Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain.
Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain.
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果蝇果蝇染色体对甲基化肽的识别。
DOI：
10.1021/pr3011205
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发表时间：
2013-03-01
影响因子：
4.4
通讯作者：
Wang W
中科院分区：
文献类型：
--
作者：
Stein RS;Li N;He W;Komives E;Wang W
赖氨酸甲基化是调节蛋白质功能的重要翻译后修饰（PTM）之一。目前，由于缺乏有效的富集方法，该PTM的蛋白质组学鉴定仍然是一个挑战。为了解决这一挑战，我们在这里提出了一个系统的方法来预测肽中赖氨酸残基可能被甲基化介导蛋白质-蛋白质相互作用。我们使用果蝇中的polycomb蛋白的染色体结构域作为模型系统来说明这种方法的成功。我们开始与分子动力学模拟和自由能分析的组蛋白肽复合的polycomb chromodomain了解如何实现的结合特异性。我们接下来进行虚拟诱变以量化每个结构域和肽残基对结构域-肽识别的贡献，基于此开发评分方案以评估任何含赖氨酸的肽被甲基化并被chromodomain识别的可能性。对一组保守组蛋白肽进行的肽微阵列实验表明，该评分方案具有令人满意的预测准确性。接下来，我们实施了一个生物信息学管道，该管道集成了多条证据线，包括保护，亚细胞定位和质谱数据，以扫描苍蝇蛋白质组，系统地识别可能的含甲基赖氨酸的肽。这些假定的染色体结合肽提示重要调节蛋白polycomb的未知功能，并为后续研究提供了候选甲基化事件的列表。
Lysine methylation is one of the important post-translational modifications (PTMs) that regulate protein functions. Up to now, proteomic identification of this PTM remains a challenge due to the lack of effective enrichment methods in mass spectrometry experiments. To address this challenge, we present here a systematic approach to predicting peptides in which lysine residues may be methylated to mediate protein–protein interactions. We used the chromodomain of the polycomb protein in Drosophila melanogaster as a model system to illustrate the success of this approach. We started with molecular dynamics simulations and free energy analyses on the histone peptides complexed with the polycomb chromodomain to understand how the binding specificity is achieved. We next conducted virtual mutagenesis to quantify each domain and peptide residue's contribution to the domain-peptide recognition, based on which scoring scheme was developed to evaluate the possibility of any lysine-containing peptides to be methylated and recognized by the chromodomain. A peptide microarray experiment on a panel of conserved histone peptides showed a satisfactory prediction accuracy of the scoring scheme. Next, we implemented a bioinformatics pipeline that integrates multiple lines of evidence including conservation, subcellular localization, and mass spectrometry data to scan the fly proteome for a systematic identification of possible methyllysine-containing peptides. These putative chromodomain-binding peptides suggest unknown functions of the important regulator protein polycomb and provide a list of candidate methylation events for follow-up investigations.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
10.5
作者：
Gdula, DA;Sandaltzopoulos, R;Wu, C
通讯作者：
Wu, C
影响因子：
2.9
作者：
Bas, Delphine C.;Rogers, David M.;Jensen, Jan H.
通讯作者：
Jensen, Jan H.
影响因子：
3
作者：
Duan, Y;Wu, C;Kollman, P
通讯作者：
Kollman, P
影响因子：
5.8
作者：
Craig, R;Beavis, RC
通讯作者：
Beavis, RC