Determinants of hydrogen bond distances in proteins

Abstract

Hydrogen bonds (H-bonds) between oxygen atoms, with the O–H bond donated to the acceptor O atom (O_donor–H⋯O_acceptor), are essential for stabilizing protein structures and facilitating enzymatic reactions. The dielectric and electrostatic environment of proteins, as well as structural constraints imposed by protein folding, influence the nature of H-bonds. In this study, we investigated how these factors affect H-bond distances in proteins. Analysis of 906 high-resolution protein structures (≤1.2 Å) from the Protein Data Bank revealed that H-bond distances for H-bonds with the same donor and acceptor groups are distributed around a value primarily determined by the pK_a difference between these groups (ΔpK_a) in water, with lower ΔpK_a values leading to shorter distances. This correlation arises from enhanced electron redistribution from the H-bond acceptor to the donor in lower ΔpK_a H-bonds, which increases the covalent character of the H-bond and decreases the H⋯O_acceptor distance. In contrast, H-bond distances are largely unaffected by whether the H-bond is buried in the protein interior or exposed to bulk water, as the strength of the electrostatic interaction between the donor and acceptor groups plays a minor role in determining distances. Furthermore, analysis of H-bonds in microbial rhodopsins using a quantum mechanical/molecular mechanical approach demonstrates that the protein environment primarily influences H-bond distances electrostatically by altering the ΔpK_a of the H-bond, while structural constraints impose a secondary influence by altering O_donor–H⋯O_acceptor angles or H⋯O_acceptor distances without changing ΔpK_a.