Art v 4 Protein Structure as a Representative Template for Allergen Profilins: Homology Modeling and Molecular Dynamics,ACS Omega

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Art v 4 Protein Structure as a Representative Template for Allergen Profilins: Homology Modeling and Molecular Dynamics
ACS Omega ( IF 3.7 ) Pub Date : 2018-12-13 00:00:00 , DOI: 10.1021/acsomega.8b02288
Haruna L. Barazorda-Ccahuana ₁ , Diego Ernesto Valencia ₁ , Jorge Alberto Aguilar-Pineda ₁ , Badhin Gómez ₁

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Profilins are panallergenic proteins of clinical relevance. We compared three groups of three-dimensional structures from six vegetable profilins. The first group was composed of crystal structures obtained by X-ray diffraction. The second and the third group structures were obtained by homology modeling; the selection criteria of the templates for these were based on the best resolution structure and the highest sequence identity, respectively. All of the structures underwent a 200 ns molecular dynamics simulation. The best template for the second group was Art v 4 and for the third group was the crystal structure corresponding to each profilin, except for Zea m 12. After molecular dynamics simulation, root-mean-square deviation, root-mean-square fluctuation, and radii of gyration values were similar in all groups, except for Amb a 8 (second group) and Zea m 12 (third group). All structures had acceptable conformation quality values, demonstrated in the Ramachandran plot and Z-score. The evaluation of epitopes did not have pertinent alterations of all of the structures. Art v 4 profilin was an acceptable template to model three-dimensional profilin structures of this work. The selection of templates based on their structural resolution and the measure of the quality is a good alternative to homology modeling of proteins of the same family.

中文翻译：

Art v 4蛋白质结构作为变应原Profilins的代表性模板：同源性建模和分子动力学

脯氨酸蛋白是具有临床意义的全变应原蛋白。我们比较了来自六个蔬菜蛋白的三组三维结构。第一组由通过X射线衍射获得的晶体结构组成。第二组和第三组结构通过同源性建模获得。这些模板的选择标准分别基于最佳分辨率结构和最高序列同一性。所有结构都进行了200 ns的分子动力学模拟。对于第二组，最好的模板是Art v 4，对于第三组，最好的模板是与每个profilin相对应的晶体结构，除了Zea m12。经过分子动力学模拟，均方根偏差，均方根波动，所有组的回转半径均相似，除了Amb a 8（第二组）和Zea m 12（第三组）。所有结构均具有可接受的构象质量值，如Ramachandran图和Z分数所示。表位的评估没有所有结构的相关改变。Art v 4 profilin是可以为这项工作的三维profilin结构建模的可接受模板。根据模板的结构分辨率和质量的衡量标准选择模板，可以很好地替代同一家族蛋白质的同源性建模。Art v 4 profilin是可以为这项工作的三维profilin结构建模的可接受模板。根据模板的结构分辨率和质量的衡量标准选择模板，可以很好地替代同一家族蛋白质的同源性建模。Art v 4 profilin是可以为这项工作的三维profilin结构建模的可接受模板。根据模板的结构分辨率和质量的衡量标准选择模板，可以很好地替代同一家族蛋白质的同源性建模。

更新日期：2018-12-13

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