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首页> 外文期刊>Journal of Molecular Biology >The recognition specificity of the CHD1 chromodomain with modified histone H3 peptides.
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The recognition specificity of the CHD1 chromodomain with modified histone H3 peptides.

机译：CHD1色域与修饰的组蛋白H3肽的识别特异性。

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摘要

Histone tail peptides comprise the flexible portion of chromatin, the substance which serves as the packaging for the eukaryotic genome. According to the histone code hypothesis, reader protein domains (chromodomains) can recognize modifications of amino acid residues within these peptides, regulating the expression of genes. We have performed simulations on models of chromodomain helicase DNA-binding protein 1 complexed with a variety of histone H3 modifications. Binding free energies for both the overall complexes and the individual residues within the protein and peptides were computed with molecular mechanics-generalized Born surface area. The simulation results agree well with experimental data and identify several chromodomain helicase DNA-binding protein 1 residues that play key roles in the interaction with each of the H3 modifications. We identified one class of protein residues that bind to H3 in all of the complexes (generally interacting hydrophobically), and a second class of residues that bind only to particular H3 modifications (generally interacting electrostatically). Additionally, we found that modifications of H3R2 and H3T3 have a dominant effect on the binding affinity; methylation of H3K4 has little effect on the interaction strength when H3R2 or H3T3 is modified. Our findings with regard to the specificity shown by the latter class of protein residues in their binding affinity to certain modifications of H3 support the histone code hypothesis.
机译：组蛋白尾部肽包含染色质的柔性部分，该部分充当真核基因组包装的物质。根据组蛋白密码假说，阅读器蛋白结构域（chromodomains）可以识别这些肽中氨基酸残基的修饰，从而调节基因的表达。我们已经对与多种组蛋白H3修饰复合的色域解旋酶DNA结合蛋白1模型进行了模拟。利用分子力学概括的Born表面积，计算蛋白质和肽中整体复合物以及各个残基的结合自由能。模拟结果与实验数据非常吻合，并鉴定了几个与每个H3修饰相互作用中起关键作用的色域解旋酶DNA结合蛋白1残基。我们鉴定出一类与所有复合物中的H3结合的蛋白质残基（通常通过疏水作用），以及第二类仅与特定的H3修饰结合的蛋白质残基（通常通过静电作用）。此外，我们发现H3R2和H3T3的修饰对结合亲和力起主要作用。修饰H3R2或H3T3时，H3K4的甲基化对相互作用强度的影响很小。关于后一类蛋白质残基对H3某些修饰的结合亲和力显示的特异性，我们的发现支持了组蛋白密码假说。

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