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Modeling the intracellular dynamics for Vif-APO mediated HIV-1 virus infection

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Chinese Science Bulletin 2010年第22期55卷 2329-2340页

作者： WANG Yi1,2.& LAI LuHua1,3 1 Center for Theoretical Biology, peking university, beijing 100871, China 2.School of Physics, peking university, beijing 100871, China 3 bnlms, state key laboratory for structural chemistry of unstable and stable species, college of chemistry and molecular engineering, peking university, beijing 100871, China Center for Theoretical Biology Peking University Beijing 100871 China School of Physics Peking University Beijing 100871 China bnlms State Key Laboratory for Structural Chemistry of Unstable and Stable Species College of Chemistry and Molecular Engineering Peking University Beijing 100871 China

The viral infectivity factor (Vif) was found to be essential for controlling HIV-1 virus infectivity. It targets cellular antiviral proteins in APOBEC family (APO) to trigger its fast degradation and inhibits APO packaging into nascent virion. In the present study, we propose a mathematical model to quantitatively study the intracellular dynamics of these typical virus-host interactions. Four sets of published experimental data were compared with simulation results to justify the model. Systematic parameter sensitivity and perturbation analysis showed that parameters related to APO are crucial to the infectivity of newly synthesized HIV-1 virus. Interestingly, we discovered that the synthesis rate of the viral structure protein Gag and the required number per nascent virion are optimized to achieve high virion production with minimal level of packaged APO, and large portion of model parameters are beneficial to virus only within a relatively small range. Furthermore, minor variations in several parameters related to viral protein Tat, the activator of viral RNA synthesis, were found to induce switch-like behaviors on both incorporated Vif and APO. These findings may provide new insights for understanding the high mutation rate of HIV-1 virus and its latency, as well as help identify key targets for therapeutic design.

关键词：病毒感染载脂蛋白 HIV 细胞内动力学抗病毒蛋白建模介导

Electron structure and substituent effects in o-,m-,p-IC_6H_4OCH_3 iodoanisoles

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Science China chemistry 2009年第11期52卷 1932-1937页

作者： TONG ShengRui,WANG WeiGang,MA ChunPing,GE MaoFa & WANG DianXun beijing National laboratory for {2. Sciences(bnlms),state key laboratory for structural chemistry of unstable and stable species,Institute of chemistry,Chinese Academy of Sciences,beijing 100190,China 1. beijing National laboratory for {2. Sciences (bnlms) State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China

The electronic structures and substituent effects in o-,m-,and p-iodoanisoles have been investigated by ultraviolet photoelectron spectroscopy(UPS).The observed UPS bands were analyzed by combining empirical arguments and theoretical *** to the electron-donating nature of both iodoand methoxy substituents,the first ionization potentials of the three iodoanisoles are lower than those of iodobenzene and *** presence of the two substituents in iodoanisoles leads to an electronrich structure,which might contribute to the observed high reactivity of iodoanisoles in a number of organic reactions.

关键词： electronic structures substituent effects ultraviolet photoelectron spectroscopy reactivity

Small Peptide Interacting with Pollen Calmodulinand their Effects on Cellular Functions

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Chinese Chemical Letters 1999年第11期10卷 929-932页

作者： Jing SU Yan Ling SONG Min HU(college of chemistry and {2. engineering, peking university, beijing 100871)(state key laboratory of Environmental Simulation and Pollution Control,peking university. beijing 100871) peking Univ Coll Chem & Mol Engn Beijing 100871 Peoples R China peking Univ State Key Lab Environm Simulat & Pollut Control Beijing 100871 Peoples R China

The interaction between dansyl-labeled pollen calmodulin (D-pCaM) and synthesized peptides was studied in the presence of Ca2. by fluorescence spectra. It is Found that Gly/L-Ala --> D-Ala substitution in peptide chains caused great changes in their affinity for pCaM. Besides. our data provided evidence on the dissimilarity of different CaMs although they have highly-conserved structures. A preliminary study was carried out on the effects of CaM-binding peptides on cellular signal transduction, cell proliferation, showing the participation of CaM in cell functions mentioned above.

关键词： pollen calmodulin affinity cellular signal transduction cell proliferation

Synthesis and Crystal Structure of 4,6Di-tert-butyl-2.hydroxy-3-(N-1-phenylethyliminomethyl) phenyl bis(triphenylphosphine)palladium bromide

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Chinese Journal of structural chemistry 1999年第4期18卷 54-59页

作者： XU JiaXi\ ZHANG ZeYing\= (college of chemistry and {2. engineering, peking university, beijing 100871, China) Coll. of Chem. and Molec. Eng. Peking University Beijing 100871 China

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１ＩＮＴＲＯＤＵＣＴＩＯＮＰａｌａｄｉｕｍｃｏｍｐｌｅｘｅｓｓｕｃｈａｓｔｅｔｒａｋｉｓ（ｔｒｉｐｈｅｎｙｌｐｈｏｓｐｈｉｎｅ）ｐａｌａｄｉｕｍａｒｅａｋｉｎｄｏｆｉｍｐｏｒｔａｎｔｃａｔａｌｙｓｔｓｉｎｔｈｅｒｅａｃｔｉｏｎｏｆｃａｒｂｏｎｃａｒ...

关键词： palladium complex synthesis molecular structure crystal structure

MB_8^(2.) (M=Be,Mg,Ca,Sr,and Ba):Planar octacoordinate alkaline earth metal atoms enclosed by boron rings

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Science China chemistry 2010年第8期53卷 1737-1745,1829-1832页

作者： PU ZhiFeng1,GE MaoFa1 & LI QianShu2.1state key {2. for {2. chemistry of unstable and stable species beijing National {2. for molecular Sciences (bnlms) Institute of chemistry,Chinese Academy of Sciences,beijing 100190,China 2.enter for Computational Quantum chemistry,South China Normal university,Guangzhou 510631,China 1. state key laboratory for structural chemistry of unstable and stable species beijing National laboratory for {2. Sciences (bnlms) Institute of chemistry Chinese Academy of Sciences Beijing 100190 China2. Center for Computational Quantum Chemistry South China Normal University Guangzhou 510631 China

Complexes involving planar octacoordinate alkaline earth metal atoms in the centers of eight-membered boron rings have been investigated by two density functional theory (DFT) ***82.with D8h symmetry is predicted to be stable,both geometrically and electronically,since a good match is achieved between the size of the central beryllium atom and the eight-membered boron *** contrast,the other alkaline earth metal atoms cannot be stabilized in the center of a planar eight-membered boron ring because of their large *** following the out-of-plane imaginary vibrational frequency,pyramidal C8v MgB82.,CaB82.,SrB82.,and BaB82.structures are *** presence of delocalized π and σ valence molecular orbitals in D8h BeB82.gives rise to aromaticity,which is reflected by the value of the nucleus-independent chemical *** D8h BeB82.structure is confirmed to be the global minimum on the potential energy surface.

关键词： density functional theory octacoordinate alkaline earth metal aromatic molecular orbital

Syntheses, structures and magnetic properties of a family of one-dimensional M(Ⅱ)-lanthanide(Ⅲ) (M = Ni(Ⅱ) and Zn(Ⅱ)) coordination polymers

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Science China chemistry 2007年第3期50卷 308-317页

作者： ZHANG Wen, ZHAO Fei, LIU Tao & GAO Song beijing National laboratory for {2. Sciences, state key laboratory of Rare Earth Materials chemistry and Applications, college of chemistry and molecular engineering, peking university, beijing 100871, China 1. beijing National laboratory for {2. Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Beijing 100871 China

A series of 1D nickel(II)/zinc(II)-lanthanide(III) coordination polymers, [M(μ-L)2.n(NO3)3]n·solvents (HL = bis(2.pyridylcarbonyl)amine; M = Ni, Ln = Gd (1·NiGd), Tb (2.NiTb), Dy (3·NiDy), Ho (4·NiHo), Y (5·NiY); M = Zn, Ln = Gd (6·ZnGd), Tb (7·ZnTb), Dy (8·ZnDy), Ho (9·ZnHo); solvents = H2. or H2.-ethanol), was synthesized and characterized. All of the complexes are isostructural at 2.3 K and crystallize in the orthorhombic space group Fddd. Magnetic measurements were performed on 1―9, where weak ferromagnetic interaction is found in 1·NiGd, ferromagnetic interaction in 2.NiTb and 3·NiDy, and antiferromagnetic interaction in 4·NiHo. A remarkable dc magnetic field dependence of ac susceptibilities was found in this series of complexes.

关键词： nickel lanthanide 3d-4f coordination polymer magnetic property

Synthesis and photophysical properties of Ir~Ⅲ-Ln~Ⅲ(Ln=Nd,Yb,Er) bimetallic complexes containing bipyrimidines as bridging ligands

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Science China chemistry 2009年第11期52卷 1808-1813页

作者： CHEN FangFang,JIANG WeiLi,LOU Bin,BIAN ZuQiang & HUANG ChunHui beijing National laboratory for {2. Sciences,state key laboratory of Rare Earth Materials chemistry and Applications,college of chemistry and {2. engineering,peking {12.,beijing 100871,China beijing National laboratory for {2. Sciences State Key Laboratory of Rare Earth Materials Chemistry and Applications College of Chemistry and Molecular Engineering Peking University Beijing China

Bipyrimidines have been chosen as(N^N)(N^N) bridging ligands for connecting metal ***Ⅲ-LnⅢ(Ln = Nd,Yb,Er) bimetallic complexes [Ir(dfppy)2.μ-bpm)Ln(TTA)3]Cl were synthesized by using Ir(dfppy)2.bpm)Cl as the ligand coordinating to lanthanide complexes Ln(TTA)3·*** stability constants between Ir(dfppy)2.bpm)Cl and lanthanide ions were measured by fluorescence *** obvious quenching of visible emission from IrⅢ complex in the IrⅢ-LnⅢ(Ln = Nd,Yb,Er) bimetallic complexes indicates that energy transfer occurred from IrⅢ center to *** emissions from NdⅢ,YbⅢ,and ErⅢ were obtained under the excitation of visible light by selective excitation of the IrⅢ-based *** was proven that Ir(dfppy)2.bpm)Cl as the ligand could effectively sensitize NIR emission from NdⅢ,YbⅢ,and ErⅢ.

关键词： bipyrimidine IrⅢ-LnⅢ bimetallic complexes stability constant NIR emission excitation of visible light

Reinvestigation on the Reaction of Salicylic Chloride with Salicylic Amide and X-ray Crystal Structure of a New Macrocyclic Polyester

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Chinese Journal of structural chemistry 2003年第5期22卷 512-516页

作者： DU Da-Ming② CHEN Xiao HUA Wen-Ting JIN Xiang-Lin (key laboratory of Bioorganic {2. and {2. engineering of Ministry of Education, college of chemistry and molecular engineering, peking university, beijing 100871, China) key laboratory of Bioorganic {2. and {2. engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University

The reaction of salicylic chloride and salicylic amide at 170 ℃ gave benzoxazine and a new macrocyclic polyester 3, whose crystal structure has been determined by single-crystal X-ray diffraction analysis. Compound 3: C2.H16O8, Mr = 480.41, monoclinic, space group P2./n, a = 15.353(3), b = 14.196(3), c = 2..147(4) ? b = 103.32.3), V = 4485(2. ?, Z = 8, F(000) = 1984, Dc = 1.42. g/cm3 and m = 0.106 mm-1. The final R = 0.0535 and wR = 0.12.5 for 7903 observed reflections (I ≥ 2.I)). In the asymmetric unit of the compound there exist two independent molecules which are connected by weak aromatic CH…O hydrogen bonding between C(47)?H(47) and atom O(7) of the carbonyl group.

关键词： salicylic chloride salicylic amide polyester macrocycle crystal structure

Systematic study of the transfer of amino acids across the water/1,2.dichloroethane interface facilitated by dibenzo-18-crown-6

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Science China chemistry 2004年第1期47卷 24-33页

作者： CHEN Yong, YUAN Yi, ZHANG Meiqin, LI Fei, SUN Peng, GAO Zhao & SHAO Yuanhuastate key {2. of Electroanalytical {2., Changchun Institute of Applied {2., Chinese Academy of Sciences, Changchun 13002., China college of {2. and molecular engineering, peking university, beijing 100871, China Lab. of Electroanalytical Chem. Changchun Inst. of Appl. Chem. Chinese Acad. of Sci. Changchun 130022 China Coll. of Chem. and molecular Eng. Peking Univ. Beijing 100871 China

Facilitated ion transfer reactions of 2. amino acids with dibenzo-18-crown-6 (DB18C6) at the water/1,2.dichloroethane (W/DCE) interfaces supported at the tips of micro- and nano-pipets were investigated systematically using cyclic voltammetry. It was found that there were only 10 amino acids, that is, Leu, Val, lie, Phe, Trp, Met, Ala, Gly, Cys, Gin (in brief), whose protonated forms as cations can give well-defined facilitated ion transfer voltammograms within the potential window, and the reaction pathway was proven to be consistent with the transfer by interfacial complexation/dissociation (TIC/TID) mechanisms. The association constants of DB 18C6 with different amino acids in the DCE (β0), and the kinetic parameters of reaction were evaluated based on the steady-state voltammetry of micro- or nano-pipets, respectively. The experimental results demonstrated that the selectivity of complexation of protonated amino acid by DB18C6 compared with that of alkali metal cations was low, which can be attributed to the vicinal effect arising from steric hindrance introduced by their side group and the steric bulk effect by lipophilic stabilization. Moreover, the association constants and the standard rate constants for different amino acids showed good correlations with their hydrophobicity (π), except Gly and Met, which inferred that the selectivity of such heterogeneous complex reaction for different amino acids with DB18C6, was not only affected by discrimination in binding these ions to the crown ether macro-cycle, but also significantly modified by the ion transfer Gibbs energy which was closely related to the structure of the transferred ions, protonated amino acids.

关键词： micro-/nano-pipet, water/1,2.dichloroethane interface, facilitated ion transfer, cyclic voltammetry, amino acid.