Keller Laura J, Lakemeyer Markus, Bogyo Matthew
Department of Chemical & Systems Biology, Stanford University, Stanford, CA, United States.
Department of Pathology, Stanford University, Stanford, CA, United States.
Methods Enzymol. 2022;664:1-22. doi: 10.1016/bs.mie.2021.11.017. Epub 2021 Dec 23.
Activity-based protein profiling (ABPP) is a commonly utilized technique to globally characterize the endogenous activity of multiple enzymes within a related family. While it has been used extensively to identify enzymes that are differentially active across various mammalian tissues, recent efforts have expanded this technique to studying bacteria. As ABPP is applied to diverse sets of bacterial strains found in microbial communities, there is also an increasing need for robust tools for assessing the conservation of enzymes across closely related bacterial species and strains. In this chapter, we detail the integration of gel-based ABPP with basic bioinformatic tools to enable the analysis of enzyme activity, distribution, and homology. We use as an example the family of serine hydrolases identified in the skin commensal bacterium Staphylococcus epidermidis.
基于活性的蛋白质谱分析（ABPP）是一种常用技术，用于全面表征相关家族中多种酶的内源性活性。虽然它已被广泛用于鉴定在各种哺乳动物组织中具有不同活性的酶，但最近的研究已将该技术扩展到细菌研究。随着ABPP应用于微生物群落中发现的各种细菌菌株，对用于评估密切相关细菌物种和菌株间酶保守性的强大工具的需求也日益增加。在本章中，我们详细介绍了基于凝胶的ABPP与基本生物信息学工具的整合，以实现对酶活性、分布和同源性的分析。我们以在皮肤共生细菌表皮葡萄球菌中鉴定出的丝氨酸水解酶家族为例进行说明。
