Figueiredo Danieli Forgiarini, Antunes Dinler A, Rigo Maurício M, Mendes Marcus F A, Silva Jader P, Mayer Fabiana Q, Matte Ursula, Giugliani Roberto, Vieira Gustavo F, Sinigaglia Marialva
NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
NBLI - Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
J Mol Graph Model. 2014 Nov;54:107-13. doi: 10.1016/j.jmgm.2014.10.004. Epub 2014 Oct 18.
Human α-L-iduronidase (IDUA) is a member of glycoside hydrolase family and is involved in the catabolism of glycosaminoglycans (GAGs), heparan sulfate (HS) and dermatan sulfate (DS). Mutations in this enzyme are responsible for mucopolysaccharidosis I (MPS I), an inherited lysosomal storage disorder. Despite great interest in determining and studying this enzyme structure, the lack of a high identity to templates and other technical issues have challenged both bioinformaticians and crystallographers, until the recent publication of an IDUA crystal structure (PDB: 4JXP). In the present work, four alternative IDUA models, generated and evaluated prior to crystallographic determination, were compared to the 4JXP structure. A combined analysis using several viability assessment tools and molecular dynamics simulations highlights the strengths and limitations of different comparative modeling protocols, all of which are based on the same low identity template (only 22%). Incorrect alignment between the target and template was confirmed to be a major bottleneck in homology modeling, regardless of the modeling software used. Moreover, secondary structure analysis during a 50ns simulation seems to be useful for indicating alignment errors and structural instabilities. The best model was achieved through the combined use of Phyre 2 and Modeller, suggesting the use of this protocol for the modeling of other proteins that still lack high identity templates.
人α-L-艾杜糖醛酸酶（IDUA）是糖苷水解酶家族的成员，参与糖胺聚糖（GAGs）、硫酸乙酰肝素（HS）和硫酸皮肤素（DS）的分解代谢。该酶的突变是导致黏多糖贮积症I型（MPS I）的原因，这是一种遗传性溶酶体贮积病。尽管人们对确定和研究这种酶的结构非常感兴趣，但由于与模板的同源性低以及其他技术问题，给生物信息学家和晶体学家都带来了挑战，直到最近IDUA晶体结构（PDB：4JXP）的发表。在本研究中，将在晶体学测定之前生成和评估的四种IDUA替代模型与4JXP结构进行了比较。使用多种可行性评估工具和分子动力学模拟的综合分析突出了不同比较建模方案的优点和局限性，所有这些方案均基于相同的低同源性模板（仅22%）。无论使用何种建模软件，目标序列与模板之间的错误比对都被证实是同源建模中的主要瓶颈。此外，在50纳秒模拟过程中的二级结构分析似乎有助于指示比对错误和结构不稳定性。通过联合使用Phyre 2和Modeller获得了最佳模型，这表明该方案可用于对仍缺乏高同源性模板的其他蛋白质进行建模。
