Department of Genetics and Molecular Biology, Bioinformatics and Computational Biology Laboratory, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.
Computational Biophysics and Molecular Modeling Group, Scientific Computing Program (PROCC), Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil.
PLoS One. 2019 Apr 18;14(4):e0215508. doi: 10.1371/journal.pone.0215508. eCollection 2019.
Brain-derived neurotrophic factor (BDNF) plays an important role in neurogenesis and synapse formation. The V66M is the most prevalent BDNF mutation in humans and impairs the function and distribution of BDNF. This mutation is related to several psychiatric disorders. The pro-region of BDNF, particularly position 66 and its adjacent residues, are determinant for the intracellular sorting and activity-dependent secretion of BDNF. However, it has not yet been fully elucidated. The present study aims to analyze the effects of the V66M mutation on BDNF structure and function. Here, we applied nine algorithms, including SIFT and PolyPhen-2, for functional and stability prediction of the V66M mutation. The complete theoretical model of BNDF was generated by Rosetta and validated by PROCHECK, RAMPAGE, ProSa, QMEAN and Verify-3D algorithms. Structural alignment was performed using TM-align. Phylogenetic analysis was performed using the ConSurf server. Molecular dynamics (MD) simulations were performed and analyzed using the GROMACS 2018.2 package. The V66M mutation was predicted as deleterious by PolyPhen-2 and SIFT in addition to being predicted as destabilizing by I-Mutant. According to SNPeffect, the V66M mutation does not affect protein aggregation, amyloid propensity, and chaperone binding. The complete theoretical structure of BDNF proved to be a reliable model. Phylogenetic analysis indicated that the V66M mutation of BDNF occurs at a non-conserved position of the protein. MD analyses indicated that the V66M mutation does not affect the BDNF flexibility and surface-to-volume ratio, but affects the BDNF essential motions, hydrogen-bonding and secondary structure particularly at its pre and pro-domain, which are crucial for its activity and distribution. Thus, considering that these parameters are determinant for protein interactions and, consequently, protein function; the alterations observed throughout the MD analyses may be related to the functional impairment of BDNF upon V66M mutation, as well as its involvement in psychiatric disorders.
脑源性神经营养因子（BDNF）在神经发生和突触形成中发挥重要作用。V66M 是人类中最常见的 BDNF 突变，会损害 BDNF 的功能和分布。这种突变与几种精神疾病有关。BDNF 的前导区，特别是第 66 位及其相邻残基，是决定 BDNF 细胞内分拣和活性依赖分泌的决定因素。然而，这一点尚未得到充分阐明。本研究旨在分析 V66M 突变对 BDNF 结构和功能的影响。在这里，我们应用了包括 SIFT 和 PolyPhen-2 在内的 9 种算法，对 V66M 突变的功能和稳定性进行预测。通过 Rosetta 生成了 BNDF 的完整理论模型，并通过 PROCHECK、RAMPAGE、ProSa、QMEAN 和 Verify-3D 算法进行了验证。使用 TM-align 进行了结构比对。使用 ConSurf 服务器进行了系统发育分析。使用 GROMACS 2018.2 包进行了分子动力学（MD）模拟并进行了分析。除了被 I-Mutant 预测为不稳定外，PolyPhen-2 和 SIFT 还预测 V66M 突变是有害的。根据 SNPeffect，V66M 突变不会影响蛋白质聚集、淀粉样倾向和伴侣蛋白结合。BDNF 的完整理论结构被证明是一个可靠的模型。系统发育分析表明，BDNF 的 V66M 突变发生在蛋白质的非保守位置。MD 分析表明，V66M 突变不会影响 BDNF 的灵活性和表面积与体积比，但会影响 BDNF 的基本运动、氢键和二级结构，特别是在其前导区和前导区，这对其活性和分布至关重要。因此，考虑到这些参数决定了蛋白质相互作用，进而决定了蛋白质的功能；在 MD 分析中观察到的改变可能与 V66M 突变后 BDNF 的功能障碍以及其在精神疾病中的参与有关。
