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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,{2. 2.School of Physics, peking University, beijing 100871,{2. 3.bnlms, state key laboratory for structural chemistry of unstable and stable species, college of chemistry and molecular engineering, peking University, beijing 100871,{2. 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

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 structural 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

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

１ＩＮＴＲＯＤＵＣＴＩＯＮＰａｌａｄｉｕｍｃｏｍｐｌｅｘｅｓｓｕｃｈａｓｔｅｔｒａｋｉｓ（ｔｒｉｐｈｅｎｙｌｐｈｏｓｐｈｉｎｅ）ｐａｌａｄｉｕｍａｒｅａｋｉｎｄｏｆｉｍｐｏｒｔａｎｔｃａｔａｌｙｓｔｓｉｎｔｈｅｒｅａ... 详细信息

１ＩＮＴＲＯＤＵＣＴＩＯＮＰａｌａｄｉｕｍｃｏｍｐｌｅｘｅｓｓｕｃｈａｓｔｅｔｒａｋｉｓ（ｔｒｉｐｈｅｎｙｌｐｈｏｓｐｈｉｎｅ）ｐａｌａｄｉｕｍａｒｅａｋｉｎｄｏｆｉｍｐｏｒｔａｎｔｃａｔａｌｙｓｔｓｉｎｔｈｅｒｅａｃｔｉｏｎｏｆｃａｒｂｏｎｃａｒ...

关键词： palladium complex synthesis molecular structure crystal structure

Novel gaseous transient species:generation and characterization

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Science china chemistry 2007年第2期50卷 145-169页

作者： ZENG XiaoQing1,2.& WANG DianXun11 state key laboratory for structural chemistry of unstable and stable species,Institute of chemistry,Chinese Academy of Sci-ences,{2. 100080,china 2.Graduate School of Chinese Academy of Sciences,{2. 100039,china 1. state key laboratory for structural chemistry of unstable and stable species Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China 2. Graduate School of Chinese Academy of Sciences Beijing 100039 China

Due to special properties of transient species, such as short-lived, unstable, reactive, and even explosive, the generation and subsequent characterization is a great challenge for experimental chemists. In our {2., systematic researches have been carried out to investigate novel transient species: reactive halogen species (RHS), short-lived free radicals, and metastable pseudohalogen compounds, based on the successive technical improvements on the Hel Photoelectron spectroscopy (PES). In this review, the topic mainly focuses on innovative methods of generating novel transient species, and subsequent geometric and electronic structure characterizations of these species combined with quantum chemical calculations.

关键词： reactive halogen species radicals pseudohalogen compounds Hel Photoelectron Spectroscopy (PES) quantum chemical calculations

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

HeI photoelectron spectroscopic (PES) studies of the electronic structure in ω-heterocycle a-cyano polyenic ethyl ester compounds

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Chinese Journal of chemistry 1996年第3期14卷 211-216页

作者： LI, Ying LI, Sheng CHEN, Ben-Ming WANG, Dian-Xunstate key {2. for structural chemistry of unstable and stable species, Institute of chemistry, Chinese Academy of Sciences, beijing 100080, china state key {2. for structural chemistry of unstable and stable species Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China

HeI photoelectron spectra of w-heterocycle a-cyano polyenic ethyl ester compounds (1-6) have been given in this paper. Assignment of the spectra is also done with the aid of HeI photoelectron spectroscopic (PES) results of smaller molecules which have similar atomic group to the molecules studied, and the aid of MNDO molecules orbital calculations. The lowest PES experimental ionization potentials (IPs in eV) of different molecules reduce gradually with the increasing number of ethylenic group. The -CO2.2.5 group can be only considered as a substituent.

关键词： HeI photoelectron spectroscopy (PES) w-heterocycle a-cyano polyenic ethyl ester compounds homologous linearity rule

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 University,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 molecular engineering of Ministry of Education, college of chemistry and molecular engineering, peking University, beijing 100871, china) key laboratory of Bioorganic {2. and molecular 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