Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.
PLoS One. 2020 Mar 2;15(3):e0229730. doi: 10.1371/journal.pone.0229730. eCollection 2020.
The tryptophan hydroxylase 2 (TPH2) enzyme catalyzes the first step of serotonin biosynthesis. Serotonin is known for its role in several homeostatic systems related to sleep, mood, and food intake. As the reaction catalyzed by TPH2 is the rate-limiting step of serotonin biosynthesis, mutations in TPH2 have been associated with several psychiatric disorders (PD). This work undertakes an in silico analysis of the effects of genetic mutations in the human TPH2 protein. Ten algorithms were used to predict the functional and stability effects of the TPH2 mutations. ConSurf was used to estimate the evolutionary conservation of TPH2 amino acids. GROMACS was used to perform molecular dynamics (MD) simulations of TPH2 WT and P260S, R303W, and R441H, which had already been associated with the development of PD. Forty-six TPH2 variants were compiled from the literature. Among the analyzed variants, those occurring at the catalytic domain were shown to be more damaging to protein structure and function. The ConSurf analysis indicated that the mutations affecting the catalytic domain were also more conserved throughout evolution. The variants S364K and S383F were predicted to be deleterious by all the functional algorithms used and occurred at conserved positions, suggesting that they might be deleterious. The MD analyses indicate that the mutations P206S, R303W, and R441H affect TPH2 flexibility and essential mobility at the catalytic and oligomerization domains. The variants P206S, R303W, and R441H also exhibited alterations in dimer binding affinity and stability throughout the simulations. Thus, these mutations may impair TPH2 functional interactions and, consequently, its function, leading to the development of PD. Furthermore, we developed a database, SNPMOL (http://www.snpmol.org/), containing the results presented in this paper. Understanding the effects of TPH2 mutations on protein structure and function may lead to improvements in existing treatments for PD and facilitate the design of further experiments.
色氨酸羟化酶 2（TPH2）酶催化 5-羟色胺生物合成的第一步。5-羟色胺以其在与睡眠、情绪和食物摄入有关的几个体内平衡系统中的作用而闻名。由于 TPH2 催化的反应是 5-羟色胺生物合成的限速步骤，因此 TPH2 中的突变与几种精神障碍（PD）有关。这项工作对人类 TPH2 蛋白中的遗传突变的影响进行了计算机分析。使用了十种算法来预测 TPH2 突变的功能和稳定性影响。ConSurf 用于估计 TPH2 氨基酸的进化保守性。GROMACS 用于对 TPH2 WT 和 P260S、R303W 和 R441H 进行分子动力学（MD）模拟，这些突变已经与 PD 的发展有关。从文献中编译了 46 种 TPH2 变体。在分析的变体中，那些发生在催化结构域的变体对蛋白质结构和功能的破坏性更大。ConSurf 分析表明，影响催化结构域的突变在整个进化过程中也更为保守。预测所有使用的功能算法都认为变体 S364K 和 S383F 是有害的，并且发生在保守位置，表明它们可能是有害的。MD 分析表明，突变 P206S、R303W 和 R441H 影响 TPH2 在催化和寡聚化结构域的灵活性和基本迁移率。在整个模拟过程中，突变 P206S、R303W 和 R441H 还表现出二聚体结合亲和力和稳定性的改变。因此，这些突变可能会损害 TPH2 的功能相互作用，从而导致 PD 的发展。此外，我们开发了一个数据库 SNPMOL（http://www.snpmol.org/），其中包含本文介绍的结果。了解 TPH2 突变对蛋白质结构和功能的影响可能会改善现有的 PD 治疗方法，并有助于进一步实验的设计。
