Chapter 9 - Hydrogen Bonds and Water Molecules in Crystalline Proteins

Abstract

This chapter discusses the role of hydrogen bonds and water molecules in crystalline proteins. The chapter states that before crystalline proteins were refined, small volumes of electron density went un-accounted for in the X-ray maps. Oftentimes, this electron density was near the surface of the crystalline protein, adjacent to an atom of nitrogen or oxygen. Due to the lack of technology, the small regions of additional electron density that could not be accounted for by protein atoms were largely ignored earlier. When it became possible to refine crystallographic coordinates, these additional volumes of electron density persisted. They were clearly a part of the protein molecule but not covalently bonded. Investigators began to assign such sites to bound water molecules. Hydrogen atoms are generally not visible in most electron density maps, because X-ray scattering is proportional to the atomic number. Later, however, neutron diffraction methods were applied to a few crystalline proteins and the ability to visualize hydrogen or deuterium atoms in maps of a crystalline protein became possible. The chapter discusses hydrogen bonding positions in proteins, neutron diffraction, and water molecules observed in crystalline proteins. The chapter also highlights the distribution of protein-bound water, and water networks in crystalline proteins.