Using hydrogen-deuterium exchange mass spectrometry to characterize Mtr4 interactions with RNA.

ABSTRACT: Hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) is a valuable technique to investigate the dynamics of protein systems. The approach compares the deuterium uptake of protein backbone amides under multiple conditions to characterize protein conformation and interaction. HDX-MS is versatile and can be applied to diverse ligands, however, challenges remain when it comes to exploring complexes containing nucleic acids. In this chapter, we present procedures for the optimization and application of HDX-MS to studying RNA-binding proteins and use the RNA helicase Mtr4 as a demonstrative example. We highlight considerations in designing on-exchange, bottom-up, comparative studies on proteins with RNA. Our protocol details preliminary testing and optimization of experimental param

SUBMITTER: Ball D 

PROVIDER: S-EPMC10204939 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature