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cDNA cloning,sequence analysis,and recombinant expression of akitonin beta,a C-type lectin-like protein from Agkistrodon acutus

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Acta Pharmacologica Sinica 2004年第3期25卷 118-123页

作者： Xiang-dong ZHA1,2.Jing LIU1,Kang-sen XU3 1 school of life {2.,University of {2. and technology,Hefei 2.002. school of life {2.,Anhui University,2.Hefei 2.0039 National Institute for Control of Pharmaceuticals and Biological Products,Beijing 100050,china 3 school of life {2. University of Science and Technology Hefei 230026 National Institute for Control of Pharmaceuticals and Biological Products 北京 100050

AIM: To clone the cDNA of a new member of snake venom C-type lectin-like proteins, to study its structure- function relationships and to achieve its recombinant production. METHODS: PCR primers were designed based on the homology and cDNA was amplified by RT-PCR using total RNA from snake venom gland as the template. The PCR products were cloned into the plasmid pGEM-T and sequenced. The deduced protein sequence was analyzed with some bioinformatic programs. A recombinant expression plasmid was constructed using pBAD- TOPO as vector and transformed into *** TOP10 competent cells. RESULTS: A novel cDNA sequence encod- ing akitonin β was found and accepted by GenBank (accession number AF387100). Akitonin β consists of a typical carbohydrate recognition domain (CRD) of C-type lectins, and it is homologous with other snake venom C-type lectin-like proteins. It was predicted to be a platelet antagonist. Upon induction with arabinose rAkitonin β express- ing in E coli was achieved at a high level (superior to 150 mg/L). The recombinant fusion protein exhibited inhibitory activities on rat platelet aggregation in vitro. CONCLUSION: A new member of snake venom C-type lectin-like proteins was discovered and characterized, and an efficient recombinant expression system was estab- lished for its production.

关键词： snake venoms cDNA akitonin C-type lectin-like proteins recombinant proteins structure- activity relationship

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Protein Secondary Structure Prediction Using Dynamic Programming

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Acta Biochimica et Biophysica Sinica 2005年第3期37卷 167-172页

作者： Jing ZHAO Pei-Ming SONG Qing FANG Jian-Hua LUO school of life {2. & technology,shanghai Jiaotong University,shanghai 2.02.0,china shanghai Center for Bioinformation and technology,shanghai 2.02.5,china Logistical Engineering University,Chongqing 400016,china school of life {2. & technology Shanghai Jiaotong UniversityShanghai 200240 China shanghai Center for Bioinformation and technologyshanghai 2.02.5 China Logistical Engineering UniversityChongqing 400016 China

In the present paper,we describe how a directed graph was constructed and then searched forthe optimum path using a dynamic programming approach,based on the secondary structure propensity ofthe protein short sequence derived from a training data *** protein secondary structure was thus pre-dicted in this *** average three-state accuracy of the algorithm used was 76.70%.

关键词： directed graph dynamic programming approach protein secondary structure

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Recognition of Gene Acceptor Site Based on Multi-objective Optimization

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Acta Biochimica et Biophysica Sinica 2005年第7期37卷 435-439页

作者： Jing ZHAO~(1,3,4) Yue-Min ZHU~2.Pei-Ming SONG~1 Qing FANG~1 Jian-Hua LUO~(1,3) 1 school of life {2. & technology,shanghai Jiaotong University,shanghai 2.02.0,china 2.CREATIS,CNRS UMR 5515,INSA Lyon,6962. Villeurbanne Cedex,France 3 shanghai Center for Bioinformation and technology,shanghai 2.02.5,china 4 Logistical Engineering University,Chongqing 400016,china school of life {2. & technology Shanghai Jiaotong UniversityShanghai 200240 China shanghai Center for Bioinformation and technologyshanghai 2.02.5 China Logistical Engineering UniversityChongqing 400016 China CREATIS CNRS UMR 5515 INSA Lyon69621 Villeurbanne Cedex France

A new method for predicting the gene acceptor site based on multi-objective optimization isintroduced in this *** models for the acceptor,branch and distance between acceptor site andbranch site were constructed according to the characteristics of the sequences from the exon-intron databaseand using common biological *** acceptor function,branch function and distance functionwere defined respectively,and the multi-objective optimization model was constructed to recognize thesplice *** test results show that the algorithm used in this study performs better than the SplicePredictor,which is one of the leading acceptor site detectors.

关键词： multi-objective optimization acceptor site recognition

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Purification and Characterization of Two Endo-β-1,4-glucanases from Mollusca,Ampullaria crossean

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Acta Biochimica et Biophysica Sinica 2005年第10期37卷 702-708页

作者： Yan-Hong LI~(1#) Rui GUO~(3#) Qiu-Yu YIN~1 Ming DING~1 Si-Liang ZHANG~3 Gen-Jun XU~(1,2. Fu-Kun ZHAO~(1,2.) 1 Key Laboratory of Proteomics,Institute of Biochemistry and Cell Biology,shanghai Institutes for Biological sciences.Graduate {2. of the Chinese Academy of sciences,Chinese Academy of sciences,shanghai 2.0031,china 2.College of life science,Zhejiang Sci-Tech University,Hangzhou 310018,china 3 Bioengineering Institute,East china University of science and {12.,shanghai 2.02.3,china Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Graduate School of the Chinese Academy of Sciences Chinese Academy of SciencesShanghai 200031 China Bioengineering Institute East China University of Science and TechnologyShanghai 200233 China College of life science Zhejiang Sci-Tech UniversityHangzhou 310018 China

Two novel endo-β-1,4-glucanases,EG45 and EG2.,were isolated from the gastric juice ofmollusca,Ampullaria crossean,by anion exchange,hydrophobic interaction,gel filtration and a secondround of anion exchange *** purified proteins EG45 and EG2. appeared as a single bandon sodium dodecylsulfate polyacrylamide gel electrophoresis with a molecular mass of 45 kDa and 2. kDa,*** optimum pH for CMC activity was 5.5 for EG45 and 4.4-4.8 for *** optimumtemperature range for EG2. was broad,between 50℃ and 60℃;for EG45 it was 50℃.The analysis on thestability of these two endo-β-1,4-glucanases showed that EG2. was acceptably stable at pH 3.0-11.0 evenwhen the incubation time was prolonged to 2. h at 30℃,whereas EG45 remained relatively stable at *** 85% of the activity of EG2. could be retained upon incubation at 60℃ for 2. ***,less than 10% residual activity of EG45 was detected at 50℃.Among different kinds of substrates,bothenzymes showed a high preference for carboxymethyl ***45,in particular,showed a carboxymethylcellulose hydrolytic activity of 146.5 IU/mg *** enzymes showed low activities to xylan (from oatspelt) and Sigmacell 101,and they were inactive to p-nitrophenyl-β-D-cellobioside,salicin and starch.

关键词： cellulase endo-β-1,4-glucanase Ampullaria crossean purification substrate specificity

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Effect of Asymmetry in a Bistable System Subject to Multiplicative Colored Noise

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Communications in Theoretical Physics 2007年第12期48卷 1059-1062页

作者： ZHOU Yu-Rong~(1,2.GUO Feng~3 and PANG Xiao-Feng~1~1 school of life {2. and technology,University of Electronic {2. and technology of china,Chengdu 610054,china~2.school of Information and Electric Engineering,Panzhihua University,Panzhihua 617000,china~3 school of Automation Engineering,University of Electronic {2. and technology of china,Chengdu 610054,china school of life {2. and technology University of Electronic Science and Technology of China Chengdu 610054 China school of Information and Electric Engineering Panzhihua University Panzhihua 617000 China school of Automation Engineering University of Electronic Science and Technology of China Chengdu 610054 China

By the method of the stochastic energetics,we investigate the stochastic resonance (SR) phenomenon of anoverdamped Brown particle in an asymmetric bistable potential,driven by external periodical signal and *** expressions have been obtained for the quasi-steady-state probability distribution *** is found thatthe input energy (IE) pumped into the system by the external driving shows an SR-like behavior as a function of thenoise strength,whereas the IE turns to be a monotonic function of the correlation time of the *** effect ofpotential asymmetry is also studied on SR and IE.

关键词： asymmetric bistable system stochastic resonance stochastic energetics

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Research on nonlinear constitutive relationship of permanent deformation in asphalt pavements

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science china(Physics,Mechanics & Astronomy) 2006年第6期49卷 671-682页

作者： PENG Miaojuan1 & XU Zhihong2.1. Department of Civil Engineering,shanghai University,shanghai 2.0072.{2. 2. school of Transportation Engineering,tongji University,shanghai 2.0092.{2. Department of Civil Engineering Shanghai University Shanghai China school of Transportation Engineering Tongji University Shanghai China

To predict correctly the rut depths in asphalt pavements,a new nonlinear viscoelastic-elastoplastic constitutive model of permanent deformation in asphalt pave-ments is presented. The model combines a generalized Maxwell model with an elasto-plastic one. Then from the creep theory,the linear and nonlinear constitutive equations of the generalized Maxwell model are obtained. From the nonlinear finite element method for the rutting of the asphalt pavement,the rut depths of 4 asphalt-aggregate mixtures are obtained. And the results are compared with the ones from the finite element method by SHRP and the experiments by SWK/UN. The results in this paper are better than the ones by SHRP,and agree with the ones of the experiment by SWK/UN. This shows that the nonlinear viscoelastic-elastoplastic constitutive model,which is presented in this paper for the rutting of the asphalt pavement,is effective. The properties,such as nonlinear elastic-ity,plasticity,viscoelasticity and nonlinear viscoelasticity,which affect the rutting of an asphalt pavement,can be shown in the model. And the characteristics of the permanent deformation of the asphalt pavement can be presented entirely in the model.

关键词： asphalt pavement,permanent deformation,nonlinear viscoelastic-elastoplastic constitutive relationship,generalized Maxwell model,creep compliance.

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CO observations of massive star forming regions at different evolutionary phases

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science china(Physics,Mechanics & Astronomy) 2006年第5期49卷 626-640页

作者： CHEN Xi1,2. XU Ye1,3, SHEN Zhiqiang1,3 & LI Jingjing1,2.1. shanghai Astronomical Observatory, Chinese Academy of sciences, shanghai 2.0030, china 2. Graduate school of the Chinese Academy of sciences, Beijing 100034, china 3. Joint Institute for Galaxy and Cosmology, shanghai Astronomical Observatory and the University of science and technology of china, shanghai 2.0030, china shanghai Astronomical Observatory Chinese Academy of Sciences Shanghai China Graduate school of the Chinese Academy of sciences Beijing China Joint Institute for Galaxy and Cosmology Shanghai Astronomical Observatory and the University of Science and Technology of China Shanghai China

The 12.O (J=1-0), 13CO (J=1-0) and C18O (J=1-0) emissions in 9 massive star forming regions, which are believed to be at different stages of massive star formation, were mapped with the 13.7 m millimeter wave telescope at Qinghai Station of Purple Mountain Observatory. Of the observed 9 sources, 13CO cores were detected in seven of them, and C18O cores in five of them. And only two sources associated with C18O cores and H2. masers showed the extended structures and strong outflows. This is the first detection of outflow associated with IRAS 2.566+582. in the observing field of S152.S153. The physical parameters of cores and outflows for these sources, derived from Local Thermal Equilibrium (LTE) analysis, are presented. These observing results suggest that the C18O cores will only appear when the gas density is high enough and the probability to have an outflow is very high when the clumps show the C18O and H2. maser simulta- neously.

关键词： star formation cloud core outflow H2. maser

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Bayesian cognitive trust model based self-clustering algorithm for MANETs

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science china(Information sciences) 2010年第3期53卷 494-505页

作者： WANG Wei1,2.3 & ZENG GuoSun1,2.31Department of Computer science & technology, {2. University, shanghai 2.0092. china 2.2. Branch, National Engineering & technology Center of High Performance Computer, shanghai 2.0092. china 3Key Loboratory of Embedded System and Service Computing, Ministry of Education, shanghai 2.0092. china Department of Computer science & technology Tongji University Shanghai China tongji Branch National Engineering & Technology Center of High Performance Computer Shanghai China Key Loboratory of Embedded System and Service Computing Ministry of Education Shanghai China

With the introduction of mobile Ad hoc networks (MANETs), nodes are able to participate in a dynamic network which lacks an underlying infrastructure. Before two nodes agree to interact, they must trust that each will satisfy the security and privacy requirements of the other. In this paper, using the cognition inspired method from the brain informatics (BI), we present a novel approach to improving the search efficiency and scalability of MANETs by clustering nodes based on cognitive trust mechanism. The trust relationship is formed by evaluating the level of trust using Bayesian statistic analysis, and clusters can be formed and maintained autonomously by nodes with only partial knowledge. Simulation experiments show that each node can form and join proper clusters, which improve the interaction performance of the entire network. The essence of the underlying reason is analyzed through the theory of complex networks, revealing great scalability of this method.

关键词： trust model MANET self-clustering Bayesian method cognitive mobile

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Molecular dynamics simulations of interaction between protein-tyrosine phosphatase 1B and a bidentate inhibitor

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Acta Pharmacologica Sinica 2006年第1期27卷 100-110页

作者： Gui-xia LIU~(2.3,4) Jin-zhi TAN~2.Chun-ying NIU~2.Jian-hua SHEN~(2.3) Xiao-min LUO~2.Xu SHEN~(2.3) Kai-xian CHEN~2.Hua-liang JIANG~(2.3,4)2.Center for Drug Discovery and Design,State Key Laboratory of Drug Research,shanghai Institute of Materia Medica,shanghai Institutes for Biological {2.s,Chinese Academy of {2.s,shanghai 2.12.3,china 3 school of Pharmacy,East china University of {2. and technology shanghai 2.02.7,china Center for Drug Discovery and Design State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China school of Pharmacy East China University of Science and Technology Shanghai China

Aim:To investigate the dynamic properties of protein-tyrosine phosphatase (PTP)1B and reveal the structural factors responsible for the high inhibitory potencyand selectivity of the inhibitor SNA for ***:We performed moleculardynamics (MD) simulations using a long time-scale for both PTP1B and PTP1Bcomplexed with the inhibitor SNA,the most potent and selective PTP1B inhibitorreported to *** trajectories were analyzed by using principal ***:Trajectory analyses showed that upon binding the ligand,theflexibility of the entire PTP1B molecule *** most notable change is themovement of the *** simulation results also indicated that electro-static interactions contribute more to PTP 1B-SNA complex conformation than thevan der Waals interactions,and that Lys41,Arg47,and Asp48 play important rolesin determining the conformation of the inhibitor SNA and in the potency andselectivity of the *** these,Arg47 contributed *** results werein agreement with previous experimental ***:The informationpresented here suggests that potent and selective PTP1B inhibitors can be de-signed by targeting the surface residues,for example the region containing Lys41,Arg47,and Asp48,instead of the second phosphate binding site (besides theactive phosphate binding site).

关键词： molecular dynamics simulation principal component analysis protein-tyrosine phosphatase 1B type 2.diabetes

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pH-Dependent Stability of EGX, A Multi-functional Cellulase from Mollusca, Ampullaria crossean

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Acta Biochimica et Biophysica Sinica 2004年第9期36卷 603-608页

作者： Wen-Ying LI2. Ji WANG1, Yan-Hong LI1, Ming DING1, Gen-Jun XU1,3, Lan-Ying LIU2. and Fu-Kun ZHAO1,3* 1Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, shanghai Institutes for Biological sciences, the Chinese Academy of sciences,Graduate school of the Chinese Academy of sciences, shanghai 2.0031, china 2.ollege of life science, Jilin University, Changchun 13002., china College of life science, Zhejiang University of science and technology, Hangzhou 310018, china College of life science Jilin UniversityChangchun 130023 China Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences the Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China College of life science Zhejiang University of Science and TechnologyHangzhou 310018 China

The cellulase activity and stability of EGX, a multi-functional cellulase previously purified from the mollusca Ampullaria crossean, was systematically studied under different pH. The pH induced con- formation and stability change of EGX have been investigated by using the intrinsic fluorescence, ANS fluorescence and CD spectrum. It has been found that the conformation and activity of this cellulase were strongly dependent on the pH. EGX was stable for both the enzyme activity and the conformation from pH 5.6 to pH 7.4. As shown by intrinsic and ANS fluorescence, no red shift of emission maximum occurred and a negligible intensity change was observed at pH 5.6–7.4. The activity of EGX remained about 80% in pH 5.6–7.4 and obviously decreased out of side the pH range. Urea-induced changes in EGX at pH 5.4 and pH 8.0 were measured by intrinsic fluorescence and CD spectrum. At pH 5.4, a significantly red shift of emission maximum occurred when the concentration of urea was 5 M compared to the concentration was 3 M at pH 8.0. The α-helix at pH 5.4 was 40.51% in the absence of urea and 31.04% in the presence of 4 M urea. At pH 8.0 the α-helix was 7.2.% in the presence of 4 M urea. The data indicated that EGX was much susceptible to urea-induced unfolding at pH 8.0 and much stable at pH 5.4. The greater pH dependent stability of EGX may allow the enzyme to adequately catalyze the hydrolysis of cellulosic materials under natural or industrial extreme conditions.

关键词： multi-functional cellulase stability Ampullaria crossean fluorescence spectroscopy pH-dependent structural change CD spectrum

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