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There are 27 papers published in subject: > since this site started. |
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1. IFGAP: a web integrated functional genomics analyzing platform | |||
HUANG Teng,LI Yan,WANG Peng,NING Shangwei,WANG Qianghu,XIAO Yun,LI Chunquan,LI Xia | |||
Biology 20 March 2012 | |||
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Abstract:The functional analysis of human genomics has been an increasing demand to help the study of human medical science. We here introduce a web-based integrative platform (IFGAP) for functional genomics analysis. IFGAP integrates functional annotation analysis, enrichment analysis and functional similarity analysis based on a unified background database. IFGAP provides comprehensive analysis of functional genomics to support molecular biology studies and generate novel biological hypothesis. We demonstrated the utility of IFGAP by analyzing associations between p53 pathway and skin cancer and our results indicated that p53 pathway is involved in the development of skin cancer. Availability: Freely available at http://bioinfo.hrbmu.edu.cn/IFGAP. | |||
TO cite this article:HUANG Teng,LI Yan,WANG Peng, et al. IFGAP: a web integrated functional genomics analyzing platform[OL].[20 March 2012] http://en.paper.edu.cn/en_releasepaper/content/4472437 |
2. Thermal stability and unfolding pathways of Sso7d and its mutant F31A by molecular dynamics simulation | |||
Xu Xianjin,Wang Cunxin | |||
Biology 13 February 2012 | |||
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Abstract:The thermo-stability and unfolding behaviors of a small hyperthermophilic protein Sso7d as well as its single-point mutation F31A are studied by molecular dynamics simulation at temperatures of 300 K and 500 K. Simulations at 300 K show that the F31A mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein’s stability. High temperature simulations at 500 K suggest that the unfolding of these two proteins evolves along different pathways. For the wild-type protein, the C-terminal alpha-helix is melted at the early unfolding stage, whereas it is destroyed much later in the unfolding process of the F31A mutant. Thus, the mutant unfolds faster than its parent protein. Besides, it is found that the triple-stranded antiparallel -sheet in the wild-type protein plays an important role in maintaining the stability of the entire structure. | |||
TO cite this article:Xu Xianjin,Wang Cunxin. Thermal stability and unfolding pathways of Sso7d and its mutant F31A by molecular dynamics simulation[OL].[13 February 2012] http://en.paper.edu.cn/en_releasepaper/content/4466109 |
3. The exploration of mammalian mitochondrial genes through integrating multiple lines of genome-wide biological evidence | |||
Xu Jiabao,Wang Sunpeng,Zhang Yizheng,Li Xiao | |||
Biology 29 December 2011 | |||
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Abstract:Mitochondria are a vital organelle of eukaryotic cells. Many diseases are caused by the mitochondrial gene mutation , therefore, there is an urgent requirement to explore the proteins of mitochondrion. In this paper we have created a list of 1086 human mitochondrial genes by combining 13 datasets from publications or genomic experiments. Then we created a functional linkage network among mitochondrial genes by integrating multiple lines of biological evidence, and utilized the network to predict the function of the mitochondrial genes, including identifying some novel components involved in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways and the MIPS complexes. Our results indicated that it is very useful to study mitochondrial biology and disease by integrated genomic and proteomic datasets. | |||
TO cite this article:Xu Jiabao,Wang Sunpeng,Zhang Yizheng, et al. The exploration of mammalian mitochondrial genes through integrating multiple lines of genome-wide biological evidence[OL].[29 December 2011] http://en.paper.edu.cn/en_releasepaper/content/4458493 |
4. PlaPID: a database of protein-protein interactions in plants | |||
Min Mingwei,Zheng Wen,Haoyang Cai,Hu Han,Zhang Yizheng,Li Xiao | |||
Biology 29 December 2011 | |||
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Abstract:PlaPID (Plant Protein Interaction Database) is a searchable database for protein-protein interactions in plants. It associates high-confidence information derived from published literatures and several databases. PlaPID aims to provide a reference and upgradeable database through comprehensive web services for studying plant protein interactions. The PlaPID database is freely accessible at http://www.PlaPID.org. | |||
TO cite this article:Min Mingwei,Zheng Wen,Haoyang Cai, et al. PlaPID: a database of protein-protein interactions in plants[OL].[29 December 2011] http://en.paper.edu.cn/en_releasepaper/content/4458490 |
5. Origin, evolution and functional diversity of bHLH gene family: insights from comparative genomics and interactomics | |||
Min Mingwei,Xu Junli,Yizheng Zhang,Yue Bisong,Li Xiao | |||
Biology 29 December 2011 | |||
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Abstract:The basic helix-loop-helix (bHLH) proteins make up of a complex multigene family of transcription factors that play the important roles in many biological processes. Although much effort has been made on their functional roles, their evolutionary origin and functional diversity remain to be clarified. In this study, we compared genomes and interactomes of bHLH gene families from model organisms such as human, fly, worm, yeast and Arabidopsis to shed light on origin, evolution and functional diversity of this gene family, inferring that bHLHs might origin in prokaryotes and undergo divergence in different linage because of distinct evolutionary force. | |||
TO cite this article:Min Mingwei,Xu Junli,Yizheng Zhang, et al. Origin, evolution and functional diversity of bHLH gene family: insights from comparative genomics and interactomics[OL].[29 December 2011] http://en.paper.edu.cn/en_releasepaper/content/4458487 |
6. Four-dimensional orthogonal electrophoresis system for screening protein complexes and protein-protein interactions combined with mass spectrometry | |||
Wang Xiaodong ,Chen Guoqiang,Liu Hui,Zhao Zhiyun ,Li Zhili | |||
Biology 21 February 2011 | |||
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Abstract:Most current approaches for purification and identification of protein complexes adopt affinity purifications combined with mass spectrometry, such as co-immunoprecipitation and tandem affinitypurification. Herein, we propose a new approach, termed as the four-dimensional orthogonal electrophoresis (4-DE) system, to find and analyze the cytoplasmic protein complexes. 4-DE system is composed of two parts: nondenaturing part (Part I) and denaturing part (Part II). Through Part I and decision procedure separations, six protein complex candidates 20S core particle of proteasome (CP), hemoglobin (Hb, α2β2), Hb (α2δ2), peroxiredoxin-2 (PRDX2), carbonic anhydrase-1 (CAH1), and heat shock protein 60 (HSP60) were separated. CP, Hb (α2β2), PRDX2, and HSP60 with different MW's and pI's were chosen for Part II proteomic analysis. The results indicate that 4-DE is not only suitable for studying protein complexes and protein-protein interactions as well as structural proteomics from complex biological samples, but can also be easy to separate and concentrate intact protein complexes from dilute complex samples. | |||
TO cite this article:Wang Xiaodong ,Chen Guoqiang,Liu Hui, et al. Four-dimensional orthogonal electrophoresis system for screening protein complexes and protein-protein interactions combined with mass spectrometry[OL].[21 February 2011] http://en.paper.edu.cn/en_releasepaper/content/4411515 |
7. Proteomic Characterization of Human Erythrocyte 20S Proteasome and Analysis of Species-dependent 20S Proteasome Heterogeneity | |||
Chen Guoqiang,Zhang Haijing,Deng Yanchun,Liu Hui,Li Zhili | |||
Biology 21 February 2011 | |||
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Abstract:A method for purification of 20S proteasome (20S core particle, CP) was developed by combining differential centrifugations with nondenaturing polyacrylamide gel electrophoresis (native-PAGE), irrespective of species origins of CPs. CP purified from human erythrocytes was subjected to proteomic analysis by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), revealing 33 spots of subunit isoforms with different molecular weights and isoelectric points, more than 14 constituent subunits. Furthermore, other four CPs were purified from yeast, mouse liver, two pancreatic cancer cell lines SW1990 and PANC-1 using this method mentioned above, and subjected to proteasome heterogeneity analysis by two-dimensional native/SDS-PAGE (native/sodium dodecyl sulphate polyacrylamide gel electrophoresis), together with CP from erythrocytes. In conclusion, the method described acts as a rapid and effective tool for CP isolations, and the results obtained may be served as a footstone for investigations of the species-dependent proteasome heterogeneity | |||
TO cite this article:Chen Guoqiang,Zhang Haijing,Deng Yanchun, et al. Proteomic Characterization of Human Erythrocyte 20S Proteasome and Analysis of Species-dependent 20S Proteasome Heterogeneity[OL].[21 February 2011] http://en.paper.edu.cn/en_releasepaper/content/4411512 |
8. The activity of myosin II motor and the volume of actin filament cooperatively regulate cytokinesis of | |||
Yang Fang,An Meiwen,Li Xiaona,Wang Li | |||
Biology 25 March 2010 | |||
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Abstract:The coordination of different cytoskeletons is an important factor in maintaining normal physiological and biochemical characteristics. In this study, normal rat kidney (NRK) cells in cytokinesis were treated with cytoskeleton inhibitors including cytochalasin D (CD), colchicine (COLC) oblebbistatin (myosin II motor activity inhibitor ). These inhibitors were released at the whole region and the localized region in two phases of cytokinesis. The influences were analyzed. It was showed that the roles of cytoskeleton inhibitors to cytokinesis were complex, for different treatment of inhibiotors corresponding to different results. The study indicated that the interaction in actin and the activity of myosin II motor is vital to cell shape and operation in every stages of cytokinesis. | |||
TO cite this article:Yang Fang,An Meiwen,Li Xiaona, et al. The activity of myosin II motor and the volume of actin filament cooperatively regulate cytokinesis of [OL].[25 March 2010] http://en.paper.edu.cn/en_releasepaper/content/41129 |
9. Selectivity and Permeation of KcsA Channel and Its Mutants | |||
Liu Yuzhi,Zhan Yong,Zhang Suhua,Yu Hui,An Hailong,Zhang Hailin | |||
Biology 20 August 2009 | |||
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Abstract:Ion selectivity is the essential problem of K+ ion channels. Peoples think that the selectivity filter which is consist of the signature sequence is the functional unit that allows K+ channels to distinguish potassium (K+) from sodium (Na+) ions. The new experimental data showed that the mutant channel of KcsA with the same signature sequence and structure has different selectivity properties when it is in the low or high [K+] conditions. It indicates that besides of the selectivity filter there must be other factor which can affect the selectivity of K+ ion channels. To answer this question, the authors executed DFT and BD simulations based on the three dimensional structure of the channels. Our data suggest that not only the signature sequence of K+ channels but also the interaction between the channels and cations determine if the channel has selectivity. | |||
TO cite this article:Liu Yuzhi,Zhan Yong,Zhang Suhua, et al. Selectivity and Permeation of KcsA Channel and Its Mutants[OL].[20 August 2009] http://en.paper.edu.cn/en_releasepaper/content/34580 |
10. The conservative gene regulatory network in HK97 and λ phages | |||
Ai Duiyuan,Qi Yanjiao | |||
Biology 08 June 2009 | |||
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Abstract:Some conservative gene regulatory elements are found in Enterobacteria phage HK97 through sequences alignment, which are very similar to λ phage. Meanwhile, the regulated genes such as c1-gene, cro-gene, Q-gene, also show homology with λ phage. All of these results suggest hk97’s gene regulatory network is as same as λ phage. It implies this regulatory network is crucial and universal to lambda group. | |||
TO cite this article:Ai Duiyuan,Qi Yanjiao. The conservative gene regulatory network in HK97 and λ phages[OL].[ 8 June 2009] http://en.paper.edu.cn/en_releasepaper/content/32942 |
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