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Interactions of Potential Endocrine-Disrupting Chemicals with Whole Human Proteome Predicted by AlphaFold2 Using an In Silico Approach

生物信息学 计算生物学 生化工程 蛋白质组 人类蛋白质组计划 内分泌系统 化学 计算机科学 环境化学 生物 生物信息学 蛋白质组学 工程类 生物化学 激素 基因
作者
Fan Zhang,Yawen Tian,Yitao Pan,Nan Sheng,Jiayin Dai
出处
期刊:Environmental Science & Technology [American Chemical Society]
被引量:5
标识
DOI:10.1021/acs.est.4c03774
摘要

Binding with proteins is a critical molecular initiating event through which environmental pollutants exert toxic effects in humans. Previous studies have been limited by the availability of three-dimensional (3D) protein structures and have focused on only a small set of environmental contaminants. Using the highly accurate 3D protein structure predicted by AlphaFold2, this study explored over 60 million interactions obtained through molecular docking between 20,503 human proteins and 1251 potential endocrine-disrupting chemicals. A total of 66,613,773 docking results were obtained, 1.2% of which were considered to be high binding, as their docking scores were lower than -7. Monocyte to macrophage differentiation factor 2 (MMD2) was predicted to interact with the highest number of environmental pollutants (526), with polychlorinated biphenyls and polychlorinated dibenzofurans accounting for a significant proportion. Dimension reduction and clustering analysis revealed distinct protein profiles characterized by high binding affinities for perfluoroalkyl and polyfluoroalkyl substances (PFAS), phthalate-like chemicals, and other pollutants, consistent with their uniquely enriched pathways. Further structural analysis indicated that binding pockets with a high proportion of charged amino acid residues, relatively low α-helix content, and high β-sheet content were more likely to bind to PFAS than others. This study provides insights into the toxicity pathways of various pollutants impacting human health and offers novel perspectives for the establishment and expansion of adverse outcome pathway-based models.
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