Most processes of life are the result of polyvalent interactions between macromolecules, often of heterogeneous types and sizes. Frequently, the times associated with these interactions are prohibitively long for interrogation using atomistic simulations. Here, we study the recognition of N6-methylated adenine (m6A) in RNA by the reader domain YTHDC1, a prototypical, cognate pair that challenges simulations through its composition and required timescales. Simulations of RNA pentanucleotides in water reveal that the unbound state can impact (un)binding kinetics in a manner that is both model- and sequence-dependent. This is important because there are two contributions to the specificity of the recognition of the Gm6AC motif: from the sequence adjacent to the central adenine and from its methylation. Next, we establish a reductionist model consisting of an RNA trinucleotide binding to the isolated reader domain in high salt. An adaptive sampling protocol allows us to quantitatively study the dissociation of this complex. Through joint analysis of a data set including both the cognate and control sequences (GAC, Am6AA, and AAA), we derive that both contributions to specificity, sequence and methylation, are significant and in good agreement with experimental numbers. Analysis of the kinetics suggests that flexibility in both the RNA and the YTHDC1 recognition loop leads to many low-populated unbinding pathways. This multiple-pathway mechanism might be dominant for the binding of unstructured polymers, including RNA and peptides, to proteins when their association is driven by polyvalent, electrostatic interactions.

中文翻译：

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关于 YTH 阅读器结构域识别 m6A-RNA 的特异性。


大多数生命过程是大分子之间多价相互作用的结果，通常具有不同的类型和大小。通常，与这些交互相关的时间对于使用原子模拟进行询问的时间长得令人望而却步。在这里，我们研究了阅读器结构域 YTHDC1 对 RNA 中 N6-甲基化腺嘌呤 （m6A） 的识别，YTHDC1 是一个原型的同源对，通过其组成和所需的时间尺度挑战模拟。水中 RNA 五核苷酸的模拟表明，未结合状态可以以模型和序列依赖性的方式影响（解）结合动力学。这很重要，因为 Gm6AC 基序识别的特异性有两个贡献：来自中央腺嘌呤附近的序列和它的甲基化。接下来，我们建立了一个还原论模型，该模型由一个 RNA 三核苷酸与高盐中分离的读者结构域结合组成。自适应采样方案使我们能够定量研究该复合物的解离。通过对包括同源序列和对照序列 （GAC、Am6AA 和 AAA） 的数据集的联合分析，我们得出对特异性、序列和甲基化的贡献都是显着的，并且与实验数字非常一致。动力学分析表明，RNA 和 YTHDC1 识别环的灵活性导致许多低填充的未结合通路。当非结构化聚合物（包括 RNA 和肽）的结合由多价静电相互作用驱动时，这种多通路机制可能是与蛋白质结合的主要因素。