Elucidating the Conformational Dynamics of YTH Domain Containing Family of Proteins

Abstract

Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) has emerged as a powerful and time-efficient technique for capturing ‘breathing motions’ and intricate conformational dynamics of proteins. Here, we conduct HDX-MS to elucidate the conformational dynamics of the YTHDF proteins. The function of the three YTHDF proteins has been debated in the scientific community. According to the prevailing model, the three YTHDF proteins (YTHDF1, YTHDF2, and YTHDF3) have different functions, while the unified model proposes shared functions. We aimed to detect whether the observed conformational dynamics between the three YTHDFs are redundant or different for the fate of the m6A-modified RNA ligand. We observed that all three YTHDFs showed significant stabilization in the bound state relative to the unbound state. However, the conformational dynamics of YTHDF2 were most different, particularly in the α2–β3 region. HDX-MS was useful in detecting unique conformational dynamics in areas influenced by allostery, such as the α2–β3 region.