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RNA Conformational Dynamics,Heterogeneity,and molecular recognition

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RNA Conformational Dynamics,Heterogeneity,and Molecular Reco...

molecular Simulations using Spherical Harmonics

第一届全国生物物理化学会议暨生物物理化学发展战略研讨会

作者： Liang Zhao,Niyati Jain,Sang Won Lee,and Tianbing Xia~* Department of molecular and Cell Biology,The University of Texas at Dallas,Richardson,Texas 75025

＜正＞RNA plays a central functional role in a number of important cellular processes,largely due to its ability to fold into intricate three-dimensional structures that rival those of proteins.But this is only part of the story.RNA molecules undergo conformational dynamics over wide ranges of time- and length scales,thus display various levels of structural heterogeneity.It has become

关键词： riboswtiches RNA aptamers ribozymes RNA conformational dynamics and heterogeneity energy landscape molecular recognition ultrafast charge transfer

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Chinese Journal of Chemistry 2003年第10期21卷 1252-1255页

作者：蔡文生徐佳维邵学广 MAIGRET Bernard Department of Chemistry UMR 7565 CNRS/UHP

Computer aided drug design is to develop a chemical that binds to a target macromolecule known to play a key role in a disease state. In recognition of ligands by their protein receptors, molecular surfaces are often used because they represent the interacting part of molecules and they should reflex the complementarity between ligand and receptor. However, assessing the surface complementarity by searching all relative position of two surfaces is often computationally expensive. The complementarity of lobe hole is very important in protein ligand interactions. Spherical harmonic models based on expansions of spherical harmonic functions were used as a fingerprint to approximate the binding cavity and the ligand, respectively. This defines a new way to identify the complementarity between lobes and holes. The advantage of this method is that two spherical harmonic surfaces to be compared can be defined separately. This method can be used as a filter to eliminate candidates among a large number of conformations, and it will speed up the docking procedure. Therefore, it is possible to select complementary ligands or complementary conformations of a ligand and the macromolecules, by comparing their fingerprints previously stored in a database.

关键词： molecular surface shape complementarity molecular docking molecular recognition spherical harmonics

Cell membrane-based nanoparticles: a new biomimetic platform for tumor diagnosis and treatment

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Acta Pharmaceutica Sinica B 2018年第1期8卷 14-22页

作者： Ruixiang Li Yuwei He Shuya Zhang Jing Qin Jianxin Wang Department of Pharmaceutics School of Pharmacy Fudan University Key Laboratory of Smart Drug Delivery Ministry of Education Institute of Materia Medica Academy of Chinese and Western Integrative Medicine Fudan University

Taking inspiration from nature, the biomimetic concept has been integrated into drug delivery systems in cancer therapy. Disguised with cell membranes, the nanoparticles can acquire various functions of natural cells. The cell membrane-coating technology has pushed the limits of common nano-systems(fast elimination in circulation) to more effectively navigate within the body. Moreover, because of the various functional molecules on the surface, cell membrane-based nanoparticles(CMBNPs) are capable of interacting with the complex biological microenvironment of the tumor. Various sources of cell membranes have been explored to camouflage CMBNPs and different tumor-targeting strategies have been developed to enhance the anti-tumor drug delivery therapy. In this review article we highlight the most recent advances in CMBNP-based cancer targeting systems and address the challenges and opportunities in this field.

关键词： Cell membrane Biomimetic nanoparticle Drug delivery Cancer targeting Circulation molecular recognition

GAS SORPTION,DIFFUSION AND PERMEATION OF ORDERED POLYMERIC MEMBRANES

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Chinese Journal of Polymer Science 2000年第4期18卷 301-307页

作者： Yoshiharu Tsujita Polymeric Materials Course Department of Materials Science and Engineering. Nagoya Institute of Technology Gokiso-cho Showa-ku Nagoya 466-8555 Japan

He, CO_2, O_2, N_2, CH_4, C_3H_8, and t-C_4H_(10) gas permeability coefficients and diffusion coefficients of poly(4-methylpentene-1) (PMP) with various degrees of crystallization were plotted against the degree of crystallization. The plotdemonstrated a linear relationship. The gas permeability coefficient and diffusion coefficient of pure amorphous and purecrystalline PMPs were evaluated by a linear extrapolation to zero and 100% crystallinity, respectively. The relationshipbetween the diffusion coefficient of crystalline parts of PMP and the kinetic diameter of penetrant gases was discussed.Syndiotactic polystyrene (SPS) could exist as δ form crystals complexed with organic solvents such as benzene, toluene,xylene, and ethylbenzene. The mesophase of SPS is prepared by annealing the δ form of crystalline complexes at a certaintemperature for 1 h. The desorption of solvent during annealing almost does not result in changes of both the conformation ofbackbone chains and the crystal lattice. We could prepare the mesophase containing molecular cavities with the size andshape of the organic solvent molecules. The mesophase could sorb the same solvent after the manner of Langmuir sorption atlow vapor pressure range while this would not be the case for solvents of different size and shape. This suggests a molecularrecognition of organic solvent, and mesophase SPS might be useful for separation membrane and adsorptive material.

关键词： Gas sorption Diffusion Poly(4-methyl pentene-l) molecular recognition

Studies on the Intramolecular Inclusion Complexes of Functionalized Calixarenes with CH_3X (X=CN, NO_2)

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Chinese Journal of Chemistry 2002年第11期20卷 1205-1211,1126页

作者：周稚仙石雅琳杜晨霞邢彦军吴养洁 Department of Chemistry Zhengzhou University Zhengzhou Heman 450052 China

Two functionalized calixarenes in cone conformation L 2-3 have been synthesized and their intramolecular inclusion complexes (1∶1) with organic neutral molecules CH 3CN and CH 3NO 2 have been prepared and characterized, respectively. The X-ray crystallographic analysis shows that L 2 in L 2·CH 3CN·C 2H 5OH has C 4 symmestry and L 3 in L 3·CH 3NO 2 exhibits C 2 symmestry. The CH-π aromatic interactions between the CH group of the guest and the phenyl rings of the calix backbond have been proved to be able to stabilize the intramolecular inclusion complexes formed. The interaction is directional, but it is independent of the acidity of the guest. To gain information on CH-π interactions, suitable geometrical parameters have been calculated from the crystal data of intramolecular inclusion complexes. The results show that L 3·CH 3NO 2 with L 3 in C 2 symmestry can also be bound stably in the intramolecular inclusion complex, being consistent with the thermal analysis. The geometrical parameters and the results of the thermal analysis of L 1·CH 3CN and L 1·CH 3NO 2 were also given and discussed.

关键词： calixarene intramolecular inclusion complex CH-π interaction molecular recognition host-guest chemistry

Imprinted membranes for sustainable separation processes

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Frontiers of Chemical Science and Engineering 2021年第4期15卷 775-792页

作者： Laura Donato Enrico Drioli Research Institute on Membrane Technology CNR-ITMUniversity of Calabria87030 Rende(CS)Italy Department of Engineering and of the Environment University of Calabria87030 Rende(CS)Italy College of Chemical Engineering Nanjing Tech UniversityNanjing 211816China Centre of Excellence in Desalination Technology King Abdulaziz UniversityJeddah 21589Saudi Arabia

The rapid industrial growth and the necessity of recovering and recycling raw materials increased the interest in the production of highly selective and efficient separation tools.In this perspective,a relevant input was given by the membrane-based technology and the production of imprinted membranes,which possess specific recognition properties at molecular and ionic level,offers the possibility of developing sustainable and green processes.Furthermore,the integration of imprinted membranes with traditional or membrane-based approaches is a promising strategy in the logic of process intensification,which means the combination of different operations in a single apparatus.This work discusses the concept and separation mechanisms of imprinted membranes.Furthermore,it presents an overview of their application in organic solvent nanofiltration,for the removal of toxic agents and recovery solvent,as well as valuable compounds.The recent advances in water treatment,such as pesticide removal and recovery of metal ions,are also discussed.Finally,potential applications of imprinted membranes in hybrid processes are highlighted,and a look into the future of membrane separations for water treatment and recovery of critical raw materials is offered.

关键词： sustainable processes membrane separation molecular recognition imprinted membranes water treatment

Selective recognition of Quaternary Ammonium Ions by Structurally Flexible Cages

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Chinese Journal of Chemistry 2021年第6期39卷 1593-1598页

作者： Qi-Cheng Huang Mao Quan Huan Yao Liu-Pan Yang Wei Jiang Shenzhen Grubbs Institute Department of ChemistryGuangdong Provincial Key Laboratory of CatalysisAcademy of Advanced Interdisciplinary StudiesSouthern University of Science and TechnologyXueyuon Blvd 1088ShenzhenGuangdong 518055China

The binding behaviors of three structurally similar and flexible cages to a series of quaternary ammonium ions have been systematically studied.The cage with phenyl sidewalls is new;moreover,its structure and conformational states have been characterized by NMR;2D NMR,and X-ray crystallography.The results reveal that the three cages show quite high binding affinities and selectivities to different guests.Enthalpy-entropy compensation was invoked to explain the different binding performance.Moreover,a six-component,high-fidelity self-sorting system was successfully constructed by using these cages and three guests.This suggests that conformationally flexible hosts may also achieve high binding affinities and selectivities,which is in contrast to the traditional point of view-only preorganized and rigid hosts are able to do so.This research advocates that conformational flexibility should also be seriously considered in host design.

关键词： Macrocycles molecular recognition Host-guest systems Supramolecular chemistry Thermodynamics

Thermo-responsive imprinted hydrogel with switchable sialic acid recognition for selective cancer cell isolation from blood

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Bioactive Materials 2021年第5期6卷 1308-1317页

作者： Yue Ma Yimei Yin Li Ni Haohan Miao Yingjia Wang Cheng Pan Xiaohua Tian Jianming Pan Tianyan You Bin Li Guoqing Pan Institute for Advanced Materials School of Materials Science and EngineeringJiangsu UniversityZhenjiangJiangsu 212013PR China School of Chemistry and Chemical Engineering Jiangsu UniversityZhenjiangJiangsu 212013PR China Jiangsu Agrochem Laboratory ChangzhouJiangsu 213022PR China Key Laboratory of Modern Agricultural Equipment and Technology Ministry of EducationSchool of Agricultural Equipment EngineeringJiangsu UniversityZhenjiangJiangsu 212013PR China Department of Orthopaedic Surgery The First Affiliated HospitalOrthopaedic InstituteMedical CollegeSoochow UniversitySuzhouJiangsu 215006PR China

In this work,a sialic acid(SA)-imprinted thermo-responsive hydrogel layer was prepared for selective capture and release of cancer cells.The SA-imprinting process was performed at 37℃ using thermo-responsive functional monomer,thus generating switchable SA-recognition sites with potent SA binding at 37℃and weak binding at a lower temperature(e.g.,25℃).Since SA is often overexpressed at the glycan terminals of cell membrane proteins or lipids,the SA-imprinted hydrogel layer could be used for selective cancer cell recognition.Our results confirmed that the hydrogel layer could efficiently capture cancer cells from not only the culture medium but also the real blood samples.In addition,the captured cells could be non-invasively released by lowing the temperature.Considering the non-invasive processing mode,considerable capture efficiency,good cell selectivity,as well as the more stable and durable SA-imprinted sites compared to natural antibodies or receptors,this thermo-responsive hydrogel layer could be used as a promising and general platform for cell-based cancer diagnosis.

关键词： molecular imprinting Cell capture and release Thermo-responsive hydrogels molecular recognition Sialic acid

Hydrogen Bonded Semi-Rigidified Bispyridyl-Incorporating Aryl Amide Oligomers： Efficient ＂C＂-Styled Receptors for Aliphatic Ammoniums, a Remarkable Protonation Effect and Chiral Induction

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Chinese Journal of Chemistry 2007年第10期25卷 1417-1422页

作者：李昌治黎占亭高翔王全瑞 Department of Chemistry Fudan University Shanghai 200433 China Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China

The complexing behaviour of two linear compounds 1 and 2 toward the trifluoroacetic acid （TFA） salts of n-dodecylamine, di-n-octylamine, n-dodecyl D- and L-phenylalaninates （3, 4, and D- and L-5） in chloroform has been described. Compounds 1 and 2 consist of two folded amide moieties with two pyridyls at the terminals which are connected directly or with an acetylene linker. The rigidified folded moieties are stabilized by intramolecular hydrogen bonding, while the whole molecules can adopt an ＂S＂- or a ＂C＂-styled conformation depending on the relative orientation of the two rigidified moieties. ^1H NMR, UV-Vis, fluorescent and circular dichroism investigations revealed that 1 and 2 could bind primary and secondary ammonium cations with their ＂C＂-styled conformation. In the presence of 1 equiv, of TFA, the binding stability was increased significantly as a result of promoted formation of the ＂C＂-styled conformation due to the monoprotonation of the peripheral pyridyl units in 1 and 2. In contrast, the addition of 2 equiv, of TFA substantially weakened the binding stability because the ＂S＂-styled conformation was favored as a result of protonation of both of their pyridyl units. Moreover, remarkable induced circular dichroisms were also displayed for the complexes of 1 and 2 with chiral D- and L-5.

关键词： molecular recognition hydrogen bonding foldamer circular dichroism aliphatic ammonium