非天然n6取代对糖尿病人RNA m6A读取器YTH结构域m6A结合的系统分子分析

IF 3.3 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Yuting Li , Peng Tan , Qianpan Liu , Huaixin Sun , Yue Wang , Siyi Chen , Weixin Kong , Xiaoyi Sun , Xiang Shao
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引用次数: 0

摘要

RNA n6 -腺苷甲基化生成n6 -甲基腺苷(m6A)是真核生物转录组中最重要的转录后修饰事件之一,受甲基转移酶(写者)、识别蛋白(读者)和去甲基化酶(擦除者)的动态调控。人类有YTHDC1、YTHDC2、YTHDF1、YTHDF2和YTHDF3 5个m6A解读子,它们通过YT521-B同源结构域特异性识别并结合甲基化的RNA m6A残基,参与了糖尿病及其多种并发症如糖尿病肾病的发病。我们在此尝试探索各种非天然n6取代对腺苷(A)与YTH结构域结合行为的分子效应,而不是天然n6甲基化。通过计算建立了40个已报道的n6 -取代腺苷(x6A)单核苷酸与5个人类读卡器YTH结构域的系统相互作用谱。启发式聚类将这些YTH结构域和这些x6A单核苷酸分别划分为两个亚族和三个类;它们代表了结构域和单核苷酸之间不同的内在相互作用模式。统计调查表明,n6取代的化学基团的体积(Vg)和疏水性(Hg)分别与x6A单核苷酸与YTH结构域的结合能(ΔGttl)呈线性和非线性相关;中等大小和弱极性的n6取代有利于x6A的结合。n6 -溴甲基腺苷(brm6A)被鉴定为YTHDF2 YTH结构域的有效结合物;其亲和力较A显著提高77.2倍,较m6A显著提高19.5倍。结构建模观察到brm6A的n6 -溴甲基紧密包裹在由YTHDF2 YTH结构域Trp432-Trp486-Trp491三联体定义的芳香笼中。电子相关分析表明,溴原子可以与芳香笼形成几何上和能量上满意的卤素-π相互作用,从而赋予结构域- brm6a相互作用相当大的亲和力和特异性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Systematic molecular profiling of non-native N6-substitution effects on m6A binding to the YTH domains of human RNA m6A readers in diabetes

Systematic molecular profiling of non-native N6-substitution effects on m6A binding to the YTH domains of human RNA m6A readers in diabetes
The RNA N6-adenosine methylation, resulting in N6-methyl adenosine (m6A), is one of the most important post-transcriptional modification events in the eukaryotic transcriptome, which is dynamically regulated by methyltransferases (writers), recognition proteins (readers) and demethylases (erasers). Human has five m6A readers namely YTHDC1, YTHDC2, YTHDF1, YTHDF2 and YTHDF3 that specifically recognize and bind to the methylated m6A residue of RNA through their YT521-B homology (YTH) domains, which have been involved in the pathogenesis of diabetes mellitus and its diverse complications such as diabetic nephropathy. Instead of the native N6-methylation, we herein attempted to explore the molecular effect of various non-native N6-substitutions on adenosine (A) binding behavior to YTH domains. A systematic interaction profile of 40 reported N6-substituted adenosine (x6A) mononucleotides with 5 human reader YTH domains was created computationally. Heuristic clustering of the profile divided these YTH domains and these x6A mononucleotides into two subfamilies and three classes, respectively; they represent distinct intrinsic interaction modes between the domains and mononucleotides. Statistical survey unraveled that the volume (Vg) and hydrophobicity (Hg) of N6-substituted chemical groups exhibit linear and nonlinear correlations with the binding energy (ΔGttl) of x6A mononucleotides to YTH domains, respectively; N6-substitutions with moderate size and weak polarity are favorable for the x6A binding. From the profile the N6-bromomethyl adenosine (brm6A) was identified as a potent binder of YTHDF2 YTH domain; its affinity was improved significantly by 77.2-fold from A and considerably by 19.5-fold from m6A. Structural modeling observed that the N6-bromomethyl group of brm6A is tightly packed against an aromatic cage defined by the Trp432-Trp486-Trp491 triad of YTHDF2 YTH domain. Electron-correlation analysis revealed that the bromine atom can form geometrically and energetically satisfactory halogen-π interactions with the aromatic cage, thus conferring considerable affinity and specificity to the domain–brm6A interaction.
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来源期刊
Biophysical chemistry
Biophysical chemistry 生物-生化与分子生物学
CiteScore
6.10
自引率
10.50%
发文量
121
审稿时长
20 days
期刊介绍: Biophysical Chemistry publishes original work and reviews in the areas of chemistry and physics directly impacting biological phenomena. Quantitative analysis of the properties of biological macromolecules, biologically active molecules, macromolecular assemblies and cell components in terms of kinetics, thermodynamics, spatio-temporal organization, NMR and X-ray structural biology, as well as single-molecule detection represent a major focus of the journal. Theoretical and computational treatments of biomacromolecular systems, macromolecular interactions, regulatory control and systems biology are also of interest to the journal.
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