Bioinformatics Analysis and Homology Modeling Study of Protein Disulfide Isomerase(mPDI) from Medicago sativa L.  

紫花苜蓿蛋白质二硫键异构酶mPDI的生物信息学分析与同源建模研究(英文)

作　　者：王海波[1] 施晓东[1] 张梅芬[1] 郭俊云[1] 

机构地区：[1]曲靖师范学院生物资源与环境科学学院,云南曲靖655011

出　　处：《Agricultural Science & Technology》2009年第5期59-64,共6页农业科学与技术（英文版）

摘　　要：pdi gene from Medicago sativa L. ,encoding Protein Disulfide Isomerase（ mPDI ）, has been cloned and sequenced. According to the mRNA and amino acid sequence, the character of mPDI such as the physical and chemical properties, hydrophilicity/hydrophobicity, signal peptide, secondary structure, coiled coil, transmembrane domains, O-glycogylation site, active site, subcellular localization, functional structural domains and three-dimensional structure were analyzed by a series of bioinformatics software. The results showed that mPDI was a hydrophobic and stable protein with 3 coiled coils, 30-glycogylation sites, 2 structural domains of thioredoxin, 2 active sites of thioredoxin, and located in rough endoplasmic reticulum. It has 512 amino acids, the theoretical pl is 4.98, and signal peptide located in 1-24AA. In the secondary structure, a-helix, random coil, extended chain is 26.37%, 53.32%, 20.31% respectively. The validation of modeling accords with the stereochemistry.利用紫花苜蓿蛋白质二硫键异构酶(mPDI)的mRNA(来自NCBI,登录号为Z11499.1)及氨基酸序列(来自UniProtKB/Swiss-Prot数据库及NCBI数据库,其登录号分别为P29828、CAA77575.1),应用生物信息学软件预测了该蛋白质的理化性质、亲疏水性、信号肽、二级结构、卷曲螺旋结构、跨膜区域、糖基化位点、活性位点、亚细胞定位、功能结构域及高级结构。结果表明:紫花苜蓿mPDI蛋白质是一个整体疏水性蛋白,细胞定位为粗面内质网,含有512个氨基酸,理论等电点为4.98,分子量为57087.4Da,原子组成为C2597H3977N651O786S6,摩尔消光系数在280nm处为37610,不稳定系数为40.12,脂肪系数为79.96,总平均亲水性为-0.357。该蛋白质由20种氨基酸组成,其中非极性R基团氨基酸占44.3%,极性R基团氨基酸占28.4%,酸性氨基酸占13.6%,碱性氨基酸占13.1%,Lys、Glu、Val、Ala含量最为丰富,Met和Cys含量最少。信号肽位于1～24号氨基酸。利用ProtScale软件的KyteandDoolittle算法对mPDI蛋白进行亲/疏水性预测,结果表明该蛋白质含有7个高疏水性区域,分别分布在40～50区域、95～105区域、120～130区域、190～200区域、285～295区域、340～350区域以及365～375区域。利用SignalP网络工具对mPDI蛋白进行信号肽的预测,神经网络法显示第24～25位点是最可能的剪切点,马可夫模型显示了同样的信号肽酶切位点。mPDI蛋白质二级结构中α-螺旋占26.37%(135AA)、无规则卷曲占53.32%(273AA)、延伸链占20.31%(104AA);包含3个卷曲螺旋结构、3个糖基化位点(分别为143位的S、148位的T、461位的S)、2个硫氧还蛋白结构域(14～144位、357～485位)、2个硫氧还蛋白活性位点(54～72位、399～417位)、1个内质网靶向序列(509～512位);Ramachandram结构检测表明此模型的三维结构符合立体化学能量规则。

关 键 词：Medicago sativa L. Protein disulfide isomerase Homology modeling 

分 类 号：S541.9[农业科学—作物学]