Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil.
J Cell Biochem. 2019 Mar;120(3):3583-3598. doi: 10.1002/jcb.27636. Epub 2018 Sep 11.
Oxidative stress is a major factor in aging processes. Superoxide dismutase 3 (SOD3) plays a key role in the protection of extracellular oxidative stress. Missense mutations in SOD3 have been described to be associated with the occurrence of pulmonary, cardiovascular, and neoplastic diseases. This study aims to analyze the effects of missense mutations on the SOD3 structure and function by modeling a complete SOD3 structure as well as analyzing the differences between the wild-types and mutants using computational simulations. Here, ten algorithms were used to predict the structural and functional effects of missense mutations. A complete model of SOD3 protein was made by ab initio and comparative modeling using the Rosetta algorithm and validated by PROCHECK, Verify 3D, QMEAN, and ProSa. Molecular dynamics (MD) simulations were performed and analyzed using the GROMACS package. The deleterious potential of the A58T and R231G mutants was not predicted by the majority of the used algorithms. The analyzed mutations were predicted as destabilizing by at least one algorithm. The MD analyses indicated that protein flexibility may be increased by all of the analyzed mutations, while the protein-ligand stability may be decreased. They also suggested that the variants A91T and R231G increase the overall dimensions of SOD3 and decrease its accessible surface area. Our findings, therefore, indicated that the analyzed mutations could affect the protein structure and its ability to interact with other molecules, which may be related to the functional impairment of SOD3 upon A58T and R231G mutations, as well as their involvement in pathologies.
氧化应激是衰老过程中的一个主要因素。超氧化物歧化酶 3（SOD3）在保护细胞外氧化应激方面起着关键作用。已经描述过 SOD3 的错义突变与肺部、心血管和肿瘤疾病的发生有关。本研究旨在通过构建完整的 SOD3 结构，并通过计算模拟分析野生型和突变体之间的差异，来分析错义突变对 SOD3 结构和功能的影响。在这里，使用了十种算法来预测错义突变对 SOD3 结构和功能的影响。使用 Rosetta 算法通过从头计算和比较建模构建了完整的 SOD3 蛋白模型，并通过 PROCHECK、Verify 3D、QMEAN 和 ProSa 进行了验证。使用 GROMACS 包进行了分子动力学（MD）模拟并进行了分析。大多数使用的算法都没有预测 A58T 和 R231G 突变的有害潜力。至少有一种算法预测分析的突变是不稳定的。MD 分析表明，所有分析的突变都可能增加蛋白质的灵活性，而降低蛋白质-配体的稳定性。它们还表明，变体 A91T 和 R231G 增加了 SOD3 的整体尺寸，并降低了其可及表面积。因此，我们的研究结果表明，分析的突变可能会影响蛋白质的结构及其与其他分子相互作用的能力，这可能与 A58T 和 R231G 突变导致 SOD3 功能受损以及它们与病理学的关系有关。
