Disprot无序蛋白数据库分析与统计
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摘要
无序蛋白是一种在天然条件下没有稳定的三维结构但却能正常行使重要生物学功能的一类蛋白质.实验以Disport无序蛋白数据库为基础,经过CD-HIT去重处理建立数据集.分别选择20种氨基酸在无序区与有序区中的分布和无序倾向性两个方面对该数据集进行对比分析.结果表明,氨基酸Ala、Asp、Glu、Gly、Lys、Pro、Gln、Ser具有形成无序区的倾向.氨基酸Leu、Thr、Val虽然在无序区和有序区中都具有倾向性,但在由DP值得到的分析中,Leu、Thr、Val不易于形成无序区;氨基酸Gln虽然在无序区和有序区中都不具有倾向性,但在DP值分析中却易于形成无序区.氨基酸Ala、Glu、Ser在二元组氨基酸对中使用最频繁.
Intrinsically disordered protein is a type of protein that does not have a stable three-dimensional structure under natural conditions but can perform properly important biological functions.The experiment was based on the Disport database and was subjected to CD-HIT de-duplication to establish the dataset.This dataset was compared and analyzed in two aspects:the distribution of 20 kinds of amino acids in the disordered and ordered regions,and the disordered tendencies.The results showed that the amino acids Ala,Asp,Glu,Gly,Lys,Pro,Gln and Ser had a tendency to form a disordered region.The amino acids Leu,Thr,and Val have the tendency of disordered and ordered regions,but Leu,Thr and Val are not prone to form disordered regions in the analysis of DPvalues;The amino acid Gln,although showing no tendency to disordered and ordered regions,tends to form an disordered region in the analysis of DPvalues.The amino acids Ala,Glu and Ser are the most frequently used in pairs of amino acid pairs.
Intrinsically disordered protein is a type of protein that does not have a stable three-dimensional structure under natural conditions but can perform properly important biological functions.The experiment was based on the Disport database and was subjected to CD-HIT de-duplication to establish the dataset.This dataset was compared and analyzed in two aspects:the distribution of 20 kinds of amino acids in the disordered and ordered regions,and the disordered tendencies.The results showed that the amino acids Ala,Asp,Glu,Gly,Lys,Pro,Gln and Ser had a tendency to form a disordered region.The amino acids Leu,Thr,and Val have the tendency of disordered and ordered regions,but Leu,Thr and Val are not prone to form disordered regions in the analysis of DPvalues;The amino acid Gln,although showing no tendency to disordered and ordered regions,tends to form an disordered region in the analysis of DPvalues.The amino acids Ala,Glu and Ser are the most frequently used in pairs of amino acid pairs.
引文
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[12]VAN D L R,BULJAN M,LANG B,et al.Classification of intrinsically disordered regions and proteins[J].Chemical reviews,2014,114(13):6 589-6 631.
[2]WRIGHT P E,DYSON H J.Intrinsically disordered proteins in cellular signalling and regulation[J].Nature Reviews Molecular Cell Biology,2015,16(1):18-29.
[3]GIBBS E B,SHOWALTER S A.Quantitative biophysical characterization of intrinsically disordered proteins[J].Biochemistry,2015,54(6):1 314-1 326.
[4]田攀,连继勤.无序蛋白[J].生命的化学,2009(2):279-282.
[5]武恩斯.基于序列多位点特征挖掘的固有无序蛋白预测[D].济南:山东师范大学,2015.
[6]UVERSKY V N,OLDFIELD C J,DUNKER A K.Intrinsically disordered proteins in human diseases:introducing the D2concept[J].Annu.Rev.Biophys.,2008,37:215-246.
[7]ROMERO P,OBRADOVIC Z,KISSINGER C,et al.Identifying disordered regions in proteins from amino acid sequence[C]//International Conference on Neural Networks.IEEE,1997,1:90-95.
[8]SRIVASTAVA N,HINTON G E,KRIZHEVSKY A,et al.Dropout:a simple way to prevent neural networks from overfitting[J].Journal of machine learning research,2014,15(1):1 929-1 958.
[9]PIOVESAN D,TABARO F,MI CˇETI C'I,et al.DisProt 7.0:a major update of the database of disordered proteins[J].Nucleic acids research,2017,45(D1):D219-D227.
[10]FU L,NIU B,ZHU Z,et al.CD-HIT:accelerated for clustering the next-generation sequencing data[J].Bioinformatics,2012,28(23):3 150-3 152.
[11]董川,曹赞霞,赵立岭,等.固有无序蛋白与蛋白质相互作用位点残基特征分析[J].生物化学与生物物理进展,2014(5):462-471.
[12]VAN D L R,BULJAN M,LANG B,et al.Classification of intrinsically disordered regions and proteins[J].Chemical reviews,2014,114(13):6 589-6 631.