Hossain Md Mainuddin, Adhikari Juthi, Dutta Amit, Khandaker Afia, Islam Sirajul, Rahman Md Masuder, Shibly Abu Zaffar
Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh.
Department of Genetic Engineering and Biotechnology, Daffodil International University, Birulia, Savar, Dhaka, Bangladesh.
PLoS One. 2025 Sep 2;20(9):e0331339. doi: 10.1371/journal.pone.0331339. eCollection 2025.
Apolipoprotein E (ApoE) plays a critical role in Alzheimer's disease (AD) by regulating amyloid beta (Aβ) clearance through direct interaction. Non-synonymous single nucleotide polymorphisms (nsSNPs) in ApoE alter its structure and impair function, contributing to disease progression. This study aimed to identify functionally damaging nsSNPs in the ApoE gene using in silico tools and to assess their structural and binding effects on Aβ in the context of AD progression. A total of 376 nsSNPs were retrieved from dbSNP, ClinVar, and DisGeNET databases. Eight predictive tools (SIFT, PolyPhen-2, PredictSNP, PhD-SNP, PANTHER, PROVEAN, Meta-SNP, and SNAP2) were employed to identify deleterious variants. Protein stability was assessed using I-Mutant 2.0, MUpro, INPS-MD, iStable, and DynaMut2, while structural effects were evaluated via HOPE, MutPred2, Swiss-PDB Viewer, and Missense3D. Domain localization was determined using InterPro. Molecular docking was performed using PyRx and AutoDock Vina. Molecular dynamic simulation (MDS) evaluate binding stability and dynamics through 100-ns by Schrödinger Maestro, analyzing RMSD, RMSF, Rg, SASA. Out of 376 nsSNPs, 10 were consistently predicted as deleterious by all eight computational tools. Among these, two variants (L107P and L122P) were classified as high-risk and located within the receptor-binding domain of ApoE. The receptor-binding domain mediates the interaction between ApoE and Aβ. Molecular docking revealed binding affinities of -5.5 kcal/mol (WT), -5.6 kcal/mol (L107P), and -6.6 kcal/mol (L122P), indicating stronger Aβ binding by L122P. Stronger binding affinity of L122P mutation may promote Aβ aggregation or hinder clearance, potentially contributing to disease severity. MDS showed L122P had the highest structural stability, with the lowest RMSD, RMSF, Rg values and increased SASA, supporting its enhanced interaction with Aβ. These findings suggest that L122P mutation may enhance Aβ aggregation or hinder its clearance, potentially worsening AD and highlight the structural and functional impact of ApoE variants and the need for experimental validation.
载脂蛋白E（ApoE）通过直接相互作用调节β-淀粉样蛋白（Aβ）的清除，在阿尔茨海默病（AD）中起着关键作用。ApoE中的非同义单核苷酸多态性（nsSNPs）改变其结构并损害功能，促进疾病进展。本研究旨在使用计算机工具鉴定ApoE基因中具有功能损伤的nsSNPs，并在AD进展的背景下评估它们对Aβ的结构和结合效应。从dbSNP、ClinVar和DisGeNET数据库中总共检索到376个nsSNPs。使用八种预测工具（SIFT、PolyPhen-2、PredictSNP、PhD-SNP、PANTHER、PROVEAN、Meta-SNP和SNAP2）来鉴定有害变异。使用I-Mutant 2.0、MUpro、INPS-MD、iStable和DynaMut2评估蛋白质稳定性，同时通过HOPE、MutPred2、Swiss-PDB Viewer和Missense3D评估结构效应。使用InterPro确定结构域定位。使用PyRx和AutoDock Vina进行分子对接。通过Schrödinger Maestro进行100纳秒的分子动力学模拟（MDS）来评估结合稳定性和动力学，分析均方根偏差（RMSD）、均方根波动（RMSF）、回旋半径（Rg）、溶剂可及表面积（SASA）。在376个nsSNPs中，有10个被所有八种计算工具一致预测为有害。其中，两个变异（L107P和L122P）被归类为高风险，且位于ApoE的受体结合结构域内。受体结合结构域介导ApoE与Aβ之间的相互作用。分子对接显示结合亲和力分别为-5.5千卡/摩尔（野生型）、-5.6千卡/摩尔（L107P）和-6.6千卡/摩尔（L122P），表明L122P与Aβ的结合更强。L122P突变更强的结合亲和力可能促进Aβ聚集或阻碍其清除，可能导致疾病严重程度增加。MDS显示L122P具有最高的结构稳定性，RMSD、RMSF、Rg值最低且SASA增加，支持其与Aβ增强的相互作用。这些发现表明L122P突变可能增强Aβ聚集或阻碍其清除，可能使AD恶化，并突出了ApoE变异的结构和功能影响以及实验验证的必要性。
