Water plays a critical role in many biological phenomena, such as correctly folding a protein, mediating oligomerization, and ligand binding. Recently, cryo-electron microscopy (cryo-EM) advanced a 2.2-Å resolution structure for β-galactosidase that identified water densities. By using molecular dynamics simulations, we compare the kinetics of the corresponding water molecules and of the water contained in the X-ray structure of the native protein. We also analyze the behavior of the conserved water molecules across all known X-ray structures for β-galactosidase. During the simulations, cryo-EM-placed water maintains its proximity to the protein better than the X-ray-placed water. Unlike X-ray, cryo-EM placed the water molecules in solvent-sheltered regions, with low accessible solvent area regardless of the residue type. Water molecules preserved in both structures are located near residues with little mobility. Our study shows that cryo-EM is able to identify a large fraction of the conserved water, which plays a crucial part in stabilizing protein structure and flexibility.<br/>

Comparing water dynamics in cryo-EM and x-ray derived molecular models

253rd National Meeting (2017)

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