水牛妊娠相关糖蛋白-1的结构建模与分析。

ISRN molecular biology Pub Date : 2012-03-12 eCollection Date: 2012-01-01 DOI:10.5402/2012/481539
Jerome Andonissamy, S K Singh, S K Agarwal
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引用次数: 4

摘要

本研究采用生物信息学方法对水牛妊娠相关糖蛋白-1 (PAG-1)的结构模型进行了设计和分析。利用PHYRE、CONSURF服务器对推断的buffalo PAG-1蛋白进行结构建模,随后使用modeleller 9.9和PyMOL软件构建其结构,并使用PROSA、WHATIF和3D-PSSM服务器分析buffalo PAG-1的结构一致性。通过BLAST分析设计水牛PAG-1蛋白结构,检索到属于天冬氨酸蛋白酶家族的蛋白结构。此外,利用PatchDock服务器与胃抑素A进行对接研究,结果显示水牛PAG-1蛋白在活性位点附近保留双叶状结构,并存在胃抑素结合裂缝。结构研究表明,含有天冬氨酸残基的氨基端和羧基端是高度保守的,并埋藏在蛋白质结构中。构造整合研究表明,90%以上的残基位于有利区和允许区。水牛PAG-1具有低能区和高能区,具有很低的蛋白水解阈值,确定了水牛PAG-1蛋白结构的稳定性。本研究描述了水牛PAG-1蛋白的结构一致性和稳定性。
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Structural Modeling and Analysis of Pregnancy-Associated Glycoprotein-1 of Buffalo (Bubalus bubalis).
The present study was conducted to design and analyze the structural model of buffalo pregnancy-associated glycoprotein-1 (PAG-1) using bioinformatics. Structural modeling of the deduced buffalo PAG-1 protein was done using PHYRE, CONSURF servers and its structure was subsequently constructed using MODELLER 9.9 and PyMOL softwares Buffalo PAG-1 structural conformity was analyzed using PROSA, WHATIF, and 3D-PSSM servers. Designed buffalo PAG-1 protein structure on BLAST analysis retrieved protein structures belonging to aspartic proteinase family. Moreover in silico analysis revealed buffalo PAG-1 protein retained bilobed structure with pepstatin-binding clefts near the active sites by docking studies with pepstatin A using PatchDock server. Structural studies revealed that the amino and carboxy terminal containing aspartic residues are highly conserved and buried within the protein structure. Structural conformity studies showed that more than 90% of the residues lie inside favored and allowed regions. It was also deduced that buffalo PAG-1 possesses low and high energy zones with a very low threshold for proteolysis ascertaining the stableness of the buffalo PAG-1 protein structure. This study depicts the structural conformity and stability of buffalo PAG-1 protein.
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