瑞士苏黎世联邦理工学院生物系Paola Picotti课题组取得最新进展。他们利用动态3D蛋白质组在高分辨率下原位揭示蛋白质功能改变。该项研究成果发表在2020年12月23日出版的《细胞》杂志上。
他们在这里证明，基于有限的蛋白水解质谱（LiP-MS）的全球蛋白质结构输出可同时和原位检测正在经历营养适应的细菌和响应急性应激的酵母中许多此类功能改变。结构输出，可视为结构条形码，捕获的酶活性变化、磷酸化、蛋白质聚集和复合物形成，具有单个调节功能位点（例如结合位点和活性位点）的分辨率。与包括其他组学数据在内的现有认知的比较表明，LiP-MS可在经过充分研究的途径中检测到许多已知的功能改变。它提出了独特的代谢物-蛋白质相互作用，并使得能够鉴定基于果糖-1,6-二磷酸的葡萄糖在大肠杆菌中的调节机制。结构输出极大地增加了经典蛋白质组学的覆盖范围，产生了机械学假说，并为原位结构系统生物学铺平了道路。
据介绍，生物过程受到分子间相互作用和不影响蛋白质水平的化学修饰的调节，从而避免了经典蛋白质组学筛选中的检测。
附：英文原文
Title: Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ
Author: Valentina Cappelletti, Thomas Hauser, Ilaria Piazza, Monika Pepelnjak, Liliana Malinovska, Tobias Fuhrer, Yaozong Li, Christian Drig, Paul Boersema, Ludovic Gillet, Jan Grossbach, Aurelien Dugourd, Julio Saez-Rodriguez, Andreas Beyer, Nicola Zamboni, Amedeo Caflisch, Natalie de Souza, Paola Picotti
Issue&Volume: 2020-12-23
Abstract: Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other ‘omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology.
DOI: 10.1016/j.cell.2020.12.021
Source: https://www.cell.com/cell/fulltext/S0092-8674(20)31691-3