Computational analysis of missense variants in MMP2 gene linked with Winchester syndrome and Nodulosis-Arthropathy-Osteolysis reveals structural shift in protein-protein and protein-ligand complexes

IF 0.8 Q4 GENETICS & HEREDITY Meta Gene Pub Date : 2021-09-01 DOI:10.1016/j.mgene.2021.100931
Nithya Rangasamy , Nachimuthu Senthil Kumar , Santhy K.S.
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引用次数: 2

Abstract

Matrix metalloproteinases - 2 (MMP2) protein stimulates multiple processes involving the nervous system, vascularization, and metastasis. Mutations in MMP2 is linked to Winchester and Nodulosis-Arthropathy-Osteolysis (NAO) syndromes. In this extensive investigation, we performed a computational analysis of 114 missense Single Nucleotide Polymorphisms (SNPs) of MMP2 protein using various in-silico algorithms. A total of 21 highly deleterious and pathogenic missense SNPs (T86K, R146H, A167T, G216E, R252P, R252L D326V, D326Y, G346S, G367S, R368L, S396R, A408P, R482C, P517L, A522E, E525K, Y543C, Y552S, K579M, M598T) were identified that probably could alter the structural and functional configuration of MMP2 gene. Moreover, conservation analysis, protein stability, TM-score and RMSD calculation, protein structure prediction and superimposition, ligand binding site prediction, protein-protein interaction, protein-ligand, and protein-protein docking studies were carried out. ConSurf analysis showed seventeen missense variants in the highly conserved regions, which were predicted as highly deleterious and pathogenic by eight in-silico platforms. Furthermore, G367S and K579M showed a greater impact on stability, structural alterations, protein-ligand and protein-protein interactions. This study will help in developing target-dependent medication for diseases and could enhance the understanding of the significance of uncharacterized missense SNPs and their interrelation with the disease. This study also contemplates the computational perception into the high-risk missense SNPs on protein structural and functional configuration.

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计算分析与温彻斯特综合征和结节-关节病-骨溶解相关的MMP2基因错义变异揭示了蛋白质-蛋白质和蛋白质-配体复合物的结构变化
基质金属蛋白酶- 2 (MMP2)蛋白刺激神经系统、血管形成和转移等多个过程。MMP2突变与温彻斯特综合征和结节性关节病-骨溶解综合征(NAO)有关。在这项广泛的研究中,我们使用各种计算机算法对MMP2蛋白的114个错义单核苷酸多态性(SNPs)进行了计算分析。共鉴定出21个极具危害性和致病性的错义snp (T86K、R146H、A167T、G216E、R252P、R252L、D326V、D326Y、G346S、G367S、R368L、S396R、A408P、R482C、P517L、A522E、E525K、Y543C、Y552S、K579M、M598T),它们可能改变MMP2基因的结构和功能构型。此外,还进行了保守性分析、蛋白质稳定性、tm评分和RMSD计算、蛋白质结构预测和叠加、配体结合位点预测、蛋白质-蛋白质相互作用、蛋白质-配体和蛋白质-蛋白质对接研究。ConSurf分析显示,在高度保守区域有17个错义变异,8个芯片平台预测这些变异具有高度致病性和危害性。此外,G367S和K579M对稳定性、结构改变、蛋白质-配体和蛋白质-蛋白质相互作用的影响更大。这项研究将有助于开发靶向性药物治疗疾病,并可以增强对未表征的错义snp的重要性及其与疾病的相互关系的理解。本研究还考虑了对蛋白质结构和功能配置的高风险错义snp的计算感知。
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来源期刊
Meta Gene
Meta Gene Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
1.10
自引率
0.00%
发文量
20
期刊介绍: Meta Gene publishes meta-analysis, polymorphism and population study papers that are relevant to both human and non-human species. Examples include but are not limited to: (Relevant to human specimens): 1Meta-Analysis Papers - statistical reviews of the published literature of human genetic variation (typically linked to medical conditionals and/or congenital diseases) 2Genome Wide Association Studies (GWAS) - examination of large patient cohorts to identify common genetic factors that influence health and disease 3Human Genetics Papers - original studies describing new data on genetic variation in smaller patient populations 4Genetic Case Reports - short communications describing novel and in formative genetic mutations or chromosomal aberrations (e.g., probands) in very small demographic groups (e.g., family or unique ethnic group). (Relevant to non-human specimens): 1Small Genome Papers - Analysis of genetic variation in organelle genomes (e.g., mitochondrial DNA) 2Microbiota Papers - Analysis of microbiological variation through analysis of DNA sequencing in different biological environments 3Ecological Diversity Papers - Geographical distribution of genetic diversity of zoological or botanical species.
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