Biochemical characterization of the epigenomic markers

组成蛋白质组的所有蛋白质可能比其基因组中的基因数量高出两到三个数量级。这一悖论，这在很大程度上是由于大量的翻译后修饰（PTM）沉积在蛋白质的主链和/或侧链，扩大了细胞机器的复杂性和微调生物途径，通过改变修饰的蛋白质的内在生化特性。此类修饰包括但不限于磷酸化、乙酰化、甲基化、泛素化和类小泛素化。信号的生物学后果将根据共价改变、潜在化学和将被修饰的残基的类型而变化。尽管蛋白质组学和基因组学工具的发展取得了很大进展，但连接乙酰基、甲基或磷酸基团的酶的生物化学和功能作用仍然难以捉摸。我的实验室采用X射线晶体学和稳态稳态动力学来表征共价修饰酶。我们的长期目标是阐明识别和修饰一个蛋白质家族的基本基础，这些蛋白质家族是DNA支架的核心，即组蛋白。组蛋白共价修饰对于控制DNA压缩以及由此的一系列细胞过程是至关重要的。作为所有真核生物的核心，确定引起组蛋白修饰的机制细节将提供一个工作模型来揭示由每个共价修饰控制的生物途径。在这个提议中，我们将阐明两个组蛋白甲基转移酶选择性地识别一个组蛋白尾部上的独特残基的机制，并确定这些蛋白质识别的共识基序。总的来说，我们的研究计划检索到的信息将1）提供组蛋白修饰酶的整体3D形状，2）阐明转录后修饰酶活性的核心驱动力的原子细节，3）确定赋予特定蛋白质底物特异性的酶的关键结合界面。

The repertoire of proteins that make up a proteome can be two to three orders of magnitude higher than the number of genes in its genome. This paradox, which is largely due to the myriad of posttranslational modifications (PTMs) deposited on protein backbones and/or side chains, expands the complexity of the cellular machinery and fine-tune biological pathways by altering the intrinsic biochemical properties of the modified proteins. Such modifications include, but are not restricted to, phosphorylation, acetylation, methylation, ubiquitinylation and sumoylation. The biological consequences of the signal will vary depending on the covalent alteration, the underlying chemistry and the type of residue that will be modified. Despite great progress in the development of proteomic and genomic tools, the biochemical and functional roles of enzymes that attach acetyl, methyl or phosphate groups have remained elusive. My laboratory employs X-ray crystallography and steady-steady-state kinetics to characterize covalent modifying enzymes. Our long-term goals are to elucidate the fundamental basis underlying the recognition and modification of a family of proteins that are central to DNA scaffolding, namely the histone proteins. Histone covalent modifications are critical for controlling DNA compaction and thereby a flurry of cellular processes. Being central to all eukaryotic organisms, determination of the mechanistic details eliciting histone modifications will provide a working model to uncover biological pathways controlled by each covalent modification. In this proposal, we will elucidate the mechanisms by which two histone methyltransferases selectively recognize unique residues on one histone tail and determine the consensus motifs recognized by these proteins. In a whole, the information retrieved by our research program will 1) provide the overall 3D-shape of histone modifying enzymes, 2) elucidate the atomic details of the driving forces central for the activity of post-transcriptional modifying enzymes and 3) determine the key binding interfaces of an enzyme conferring specificity for a given protein substrate.