Measurement of charges and chemical bonding in a cryo-EM structure

Hydrogen bonding, bond polarity, and charges in protein molecules are crucial for protein structure stabilization and function. This study uses cryo-EM to measure these properties in a sub-1.2 Å resolution structure of apoferritin. A weighted difference map reveals positive densities for most hydrogen atoms in the core, and negative densities around acidic amino acid side chains, likely indicating negative charges. The positive densities help identify amino- and oxo-termini of asparagine and glutamine. Spatial-resolution selection and dose-dependent analysis validate these findings, showing the average hydrogen density position depends on the bonded atom type.

Saori Maki-Yonekura, Keisuke Kawakami, Kiyofumi Takaba, Tasuku Hamaguchi, Koji Yonekura