PROTEOME-WIDE PREDICTION OF ACETYLATION SUBSTRATES

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 乙酰化是一种被广泛研究的翻译后修饰，与广泛的生物学过程有关，特别是基因调控。许多研究有助于我们了解乙酰化的酶学基础，包括努力了解几种乙酰基转移酶识别底物的分子机制，但传统的实验已经被证明是具有挑战性的，以确定底物位置特异性的内在特征。在这里，我们将实验方法与蛋白质序列的聚类分析相结合，利用我们独特的预测工具PredMod，基于组蛋白中乙酰化赖氨酸的序列特征来预测蛋白质乙酰化。我们通过对组蛋白和非组蛋白序列进行聚类分析，定义了一个局部氨基酸序列组成，它代表了潜在的乙酰化位点。我们表明，该序列组成对两个独立的乙酰化标记实验数据集具有预测能力。最后，我们用质谱仪检测了选定的假定底物的乙酰化，并报道了几种在发芽酵母中的非组蛋白乙酰化底物。我们的方法，结合更传统的实验方法，可能有助于在蛋白质组范围内识别乙酰化底物。一篇描述这些结果的论文已经发表： 蛋白质组对乙酰化底物的预测 巴苏A，罗克伦，张锦明，等. PNAS106(2009年)13785-13790

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Acetylation is a well-studied posttranslational modification that has been associated with a broad spectrum of biological processes, notably gene regulation. Many studies have contributed to our knowledge of the enzymology underlying acetylation, including efforts to understand the molecular mechanism of substrate recognition by several acetyltransferases, but traditional experiments to determine intrinsic features of substrate site specificity have proven challenging. Here, we combine experimental methods with clustering analysis of protein sequences to predict protein acetylation based on the sequence characteristics of acetylated lysines within histones with our unique prediction tool PredMod. We define a local amino acid sequence composition that represents potential acetylation sites by implementing a clustering analysis of histone and nonhistone sequences. We show that this sequence composition has predictive power on 2 independent experimental datasets of acetylation marks. Finally, we detect acetylation for selected putative substrates using mass spectrometry, and report several nonhistone acetylated substrates in budding yeast. Our approach, combined with more traditional experimental methods, may be useful for identifying acetylated substrates proteome-wide. A paper describing these results has been published: Proteome-wide prediction of acetylation substrates Basu A, Rose KL, Zhang JM, et al. PNAS 106 (2009) 13785-13790