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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, {2., china 2.School of Physics, peking university, {2., china 3 BNLMS, state key laboratory for structural chemistry of Un{12. and {12. species, college of chemistry and molecular engineering, peking university, {2., 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 {2. for molecular Sciences(BNLMS),state key {2. for structural chemistry of Unstable and stable species,Institute of chemistry,Chinese Academy of Sciences,beijing 100190,china 1. beijing national {2. for molecular 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 {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 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 {2. *** 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

Study on the atmospheric photochemical reaction of CF_3 radicals using ultraviolet photoelectron and photoionization mass spectrometer

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Science china chemistry 2008年第4期51卷 316-321页

作者： YAO Li1,2. DU Lin1,2. YIN Shi1,2.& GE MaoFa1 1 beijing national {2. for molecular Sciences (BNLMS), state key {2. for structural chemistry of Unstable and stable species, Institute of chemistry, Chinese Academy of Sciences, beijing 100080, china 2.Graduate university of Chinese Academy of Sciences, beijing 100080, china 1. beijing national {2. for molecular Sciences (BNLMS) State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China 2. Graduate university of Chinese Academy of Sciences Beijing 100080 China

A study of the atmospheric photochemical reaction of CF3 radical with CO and O2.was performed by using a homemade ultraviolet photoelectron spectrometer-photoionization mass spectrometer (PES- PIMS). The electronic structures and mechanism of ionization and dissociation of CF3OC(O)OOC(O)- OCF3 were investigated. It was indicated that the two bands on the photoelectron spectrum of CF3OC(O)OOC(O)OCF3 are the result of ionization of an electron from a lone pair of oxygen and a fluo- rine lone pair of CF3 group. The outermost electrons reside in the oxygen lone pair. The experimental and theoretical first vertical ionization energy is 13.2. and 13.178 eV, respectively, with the PES and OVGF method. They are in good agreement. The photo ionization and dissociation processes were discussed with the help of theoretical calculations and PES-PIMS experiment. After ionization, the parent ions prefer the dissociation of the C-O bond and giving the fragments CF3OCO+ and CF3+. It demonstrated that the ultraviolet photoelectron and photoionization mass spectrometer could be ap- plied widely in the study of atmospheric photochemical reaction.

关键词： photochemical reaction CF3 radical ultraviolet photoelectron and photoionization mass spectroscopy transient species

Fluorescence dynamics of interactions between polyamide PyPyPyβDp and DNA

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Science china chemistry 2006年第1期49卷 75-80页

作者： ZHANG Huijuan1,2. WANG Jin3, WU Yishi1, YUAN Gu3, AI Xicheng1, WANG Li4 & ZHANG Jianping1 1. state key {2. for structural chemistry of Unstable and stable species, Institute of chemistry, Chinese Academy of Sciences, beijing 100080, china 2. School of Life Science and Technology, beijing Institute of Technology, beijing 100081, china 3. college of chemistry and molecular engineering, peking university, beijing 100080, china 4. Center for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, beijing 100080, china Correspondence should be addressed to Ai Xicheng and Zhang Jianping 1. state key {2. for structural chemistry of Unstable and stable species Institute of Chemistry Chinese Academy of Sciences Beijing 100080 China 2. School of Life Science and Technology Beijing Institute of Technology Beijing 100081 China 3. college of chemistry and molecular engineering Peking University Beijing 100080 China 4. Center for Condensed Matter Physics Institute of Physics Chinese Academy of Sciences Beijing 100080 China

The photophysical properties of the polyamide PyPyPyβDp (PPP) were investigated by means of steady-state absorption and fluorescence spectroscopies, as well as time-resolved fluo-rescence spectroscopy. It was found that the excited-state properties of PPP are very sensitive to solvents. In TKMC buffer PPP exhibited weak fluorescence with a decay time constant of 16 ps, while with the decrease of the solvent polarity PPP showed the blue-shifted peak position, increased inten-sity and lengthened life-time for its fluorescence behavior. In the presence of calf thymus DNA, it was observed that the fluorescence intensity was enhanced and the fluorescence lifetime increased from 16 to 32.ps for PPP, which verified that PPP bound into the minor groove of DNA duplex.

关键词： polyamide (PPP), calf thymus DNA (ctDNA), time-resolved fluorescence spectroscopy, recognition dynamics.

Probing biological Process via Single Molecule Detection

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Probing biological Process via Single Molecule Detection

第五届全国化学生物学学术会议

作者： Xin Sheng Zhao beijing national {2. for molecular Sciences,state key {2. for structural chemistry of Unstable and stable species,{12.,college of chemistry and molecular engineering,peking university,beijing 100871,china.

＜正＞Single molecule detection（SMD）emerges as a powerful tool to investigate biological process in vitro and in *** have applied SMD to study the dynamics of DNA hybridization,protein

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Qualitative and Quantitative Protein Detection in Undiluted Serum with Gold Nanoparticles

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Qualitative and Quantitative Protein Detection in Undiluted ...

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： Jing Ge,Xin Sheng Zhao~* beijing national {2. for molecular Sciences,state key {2. for structural chemistry of Unstable and stable species,{12.,college of chemistry and molecular engineering,peking university,beijing 100871,china

＜正＞One of the key challenges in bioanalytical chemistry is the detection of disease-related protein and metabolites in biological *** great efforts have been made to develop protein biosensors,so far only a few met...

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Enzyme Dynamics of AIKB

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Enzyme Dynamics of AIKB

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： Xun Li,Xin Sheng Zhao~* beijing national {2. for molecular Sciences,state key {2. for structural chemistry of Unstable and stable species,{12.,college of chemistry and molecular engineering,peking university,beijing 100871,china

A1KB is a kind of enzyme that repairs *** phenomenon that double strand DNA(dsDNA) will be contorted when complex is formed may decide the enzyme catalyze rate according to the study from He and *** used three kinds o... 详细信息

关键词： A1KB dynamic enzyme

Silver Enhancement-Aptamer-Gold Nanoparticles Aggregation Based Assay for Simple and Sensitive Detection of Adenosine

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Silver Enhancement-Aptamer-Gold Nanoparticles Aggregation Ba...

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： Zhaofang Liu,Jing Ge,and Xin Sheng Zhao~* beijing national {2. for molecular Sciences,state key {2. for structural chemistry of Unstable and stable species,{12.,college of chemistry and molecular engineering,peking university,beijing 100871,china

＜正＞Aptamers are oligonucleic acid or peptide molecules that bind to wide range specific targets from metal ions,small molecules,to large proteins,even *** gold nanoparticles （AuNPs） and silver enhancement were introduced to detect the target molecules[1]. Previous work in our group has prepared aptamer-Gold nanoparticles（Apt-AuNPs） by

关键词： Aptamer Gold nanoparticles Adenosine detection Silver enhancement