Structural Characterization of the Histone Multimers in the Gas Phase using Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation

The nucleosome core particle (NCP) is the minimum structural unit of chromatin and is composed of a histone octamer and 146 base pairs of DNA. The DNA is wrapped around the histone octamer, which consists of two H2A/H2B dimers and one (H3/H4)2 tetramer. These histone multimers contain intrinsically disordered tail regions that are functionally important for NCP assembly and disassembly, which are highly relevant to gene expression. In order to elucidate the mechanisms underlying these processes, it is of importance to characterize structures of the H2A/H2B dimer and (H3/H4)2 tetramer. In the present study, we investigated gas-phase structures of these two histone multimers having disordered tail regions using electrospray ionization ion mobility-mass spectrometry (IM-MS) and molecular dynamics (MD) simulation. IM-MS experiments of the histone multimers showed that their arrival-time distributions were rather wide, implying that each histone multimer could have multiple conformers in the gas phase. To examine their structures, MD simulations of the histone multimers were performed first in solution and then in vacuo at four temperatures, providing a variety of their gas-phase structures. By calculating theoretical collision cross-section (CCS) values of these structures, it was found that histone multimer structures with smaller CCS values had more compact tail regions than those with larger CCS values. This finding suggests that multiple conformers of the histone multimers are primarily due to the random behaviors of the tail regions in the gas phase. Thus, the combination use of IM-MS and MD simulation enables us to clearly characterize gas-phase structures of proteins containing disordered tails.