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Applying genetic algorithms to the study of protein mutation theory

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Chinese Science Bulletin 1998年第23期43卷 1977-1982页

作者： zhirong sun Hao Han Wang Tsing Hua Univ Dept Biol Sci & Biotechnol Beijing 100084 Peoples R China

Genetic algorithms were applied to the study of simulation of protein mutation carried out on two_dimensional lattice model; to the study of effects of single mutation and double mutation on protein folding and protein structure stability. It is found that in two_dimensional lattice models, replacement of inner core hydrophobic residue by hydrophilic residue will result in reduction of protein stability; at the same time the number of residues of protein surface relatively grows with increase of protein chain length; and most mutations occur in residues of protein surface, these mutations are all neutral and have no effects on protein natural structure. The two mutations of double mutation are interactive and related to each other.

关键词： genetic algorithm two_dimensional lattice model single mutation double mutation.

Identifying changed protein-protein interactions in biological processes by gene coexpression analysis

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Chinese Science Bulletin 2010年第14期55卷 1396-1402页

作者： ZHANG Ting ZHANG XueGong sun zhirong Key Laboratory of Bioinformatics of Ministry of Education State Key Laboratory of Biomembrane and Membrane Biotechnology Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China Bioinformatics Division TNLIST/Department of Automation Tsinghua Un-iversi-ty Beijing 100084 China

The interaction strength between 2 proteins is not constant but variable under different conditions. For a given biological process, identification of protein-protein interactions (PPIs) undergoing dynamic change in interaction strength is highly valuable but never achieved before. In this work, we presented a computational approach to identify changed PPIs (cPPIs) on a global scale by analyzing the coexpression level of genes encoding the interacting protein pairs. This approach stemmed from the biological con-ception that the change of protein-protein interaction bore imprint at the gene coexpression level. We applied this method to identify cPPIs in cells treated with a cytokine TGFβ, as well as cPPIs in rheumatoid arthritis (RA) patients. The accuracy of identification was evaluated by comparing our results with data from the high-throughput experiment and literature mining. Our analysis demonstrated that this is a simple and effective method to infer cPPIs from a given set of PPIs or even from the whole interactome. Further analysis uncovered the biological functions of the cPPIs in RA patients, which included muscle contraction and antigen presentation. Our method could help to elucidate molecular mechanisms of dynamic biological processes.

关键词：蛋白质相互作用相互作用力生物过程表达分析基因识别价格指数转化生长因子

GO molecular function coding based protein subcellular localization prediction

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Chinese Science Bulletin 2007年第16期52卷 2240-2245页

作者： SHEN JinCheng SONG Zhang sun zhirong MOE Key Laboratory of Bioinformatics/Department of Biology Tsinghua University Beijing 100084 China

Subcellular localization is an important feature of proteins which is closely correlated to their function. In this work,we tried to develop a new coding method of using those location predictive molecular function terms of protein as the input for the prediction of subcellular localization. Combined with the amino acid pair composition of the sequence,this coding system is proved to be efficient for support vector machine (SVM) and to have satisfied performance when tested on the RH dataset. Meanwhile,the model also shows robustness against N-terminal uncertainties in sequences.

关键词：蛋白质细胞内定位氨基酸支持向量机

Bioinformatical study on the proteomics and evolution of SARS-CoV

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Chinese Science Bulletin 2003年第13期48卷 1277-1287页

作者： LIU Shuqun GUO Tao JI Xinglai sun zhirong Institute of Bioinformatics Department of Biological Sciences andBiotechnologyTsinghua UniversityBeijing 100084China

A novel coronavirus has been identified as the causative agent of the severe acute respiratory syndrome(SARS). For all the SARS-CoV associated proteins derivatedfrom the SARS-CoV genome, the physiochemical propertiessuch as the molecular weight, isoelectric point and extinction coefficient of each protein were calculated. Thetransmembrane segments and subcellular localization(SubLocation) prediction and conserved protein motifssearch against database were employed to analyze thefunction of SARS-CoV proteins. Also, the homology protein sequence alignment and evolutionary distance matrixcalculation between SARS-CoV associated proteins and the corresponding proteins of other coronaviruses wereemployed to identify the classification and phylogeneticrelationship between SARS-CoV and other *** results showed that SARS-CoV is a novel coronavirus which is different from any of the three previously knowngroups of coronviruses, but it is closer to BoCoV and MHV than to other coronaviruses. This study is in aid ofexperimental determination of SARS-CoV proteomics andthe development of antiviral vaccine.

关键词：生物信息学 SARS 非典型肺炎冠状病毒疾病防治

Electrochemical dechlorination of chloroform in neutral aqueous solution on palladium/foam-nickel and palladium/polymeric pyrrole film/foam-nickel electrodes

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Journal of Environmental Sciences 2008年第3期20卷 268-272页

作者： sun zhirong LI Baohua HU Xiang SHI Min HOU Qingnan PENG Yongzhen Key Laboratory for Water Quality Science and Water Environment Recovery Engineering Beijing University of Technology Beijing 100022 China College of Chemical Engineering Beijing University of Chemical Technology Beijing 100029 China

Electrochemical dechlorination of chloroform in neutral aqueous solution was investigated using palladium-loaded electrodes at ambient temperature. Palladium/foam-nickel （Pd/foam-Ni） and palladium/polymeric pyrrole film/foam-nickel （Pd/PPy/foam-Ni） composite electrodes which provided catalytic surface for reductive dechlorination of chloroform in aqueous solution were prepared using an electrodepositing method. Scanning electron microscope （SEM） micrographs showed that polymeric pyrrole film modified the electrode-surface characteristics and resulted in the uniform dispersion of needle-shaped palladium particles on foam-Ni supporting electrode. The experimental results of dechlorination indicated that the removal efficiency of chloroform and current efficiency in neutral aqueous solution on Pd/PPy/foam-Ni electrode could be up to 36.8% and 33.0% at dechlorination current of 0.1 mA and dechlorination time of 180 min, which is much higher than that of Pd/foam-Ni electrode.

关键词： chloroform electrochemical dechlorination removal efficiency Pd/foam-Ni electrode Pd/PPy/foam-Ni electrode

Efficient and reproducible folding simulations of the Trp-cage protein with multiscale molecular dynamics

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Chinese Science Bulletin 2008年第11期53卷 1699-1707页

作者： XIA XueFeng ZHANG Song HUANG Bo ZHOU Yun sun zhirong Department of Biology/MOE Key Laboratory of Bioinforrnatics State Key Laboratory of Biomembrane and Membrane BiotechnologyTsinghua University Beijing 100084 China

Folding simulations are often time-consuming or highly sensitive to the initial conformation of the si-mulation even for mini protein like the Trp-cage. Here, we present a multiscale molecular dynamics method which appears to be both efficient and insensitive to the starting conformation based on the testing results from the Trp-cage protein. In this method the simulated system is simultaneously mod-eled on atoms and coarse-grained particles with incremental coarsening levels. The dynamics of coarse-grained particles are adapted to the recent trajectories of finer-grained particles instead of fixed and parameterized energy functions as used in previous coarse-grained models. In addition, the com-positions of coarse-grained particles are allowed to be updated automatically based on the coherence during its history. Starting from the fully extended conformation and other several different conforma-tions of the Trp-cage protein, our method successfully finds out the native-like conformations of the Trp-cage protein in the largest cluster of the trajectories in all of the eight performed simulations within at most 10 ns simulation time. The results show that approaches based on multiscale modeling are promising for ab initio protein structure prediction.

关键词：蛋白质分子动力学分子结构结构模拟

A new method of research on molecular evolution of proteinase superfamily

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Chinese Science Bulletin 2001年第7期46卷 578-582页

作者： sun zhirong JI Xinglai HU Shengmin WANG Yu HE Fuchu Department of Biology Tsinghua UniversityBeijing 100084China Radiate Medicine Institute Academy of Military Medical SciencesBeijing 100850China

The molecular evolutionary tree, also known as a phylogenetic tree, of the serine proteinase superfamily was constructed by means of structural alignment. Three-dimensional structures of proteins were aligned by the SSAP program of Orengo and Taylor to obtain evolutionary distances. The resulting evolutionary tree provides a topology graph that can reflect the evolution of structure and function of homology proteinase. Moreover, study on evolution of the serine proteinase superfamily can lead to better understanding of the relationship and evolutionary difference among proteins of the superfamily, and is of significance to protein engineering, molecular design and protein structure prediction. Structure alignment is one of the useful methods of research on molecular evolution of protein.

关键词： molecular evolution SSAP algorithm structure alignment evolutionary tree serine proteinase superfamily.

The 7th National Conference on Bioinformatics and Systems Biology of China

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Frontiers of Electrical and Electronic Engineering in China 2017年第2期5卷 199-201页

作者： zhirong sun Kui Hua Xuegong Zhang Feng-Biao Guo Jian Huang MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic & Systems Biology TNLIST Department of Automation Tsinghua University Beijing 100084 China Bioinformatics Center in School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China Center of Bioinformatics (COBI) Key Laboratory for Neuro Information of Ministry of Education University of Electronic Science and Technology of China Chengdu 610054 China

The 7th National Conference on Bioinformatics and System Biology and the International Workshop on Advanced Bioinformatics and Precision Medicine was successfully held in Chengdu, Sichuan Province, China, on October 7-9, 2016. The conference is organized by Chinese Society for Cell Biology （CSCB）, National Natural Science Foundation of China （NSFC）, and MOE Key Laboratory of Bioinformatics, Tsinghua University, and hosted by University of Electronic Science and Technology of China （UESTC）. Prof. Runsheng Chen of Institute of Biophysics, CAS, is the organizing chair of the conference, and Prof. zhirong sun of Tsinghua University is the general secretary. Professors Feng-Biao Guo and Jian Huang of UESTC led the local organization team. A total of about 1,047 professionals and graduate students from all over the country and several US universities attended the conference.

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Characterizing the tumor microenvironmental changes in a network perspective

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Characterizing the tumor microenvironmental changes in a net...