检索结果-南通市图书馆

Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

在线全文

学校读者我要写书评

暂无评论

Chinese Chemical Letters 2021年第4期32卷 1515-1518页

作者： Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional materials.Although NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE property.In this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related polymers.In order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB conformation.This rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

关键词： Negative thermal expansion conformational change Polyarylamides Density-functional theory Dibenzocyclooctadiene

Single-molecule fluorescence studies on the conformational change of the ABC transporter MsbA

在线全文

学校读者我要写书评

暂无评论

Biophysics Reports 2018年第3期4卷 153-165页

作者： Yanqing Liu Yue Liu Lingli He Yongfang Zhao Xuejun C.Zhang National Laboratory of Biomacromolecules National CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences College of Life Science University of Chinese Academy of Sciences

ATP-binding cassette(ABC) transporters are found in all forms of life from microbes to humans, and transport a wide variety of substrates across the cell membrane using the energy released from ATP hydrolysis and an alternating-access mechanism. Msb A is a homodimeric ABC exporter from Gramnegative bacteria, and transports amphipathic substrates including precursors of lipopolysaccharides from the inner leaflet to the outer leaflet of the cytoplasmic membrane. Despite extensive structural and functional studies, controversies remain regarding the dynamic properties of the conformational changes of Msb A during its transport cycle in the lipid environment. Here, we used single-molecule fluorescence resonance energy transfer(sm FRET) to explore the dynamic behaviors of Msb A in detergent micelles, nanodiscs, and proteoliposomes. Msb A reconstituted into liposomes showed higher transition frequency between different states on the cytoplasmic side, whereas detergent-solubilized Msb A showed higher transition frequency on the periplasmic side. Three major states were identified from this sm FRET study in the functional cycle of Msb A, including an intermediate conformation between the fully opened and fully closed cytoplasmic conformations, associated with both ATP binding and hydrolysis.

关键词： ABC transporter conformational change Single-molecule fluorescence resonance energy transfer (smFRET)

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

同方期刊数据库

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 dinucleotides.It blocks the entrance of DNA into the catalytic pocket via the replication foci targeting sequence(RFTS)domain.Recent studies have shown that an H3-tail-conjugated two-mono-ubiquitin mark(H3Ub2)activates DNMT1 by binding to the RFTS domain.However,the activation mechanism of DNMT1 remains unclear.In 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 DNMT1.Geometric 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 DNMT1.These 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

Selecting small molecule DNA aptamers with significant conformational changes for constructing transcriptional switches and biosensors

在线全文

学校读者我要写书评

暂无评论

Science China Chemistry 2023年第5期66卷 1529-1536页

作者： Shaobin Guo Jingjing Lin Lujie Lin Wen Xu Yan Guo Zipeng Xu Chunhua Lu Xianai Shi Lanlan Chen Huanghao Yang College of Biological Science and Engineering Fuzhou UniversityFuzhou 350108China School of Pharmacy Fujian University of Traditional Chinese MedicineFuzhou 350122China Key Laboratory for Analytical Science of Food Safety and Biology of Ministry of Education Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food SafetyState Key Laboratory of Photocatalysis on Energy and EnvironmentCollege of ChemistryFuzhou UniversityFuzhou 350108China Fujian Key Laboratory of Medical Instrument and Pharmaceutical Technology Fuzhou UniversityFuzhou 350108China

Small molecule aptamers discovered by traditional selection methods usually lack conformational changes upon target binding.This limits the use of aptamers as molecular probes for small molecule detection and regulatory elements of genetic circuits.Here,we report a new method called capture and in vitro transcription-systematic evolution of ligands by exponential enrichment(CIVT-SELEX)to select DNA aptamers that can not only bind to small molecule ligands but also undergo significant conformational changes.Through this method,we select a structure-switching aptamer of uridine-5′-diphosphate(UDP).Taking advantage of its conformational changes,we first construct a UDP-responsive transcriptional switch by inserting the aptamer in a genetic circuit and demonstrate that it can respond to the addition of UDP and regulate the transcription of downstream genes.We also build a UDP aptamer-based biosensor that can be used for active glycosyltransferase screening.We believe this method can provide a universal platform for selecting small molecule aptamers with conformational changes and expand the use of aptamers in small molecule detection and genetic regulation.

关键词： aptamers conformational change CIVT-SELEX small molecule biosensors

Monitoring Molecular Dynamics with Single-Molecule Electronic Devices and Fluorescence Techniques

在线全文

学校读者我要写书评

暂无评论

Chinese Journal of Chemistry 2023年第21期41卷 2889-2907页

作者： Lan Yang Zhizhuo Zhang Cong Zhao Yani Huo Enyu Zhang Suhang He Chuancheng Jia Xuefeng Guo Center of Single-Molecule Sciences Institute of Modern OpticsTianjin Key Laboratory of Micro-scale Optical Information Science and TechnologyFrontiers Science Center for New Organic MatterCollege of Electronic Information and Optical EngineeringNankai University38 Tongyan RoadJinnan DistrictTianjin300350 China Beijing National Laboratory for Molecular Sciences National Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu RoadHaidian DistrictBeijing100871 China

Monitoring the dynamics of a single molecule provides unique insights into the fundamental physical and chemical properties of individual molecules.Over the past few decades,various approaches have been developed to enable the real-time and high-resolution detection at the single-molecule level.Among them,electrical and optical methods are the most promising tools,for the reason that electrical detection offers high resolution while optical technology provides non-invasive,targeted measurement with the added benefit of visualization.In this review,we summarized the current state-of-the-art electrical and optical techniques for single-molecule measurement and discussed their applications in detecting dynamic events such as conformational isomerizations,intermolecular interactions,chemical reactions,and biomolecular activities.In addition,we discussed the challenges and opportunities in this area and proposed possible directions for future development.

关键词： Single-molecule dynamics Single-molecule junction Fluorescence conformational change Reaction mechanisms Enzymes Host-guestsystems Molecularelectronics

Different conformational responses of the β2-adrenergic receptor-Gs complex upon binding of the partial agonist salbutamol or the full agonist isoprenaline

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

National Science Review 2021年第9期8卷 111-120页

作者： Fan Yang Shenglong Ling Yingxin Zhou Yanan Zhang Pei Lv Sanling Liu Wei Fang Wenjing Sun Liaoyuan A.Hu Longhua Zhang Pan Shi Changlin Tian Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Amgen Asia R&D Center Amgen Research Shanghai 201210 China3High Magnetic Field Laboratory Chinese Academy of Sciences

G protein-coupled receptors(GPCRs) are responsible for most cytoplasmic signaling in response to extracellular ligands with different efficacy profiles. Various spectroscopic techniques have identified that agonists exhibiting varying efficacies can selectively stabilize a specific conformation of the receptor.However, the structural basis for activation of the GPCR-G protein complex by ligands with different efficacies is incompletely understood. To better understand the structural basis underlying the mechanisms by which ligands with varying efficacies differentially regulate the conformations of receptors and G proteins, we determined the structures of β2AR-Gαsβγ bound with partial agonist salbutamol or bound with full agonist isoprenaline using single-particle cryo-electron microscopy at resolutions of 3.26 ?A and3.80 ?A, respectively. Structural comparisons between the β2AR-Gs-salbutamol and β2AR-Gs-isoprenaline complexes demonstrated that the decreased binding affinity and efficacy of salbutamol compared with those of isoprenaline might be attributed to weakened hydrogen bonding interactions, attenuated hydrophobic interactions in the orthosteric binding pocket and different conformational changes in the rotamer toggle switch in TM6. Moreover, the observed stronger interactions between the intracellular loop 2 or 3(ICL2 or ICL3) of β2AR and Gαswith binding of salbutamol versus isoprenaline might decrease phosphorylation in the salbutamol-activated β2AR-Gs complex. From the observed structural differences between these complexes of β2AR, a mechanism of β2AR activation by partial and full agonists is proposed to provide structural insights into β2AR desensitization.

关键词： cryo-EM structure G protein-coupled receptor (GPCR) partial and full agonists conformational change desensitization

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

在线全文

同方期刊数据库

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 mode.Co-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 simulations.Small-angle X-ray scattering experiments demonstrate a direct link between ligand binding and E-selectin conformational transition under static conditions in solution.This 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 recruitment.The detailed molecular view of the binding site paves the way for the design of a new generation of selectin antagonists.This 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

Structural understanding of T cell receptor triggering

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

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 mysterious.As 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 events.Whether conformational change plays an important role in the transmembrane signal transduction of TCR is under debate.Attracted by the complexity and functional importance of TCR,many groups have been studying TCR structure and triggering for decades using diverse biochemical and biophysical tools.Here,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

Dynamic mechanism for encapsulating two HIV replication inhibitor peptides with carbon nanotubes

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

Chinese Physics B 2012年第8期21卷 152-155页

作者：陈保栋杨传路王美山马晓光 School of Physics and Optoelectric Engineering Ludong University

Encapsulation of biomolecules inside a carbon nanotube （CNT） has attracted great interest because it could enable the delivery of nanoscale pharmaceutical drugs with CNT-based devices. Using a molecular dynamics simulation, we investigate the dynamic process by which human immunodeficiency virus （HIV） replication inhibitor peptides （HRIPs） are encapsulated in a water solution contained inside a CNT. The van der Waals attraction between the HRIPs and the CNT and the root-mean-square deviation are used to analyse the evolution of the encapsulation. It is found that the interaction between the HRIPs and the CNT is the main driving force for the encapsulation process, which does not cause an obvious conformational change to the HRIPs.

关键词： molecular dynamics simulation drug delivery peptide-CNT interaction spontaneous encapsulation conformational change