Krebs Bruna Baumgarten, De Mesquita Joelma Freire
Laboratory of Bioinformatics and Computational Biology, Department of Genetics and Molecular Biology, Federal University of Rio de Janeiro State (UNIRIO), Rio de Janeiro, Brazil.
PLoS One. 2016 Jul 14;11(7):e0158939. doi: 10.1371/journal.pone.0158939. eCollection 2016.
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects the upper and lower motor neurons. 5-10% of cases are genetically inherited, including ALS type 20, which is caused by mutations in the hnRNPA1 gene. The goals of this work are to analyze the effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on hnRNPA1 protein function, to model the complete tridimensional structure of the protein using computational methods and to assess structural and functional differences between the wild type and its variants through Molecular Dynamics simulations. nsSNP, PhD-SNP, Polyphen2, SIFT, SNAP, SNPs&GO, SNPeffect and PROVEAN were used to predict the functional effects of nsSNPs. Ab initio modeling of hnRNPA1 was made using Rosetta and refined using KoBaMIN. The structure was validated by PROCHECK, Rampage, ERRAT, Verify3D, ProSA and Qmean. TM-align was used for the structural alignment. FoldIndex, DICHOT, ELM, D2P2, Disopred and DisEMBL were used to predict disordered regions within the protein. Amino acid conservation analysis was assessed by Consurf, and the molecular dynamics simulations were performed using GROMACS. Mutations D314V and D314N were predicted to increase amyloid propensity, and predicted as deleterious by at least three algorithms, while mutation N73S was predicted as neutral by all the algorithms. D314N and D314V occur in a highly conserved amino acid. The Molecular Dynamics results indicate that all mutations increase protein stability when compared to the wild type. Mutants D314N and N319S showed higher overall dimensions and accessible surface when compared to the wild type. The flexibility level of the C-terminal residues of hnRNPA1 is affected by all mutations, which may affect protein function, especially regarding the protein ability to interact with other proteins.
肌萎缩侧索硬化症（ALS）是一种致命的神经退行性疾病，会影响上下运动神经元。5%-10%的病例是遗传继承的，包括20型ALS，它由hnRNPA1基因突变引起。这项工作的目标是分析非同义单核苷酸多态性（nsSNP）对hnRNPA1蛋白功能的影响，使用计算方法对该蛋白的完整三维结构进行建模，并通过分子动力学模拟评估野生型及其变体之间的结构和功能差异。使用nsSNP、PhD-SNP、Polyphen2、SIFT、SNAP、SNPs&GO、SNPeffect和PROVEAN来预测nsSNP的功能影响。使用Rosetta对hnRNPA1进行从头建模，并使用KoBaMIN进行优化。通过PROCHECK、Rampage、ERRAT、Verify3D、ProSA和Qmean对结构进行验证。使用TM-align进行结构比对。使用FoldIndex、DICHOT、ELM、D2P2、Disopred和DisEMBL来预测蛋白内的无序区域。通过Consurf评估氨基酸保守性分析，并使用GROMACS进行分子动力学模拟。预测突变D314V和D314N会增加淀粉样蛋白倾向，并且至少被三种算法预测为有害，而突变N73S被所有算法预测为中性。D314N和D314V发生在一个高度保守的氨基酸中。分子动力学结果表明，与野生型相比，所有突变均增加了蛋白稳定性。与野生型相比，突变体D314N和N319S显示出更大的整体尺寸和可及表面积。hnRNPA1 C末端残基的灵活性水平受到所有突变的影响，这可能会影响蛋白功能，特别是在蛋白与其他蛋白相互作用的能力方面。
