Padarti Akhil, Belkin Ofek, Abou-Fadel Johnathan, Zhang Jun
Departments of Molecular & Translational Medicine (MTM), Texas Tech University Health Science Center El Paso (TTUHSCEP), El Paso, TX, 79905, USA.
Department of Neurology, University of South Alabama School of Medicine, 5795 USA N Dr., Mobile, AL, 36608, USA.
Biochem Biophys Rep. 2022 Jan 27;29:101218. doi: 10.1016/j.bbrep.2022.101218. eCollection 2022 Mar.
The objective of this study is to validate the existence of dual cores within the typical phosphotyrosine binding (PTB) domain and to identify potentially damaging and pathogenic nonsynonymous coding single nuclear polymorphisms (nsSNPs) in the canonical PTB domain of the CCM2 gene that causes cerebral cavernous malformations (CCMs).
The nsSNPs within the coding sequence for PTB domain of human CCM2 gene, retrieved from exclusive database searches, were analyzed for their functional and structural impact using a series of bioinformatic tools. The effects of mutations on the tertiary structure of the PTB domain in human CCM2 protein were predicted to examine the effect of nsSNPs on the tertiary structure of PTB Cores.
Our mutation analysis, through alignment of protein structures between wildtype CCM2 and mutant, predicted that the structural impacts of pathogenic nsSNPs is biophysically limited to only the spatially adjacent substituted amino acid site with minimal structural influence on the adjacent core of the PTB domain, suggesting both cores are independently functional and essential for proper CCM2 PTB function.
Utilizing a combination of protein conservation and structure-based analysis, we analyzed the structural effects of inherited pathogenic mutations within the CCM2 PTB domain. Our results predicted that the pathogenic amino acid substitutions lead to only subtle changes locally, confined to the surrounding tertiary structure of the PTB core within which it resides, while no structural disturbance to the neighboring PTB core was observed, reaffirming the presence of independently functional dual cores in the CCM2 typical PTB domain.
本研究的目的是验证典型的磷酸酪氨酸结合（PTB）结构域内双核的存在，并鉴定导致脑海绵状血管畸形（CCM）的CCM2基因的典型PTB结构域中潜在的有害和致病性非同义编码单核苷酸多态性（nsSNP）。
从独家数据库搜索中检索出人类CCM2基因PTB结构域编码序列内的nsSNP，使用一系列生物信息学工具分析它们对功能和结构的影响。预测突变对人类CCM2蛋白PTB结构域三级结构的影响，以检查nsSNP对PTB核心三级结构的影响。
我们通过野生型CCM2和突变体之间的蛋白质结构比对进行的突变分析预测，致病性nsSNP的结构影响在生物物理上仅局限于空间上相邻的取代氨基酸位点，对PTB结构域的相邻核心结构影响最小，这表明两个核心都是独立发挥功能的，并且对于CCM2 PTB的正常功能至关重要。
利用蛋白质保守性和基于结构的分析相结合的方法，我们分析了CCM2 PTB结构域内遗传性致病突变的结构效应。我们的结果预测，致病性氨基酸取代仅导致局部细微变化，局限于其所在的PTB核心周围的三级结构，而未观察到对相邻PTB核心的结构干扰，再次证实了CCM2典型PTB结构域中存在独立发挥功能的双核。
