Efficient leukocyte recruitment under vascular flow conditions depends on an increased lifetime of E-selectin/ligand complexes under tensile force in a so-called catch-bond binding ***-crystal structures of a representative fragment of the extracellular E-selectin region with sLex and a glycomimetic antagonist thereof reveal an extended E-selectin conformation,which is identified as a high-affinity binding state of E-selectin by molecular dynamics ***-angle X-ray scattering experiments demonstrate a direct link between ligand binding and E-selectin conformational transition under static conditions in *** permits tracing a series of concerted structural changes connecting ligand binding to conformational stretching as the structural basis of E-selectin catch-bond-mediated leukocyte *** detailed molecular view of the binding site paves the way for the design of a new generation of selectin *** is of special interest,since their therapeutic potentialwas recently demonstrated with the pan-selectin antagonists GMI-1070(Rivipansel).

关键词： inﬂammation leukocyte adhesion E-selectin glycomimetic antagonist sialyl Lewisx conformational change

Molecular recognition: monomer of the yeast transcriptional activator GCN4 recognizes its dimer DNA binding target sites specifically

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Science China Chemistry 2000年第5期43卷 466-476页

作者：曹炜刘亮来鲁华唐有祺 Institute of Physical Chemistry College of Chemistry and Molecular Engineering Peking University Beijing 100871China

It is widely believed that dimerization is a requirement for the yeast transcriptional activator GCN4 to recognize its specific DNA target sites. We used the basic region (226-252) of the yeast transcriptional activator GCN4, as both a monomeric peptide and a disulfide-linked dimer to investigate the interaction of the peptides with the DNA target sites AP-1 and CRE. CD and ITC experiments indicate that although the monomeric peptide GCN4-M has a weaker affinity with the DNA relative to the disulfide-linked dimer peptide GCN4-D, it recognizes AP-1 and CRE target sites specifically.

关键词： molecular recognition conformational change thermodynamic parameter ITC CD

Structural understanding of T cell receptor triggering

在线全文

学校读者我要写书评

暂无评论

Cellular & Molecular Immunology 2020年第3期17卷 193-202页

作者： Xinyi Xu Hua Li Chenqi Xu State Key Laboratory of Molecular Biology Shanghai Science Research CenterCAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesUniversity of Chinese Academy of Sciences320 Yueyang Road200031 ShanghaiChina School of Life Science and Technology ShanghaiTech University100 Haike Road201210 ShanghaiChina

The T cell receptor(TCR)is one of the most complicated receptors in mammalian cells,and its triggering mechanism remains *** an octamer complex,TCR comprises an antigen-binding subunit(TCRαβ)and three CD3 signaling subunits(CD3ζζ,CD3δε,and CD3γε).Engagement of TCRαβwith an antigen peptide presented on the MHC leads to tyrosine phosphorylation of the immunoreceptor tyrosine-based activation motif(ITAM)in CD3 cytoplasmic domains(CDs),thus translating extracellular binding kinetics to intracellular signaling *** conformational change plays an important role in the transmembrane signal transduction of TCR is under *** by the complexity and functional importance of TCR,many groups have been studying TCR structure and triggering for decades using diverse biochemical and biophysical ***,we synthesize these structural studies and discuss the relevance of the conformational change model in TCR triggering.

关键词： T Cell Receptor Structure conformational change Triggering

Effect of Calcium Cation on Thermophilic Acylamino Acid-releasing Enzyme Ape1547 from Aeropyrum pernix K1

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Chemical Research in Chinese Universities 2009年第4期25卷 513-517页

作者： ZHOU Jun XIE Gui-qiu CAO Shu-gui GAO Ren-jun Key Laboratory for Molecular Enzymology and Engineering Ministry of Education School of Pharmaceutical Sciences Jilin University Changchun 130021 P. R. China

The gene of enzyme（Ape1547） was cloned from hyperthermophilic archaeon Aeropyrum pernix K1 and expressed in Escherichia *** effect of calcium cation on the properties of Ape1547 was ***1547 exhibits both peptidase activity and esterase *** fluorescence spectrum shows that calcium cation quenches the fluorescence of the enzyme through static quenching mechanism,indicating that calcium cation was bound to the *** on the study of calcium cation on CD ellipticity of Ape1547 by circular dichroism,we concluded that the change of enzyme structure induced by calcium cation may be responsible for the change of enzyme *** cation has dual effects on Ape1547：it could activate the enzyme activity when its concentration was 0.1 mol/L,and the enzyme had the highest activity;however,when its concentration was higher than 0.2 mol/L,the enzyme activity was *** results indicate that the activity center of peptidase activity might involve more amino acid residues than that of esterase activity.

关键词： Acylamino acid-releasing enzyme Aeropyrum pernix K1 conformational change Calcium cation

Molecular Dynamics Simulations and Steered Molecular Dynamics Simulations of Glabridin Bound to Wild Type and V30A Mutant Transthyretin： Ligand-linked Perturbation of Tertiary Conformation

在线全文

学校读者我要写书评

暂无评论

Chemical Research in Chinese Universities 2018年第6期34卷 995-1003页

作者： YU Zhengfei HAN Jiarui LIU Ye ZHU Jingxuan TIAN Xiaopian HAN Weiwei Key Laboratory for Molecular Enzymology and Engineering Ministry of Education School of Life Sciences Jilin University Changchun 130012 P. R. China

Transthyretin（TTR）, as a tetrameric protein, functions as a neuroprotector. The native TTR homotetramer dissociates into dimers and monomers. Dimers and monomers self-assemble into amyloid fibrils, and this process can lead to some diseases. Native TTR homotetramer is a widely accepted model for TTR amyloid formation. In this study, simulations using molecular dynamics（MD） and steered MD（SMD） were performed to explore the mechanisms for glabridin（Glab）, a specific inhibitor for TTR binding, for V30A mutant and wild-type（WT） TTR. MD simulation results indicate that, compared with Glab binding to WT and V30A mutant, the WT TTR could lead to the collapse of β-strands from Ser52 to His56 at chain A. This phenomenon facilitated the easy dissociation of chains A and C. Calculations of the binding free energy between the two chains showed that the V30A-Glab TTR complex displayed a lower binding energy than other systems（WT TTR and WT-Glab TTR）. Then, SMD simulation was performed to ex- plore the unbinding pathway for Glab through the WT and V30A mutant TTR. The results show that Lysl 5（chain A） produced a hydrogen bond with Glab at the force peak via the WT TTR tunnel. Meanwhile, in the V30A TTR mutant, the hydrogen bond between Lysl 5（chain A） and Glab was broken at the force peak. This condition was beneficial for Glab to be taken off from the protein. Our theoretical results will be useful in designing a new specific inhibitor of TTR protein to control the TTR homotetramer dissociation.

关键词： Transthyretin Glabridin conformational change Molecular mechanics-poisson Boltzmann surface area(MM-PBSA)

Urea-induced Inactivation and Unfolding of Recombinant Phospholipid Hydroperoxide Glutathione Peroxidase from Oryza sativa

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Chemical Research in Chinese Universities 2007年第5期23卷 562-566页

作者： WANG Feng ZHOU Hui-ping KONG Bao-hua FAN Jing-hua CHEN Hai-ru LIU Jin-yuan Key Laboratory of Molecular Biology and Protein Science of Ministry of Education Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 P. R. China Key Laboratory for Plant Pathology of Yunnan Province Yunnan Agricultural University Kunming 650201 P. R. China

Phospholipid hydroperoxide glutathione peroxidase is an antioxidant enzyme that has the highest capability of reducing membrane-bound hydroperoxy lipids as compared to free organic and inorganic hydroperoxides amongst the glutathione *** this study,urea-induced effects on the inactivation and unfolding of a recombinant phospholipid hydroperoxide glutathione peroxidase（PHGPx）from Oryza sativa were investigated by means of circular dichroism and fluorescence *** the increase of urea concentration,the residual activity of OsPHGPx decreases *** the urea concentration is above 5.0 mol/L,there was no residual *** addition,the observed changes in intrinsic tryptophan fluorescence,the binding of the hydrophobic fluorescence probe ANS,and the far UV CD describe a common dependence on the concentration of urea suggesting that the conformational features of the native OsPHGPx are lost in a highly cooperative single *** unfolding process comprises of three zones：the native base-line zone between 0 and 2.5 mol/L urea,the transition zone between 2.5 and 5.5 mol/L urea,and the denatured base-line zone above 5.5 mol/L *** transition zone has a midpoint at about 4.0 mol/L urea.

关键词： Circular dichroism Fluorescence conformational change Phospholipid hydroperoxide glutathione peroxidase(PHGPx) Urea titration

Conformation Disturbance of CopC by α-Naphthylamine

在线全文

学校读者我要写书评

暂无评论

Chemical Research in Chinese Universities 2009年第3期25卷 269-272页

作者： LI Hui-qing ZHENG Xiao-yan ZHAO Ya-qin YANG Bin-sheng Institute of Molecular Science Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education Shanxi University Taiyuan 030006 P. R. China

It is known that urea and guanidine hydrochloride（GuHC1） induce conformational change of proteins in a certain range of molar ratios. In our research, a-naphthylamine（NA） above 10^-4 mol/L at pH 7.0 was discovered to perturb the conformation of CopC, a copper resistant protein with a Greek fl-barrel motif; this was reflected by the greater fluorescence quenching and red-shifted emission peak of CopC. The conformation change of CopC was also verified in acrylamide collision experiment by comparing quenching levels of CopC in the presence or the abscence of NA. Comparison of emission change of CopC-Cu^2＋ with that of apo-CopC showed a consistent result with their denaturation in GuHCl. And decreasing fluorescence polarization of CopC with increasing NA concentration is consistent with a more extend conformation of CopC. Interaction mechanism was also explored.

关键词： α-Naphthylamine(NA) CopC conformational change

Effect of solution conditions on depression of chlorite using CMC as depressant

在线全文

学校读者我要写书评

暂无评论

Journal of Central South University 2013年第4期20卷 1034-1038页

作者：冯博冯其明卢毅屏李浩 School of Mineral Processing and Bioengineering Central South University

The effect of solution conditions on the depression of chlorite using CMC (carboxymethyl cellulose) as depressant was studied through flotation tests and adsorption measurements. Flotation and adsorption tests were first studied as a function of initial solution conditions. The results show that electrostatic repulsion between CMC molecules and chlorite surface hinders the approach of the CMC molecules to the chlorite surface and CMC adsorbs to a great extent at high ionic concentration (10-4 mol/L ions as opposed to 0 mol/L ions) or low pH (3 as opposed to 9). The enhanced adsorption density is attributed to the decreased electrostatic repulsion between CMC and mineral surface. The solution condition that yielded the lowest initial adsorbed amount (0 mol/L ions, pH 9) was used as a reference to investigate the response of the adsorbed CMC layer to a switch in solution conditions after adsorption. The two kinds of solution switches (reducing the solution pH or increasing ionic concentration) result in an increased depression effect of CMC on chlorite flotation, as a result of conformational change of CMC pre-adsorbed layer. The change in the flotation recovery of the CMC-coated chlorite following the solution switches is reversible.

关键词： chlorite carboxymethyl cellulose ion pH conformational change