甲型流感病毒蛋白质空间结构预测
发布时间：2018-08-25 16:49
【摘要】：甲型流感病毒具有极强的变异性，是历史上导致病患死亡人数最多的流行病毒之一。每一次甲型流感大爆发都是由其变异得到的新亚型和之前出现过的亚型流感病毒再次出现而引起。自20世纪以来，历史上共发生四次较大规模的流感病毒大流行，其每一次都对人类公共卫生和社会经济发展造成极大的破坏，因此对甲型流感病毒的研究已逐渐成为众多研究者的重要研究方向。目前对甲型流感病毒的研究主要是关于其DNA、RNA和蛋白质序列，从生物化学、生物物理学以及统计学等多角度去研究其序列的变化情况，并找到其中的变化规律。 文章首先介绍了最近甲型流感病毒的变异和流行情况，以其10种组成蛋白作为研究对象，在NCBI数据库中获得1902-2013年间关于甲型流感病毒10种组成蛋白的所有氨基酸序列，利用MATLAB进行大数据编程分析，结合详细的HP模型，并基于CGR-Walk模型将全部甲型流感病毒蛋白质序列转化为数据形式，引入时间序列ARFIMA(p,d,q)模型拟合所有数据化序列，分析10种组成蛋白的序列在1902-2013年间的变化趋势，并进一步对其未来10年的发展趋势进行预测。然后以甲型流感病毒蛋白质氨基酸序列变化规律的研究作为基础，运用从头计算的思想选择甲型H1N1流感病毒的蛋白质作为研究对象对其空间结构进行研究。基于蛋白质空间结构的HP模型，文中构建了甲型H1N1流感病毒蛋白质空间结构的3DHP模型，并利用优化的遗传算法找到具有最小自由能的优化结构，从而对甲型H1N1流感病毒蛋白质三维空间结构进行初步模建预测。之后鉴于HP格点模型过于简单，则根据甲型H1N1流感病毒的典型病毒颗粒呈球状这一特性，，利用这样的球状结构中氨基酸残基间形成的紧密接触对的能力不同，将20种氨基酸分成四类，并得到HNXP三维空间格点模型。采用优化的遗传算法得到其自由能最小的蛋白质HNXP三维空间结构，并采用稀疏典型相关性分析法将模建得到的结构与真实蛋白质空间结构进行对比分析，经检验得两者在结构上高度相似。 本文利用组成其序列的20种氨基酸之间所包含的生物信息对甲型流感病毒的三维空间结构进行预测，将目前关于甲型流感病毒对蛋白质氨基酸序列的研究进一步拓展至三维。研究结果可为甲型流感病毒蛋白质氨基酸序列空间结构的预测提供借鉴。
[Abstract]:Influenza A virus is one of the most prevalent viruses with the highest number of deaths in history. Each outbreak of influenza A is caused by the reappearance of new subtypes and previous subtypes of influenza viruses. Since the 20th century, there have been four large-scale pandemics of influenza viruses, each of which has caused great damage to human public health and socio-economic development. Therefore, the study of influenza A virus has gradually become an important research direction of many researchers. At present, the study of influenza A virus is mainly about its DNA,RNA and protein sequences. The changes of the sequences are studied from the aspects of biochemistry, biophysics and statistics, and the changing rules are found. This paper first introduces the variation and prevalence of influenza A virus recently. Taking its 10 constituent proteins as the research object, all the amino acid sequences of 10 components of influenza A virus from 1902 to 2013 were obtained in NCBI database. Big data programming analysis was carried out with MATLAB, combined with the detailed HP model, and based on the CGR-Walk model, all the protein sequences of influenza A virus were transformed into data form, and the time series ARFIMA model was introduced to fit all the digitized sequences. The variation trend of 10 kinds of protein sequences from 1902 to 2013 was analyzed, and the trend of development in the next 10 years was forecasted. Based on the study of amino acid sequence variation of influenza A virus protein, the spatial structure of influenza A H1N1 virus was studied by ab initio method. Based on the HP model of protein spatial structure, the 3DHP model of protein spatial structure of A H1N1 influenza virus is constructed, and the optimized structure with minimum free energy is found by using the optimized genetic algorithm. Thus the three-dimensional spatial structure of influenza A H1N1 virus protein was predicted. Then, given that the HP lattice model is too simple, the ability to make use of the tight contact pairs formed between amino acid residues in such a spherical structure is different according to the characteristic that the typical virus particles of A / H1N1 influenza virus are spherical. The 20 amino acids were divided into four classes and the HNXP three dimensional lattice model was obtained. The three-dimension structure of protein HNXP with minimal free energy was obtained by using the optimized genetic algorithm, and the structure of the model was compared with that of the real protein by sparse canonical correlation analysis. It has been tested that the two are highly similar in structure. In this paper, the three-dimensional structure of influenza A virus is predicted by the biological information contained among the 20 amino acids that make up its sequence, and the current research on the amino acid sequence of protein of influenza A virus is further expanded to three dimensions. The results can be used for prediction of amino acid sequence spatial structure of influenza A virus protein.
【学位授予单位】：江南大学
【学位级别】：硕士
【学位授予年份】：2014
【分类号】：R373;O175
本文编号：2203514
[Abstract]:Influenza A virus is one of the most prevalent viruses with the highest number of deaths in history. Each outbreak of influenza A is caused by the reappearance of new subtypes and previous subtypes of influenza viruses. Since the 20th century, there have been four large-scale pandemics of influenza viruses, each of which has caused great damage to human public health and socio-economic development. Therefore, the study of influenza A virus has gradually become an important research direction of many researchers. At present, the study of influenza A virus is mainly about its DNA,RNA and protein sequences. The changes of the sequences are studied from the aspects of biochemistry, biophysics and statistics, and the changing rules are found. This paper first introduces the variation and prevalence of influenza A virus recently. Taking its 10 constituent proteins as the research object, all the amino acid sequences of 10 components of influenza A virus from 1902 to 2013 were obtained in NCBI database. Big data programming analysis was carried out with MATLAB, combined with the detailed HP model, and based on the CGR-Walk model, all the protein sequences of influenza A virus were transformed into data form, and the time series ARFIMA model was introduced to fit all the digitized sequences. The variation trend of 10 kinds of protein sequences from 1902 to 2013 was analyzed, and the trend of development in the next 10 years was forecasted. Based on the study of amino acid sequence variation of influenza A virus protein, the spatial structure of influenza A H1N1 virus was studied by ab initio method. Based on the HP model of protein spatial structure, the 3DHP model of protein spatial structure of A H1N1 influenza virus is constructed, and the optimized structure with minimum free energy is found by using the optimized genetic algorithm. Thus the three-dimensional spatial structure of influenza A H1N1 virus protein was predicted. Then, given that the HP lattice model is too simple, the ability to make use of the tight contact pairs formed between amino acid residues in such a spherical structure is different according to the characteristic that the typical virus particles of A / H1N1 influenza virus are spherical. The 20 amino acids were divided into four classes and the HNXP three dimensional lattice model was obtained. The three-dimension structure of protein HNXP with minimal free energy was obtained by using the optimized genetic algorithm, and the structure of the model was compared with that of the real protein by sparse canonical correlation analysis. It has been tested that the two are highly similar in structure. In this paper, the three-dimensional structure of influenza A virus is predicted by the biological information contained among the 20 amino acids that make up its sequence, and the current research on the amino acid sequence of protein of influenza A virus is further expanded to three dimensions. The results can be used for prediction of amino acid sequence spatial structure of influenza A virus protein.
【学位授予单位】：江南大学
【学位级别】：硕士
【学位授予年份】：2014
【分类号】：R373;O175
【参考文献】
相关期刊论文 前3条
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2 王革非;李康生;;新世纪流感大流行的思考[J];生物化学与生物物理进展;2009年08期
3 张玲;高洁;;甲型H1N1流感病毒蛋白质序列的预测[J];生物技术;2012年06期
本文编号：2203514
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