Panoramic Perspective on Human Phosphosites

Protein
phosphorylation is the most common reversible post-translational
modification of proteins and is key in the regulation of many cellular
processes. Due to this importance, phosphorylation is extensively
studied, resulting in the availability of a large amount of mass spectrometry-based
phospho-proteomics data. Here, we leverage the information in these
large-scale phospho-proteomics data sets, as contained in Scop3P,
to analyze and characterize proteome-wide protein phosphorylation
sites (P-sites). First, we set out to differentiate correctly observed
P-sites from false-positive sites using five complementary site properties.
We then describe the context of these P-sites in terms of the protein
structure, solvent accessibility, structural transitions and disorder,
and biophysical properties. We also investigate the relative prevalence
of disease-linked mutations on and around P-sites. Moreover, we assess
the structural dynamics of P-sites in their phosphorylated and unphosphorylated
states. As a result, we show how large-scale reprocessing of available
proteomics experiments can enable a more reliable view on proteome-wide
P-sites. Furthermore, adding the structural context of proteins around
P-sites helps uncover possible conformational switches upon phosphorylation.
Moreover, by placing sites in different biophysical contexts, we show
the differential preference in protein dynamics at phosphorylated
sites when compared to the nonphosphorylated counterparts.

蛋白质磷酸化是最为常见的蛋白质可逆翻译后修饰类型，在众多细胞进程的调控中扮演核心角色。鉴于其生物学重要性，磷酸化靶点被广泛研究，由此产生了海量基于质谱的磷酸化蛋白质组学数据。
本研究依托Scop3P数据库收录的大规模磷酸化蛋白质组学数据集信息，对全蛋白质组范围内的蛋白质磷酸化位点（P-sites）开展分析与表征。首先，我们拟通过五种互补的位点特征，将真实观测到的P-sites与假阳性位点加以区分。随后，我们从蛋白质结构、溶剂可及性、结构转变与无序性，以及生物物理特性等维度，阐明这些P-sites的所处环境。此外，我们探究了磷酸化位点及其周边区域与疾病相关突变的相对分布频率。更进一步，我们评估了P-sites在磷酸化与非磷酸化状态下的结构动力学特征。
研究结果显示，对现有蛋白质组学实验进行大规模重新处理，能够为全蛋白质组P-sites提供更为可靠的认知视角。此外，添加磷酸化位点周边蛋白质的结构上下文信息，有助于揭示磷酸化诱导的潜在构象转换。再者，通过将位点划分至不同生物物理环境中，我们证实了相较于非磷酸化对应位点，磷酸化位点在蛋白质动力学上存在显著的差异化偏好。