Kitchen James, Saunders Rebecca E, Warwicker Jim
Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
BMC Struct Biol. 2008 Mar 25;8:19. doi: 10.1186/1472-6807-8-19.
Phosphorylation is a central feature in many biological processes. Structural analyses have identified the importance of charge-charge interactions, for example mediating phosphorylation-driven allosteric change and protein binding to phosphopeptides. Here, we examine computationally the prevalence of charge stabilisation around phosphorylated sites in the structural database, through comparison with locations that are not phosphorylated in the same structures.
A significant fraction of phosphorylated sites appear to be electrostatically stabilised, largely through interaction with sidechains. Some examples of stabilisation across a subunit interface are evident from calculations with biological units. When considering the immediately surrounding environment, in many cases favourable interactions are only apparent after conformational change that accompanies phosphorylation. A simple calculation of potential interactions at longer-range, applied to non-phosphorylated structures, recovers the separation exhibited by phosphorylated structures. In a study of sites in the Phospho.ELM dataset, for which structural annotation is provided by non-phosphorylated proteins, there is little separation of the known phospho-acceptor sites relative to background, even using the wider interaction radius. However, there are differences in the distributions of patch polarity for acceptor and background sites in the Phospho.ELM dataset.
In this study, an easy to implement procedure is developed that could contribute to the identification of phospho-acceptor sites associated with charge-charge interactions and conformational change. Since the method gives information about potential anchoring interactions subsequent to phosphorylation, it could be combined with simulations that probe conformational change. Our analysis of the Phospho.ELM dataset also shows evidence for mediation of phosphorylation effects through (i) conformational change associated with making a solvent inaccessible phospho-acceptor site accessible, and (ii) modulation of protein-protein interactions.
磷酸化是许多生物过程的核心特征。结构分析已确定了电荷-电荷相互作用的重要性，例如介导磷酸化驱动的变构变化以及蛋白质与磷酸肽的结合。在此，我们通过与同一结构中未磷酸化的位置进行比较，对结构数据库中磷酸化位点周围电荷稳定化的普遍性进行了计算研究。
相当一部分磷酸化位点似乎通过与侧链的相互作用在静电上得到稳定。从生物单元的计算中可以明显看出一些跨亚基界面的稳定化实例。在考虑紧邻的周围环境时，在许多情况下，有利的相互作用仅在磷酸化伴随的构象变化之后才明显。对非磷酸化结构应用简单的远程潜在相互作用计算，可恢复磷酸化结构所呈现的分离状态。在对Phospho.ELM数据集中的位点进行的一项研究中，对于由非磷酸化蛋白质提供结构注释的情况，即使使用更宽的相互作用半径，已知的磷酸化受体位点相对于背景也几乎没有分离。然而，Phospho.ELM数据集中受体位点和背景位点的斑块极性分布存在差异。
在本研究中，开发了一种易于实施的程序，该程序可能有助于识别与电荷-电荷相互作用和构象变化相关的磷酸化受体位点。由于该方法提供了磷酸化后潜在锚定相互作用的信息，它可以与探测构象变化的模拟相结合。我们对Phospho.ELM数据集的分析还显示了通过以下方式介导磷酸化效应的证据：（i）与使溶剂不可及的磷酸化受体位点变得可及相关的构象变化，以及（ii）蛋白质-蛋白质相互作用的调节。
