Filandrova Ruzena, Kavan Daniel, Kadek Alan, Novak Petr, Man Petr
Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
Faculty of Sciences, Charles University, Prague, Czech Republic.
Methods Mol Biol. 2021;2247:193-219. doi: 10.1007/978-1-0716-1126-5_11.
Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different experimental conditions. It is often described as a method with virtually no limitations in terms of protein size or sample composition. While this is generally true, there are, however, ligands or buffer components that can significantly complicate the analysis. One such compound, that can make HDX-MS troublesome, is DNA. In this chapter, we will focus on the analysis of protein-DNA interactions, describe the detailed protocol, and point out ways to overcome the complications arising from the presence of DNA.
蛋白质氢/氘交换（HDX）与质谱（MS）联用可用于研究蛋白质与各种配体的相互作用、描述突变的影响或揭示蛋白质对不同实验条件的结构响应。它通常被描述为一种在蛋白质大小或样品组成方面几乎没有限制的方法。虽然总体上确实如此，但然而，有些配体或缓冲液成分会使分析显著复杂化。一种会给HDX-MS带来麻烦的化合物就是DNA。在本章中，我们将重点关注蛋白质-DNA相互作用的分析，描述详细的实验方案，并指出克服因DNA存在而产生的复杂性的方法。
