Imidazole Nitrogens of Two Histidine Residues Participating in N-H center dot center dot center dot N Hydrogen Bonds in Protein Structures: Structural Bioinformatics Approach Combined with Quantum Chemical Calculations

摘要

Protein structures are stabilized by different types of hydrogen bonds. However, unlike the DNA double helical structure, the N-H center dot center dot center dot N type of hydrogen bonds is relatively rare in proteins. N-H center dot center dot center dot N hydrogen bonds formed by imidazole groups of two histidine residues have not been investigated. We have systematically analyzed 5333 high-resolution protein structures with resolution 1.8 angstrom or better and identified 285 histidine pairs in which the nitrogen atoms of the imidazole side chains can potentially participate in N-H center dot center dot center dot N hydrogen bonds. The histidine pairs were further divided into two groups, neutral-neutral and protonated-neutral, depending on the protonation state of the donor histidine. Quantum chemical calculations were performed on imidazole groups adopting the same geometry observed in the protein structures. Average interaction energies between the interacting imidazole groups are -6.45 and -22.5 kcal/mol for neutral-neutral and protonated-neutral, respectively. Hydrogen bond interaction between the imidazole moieties is further confirmed by natural bond orbital analyses of the model compounds. Histidine residues involved in N-H center dot center dot center dot N hydrogen bonds are relatively more buried and have low B-factor values in the protein structures. N-H center dot center dot center dot N hydrogen bond formed by a pair of buried histidine residues can significantly contribute to the structural stability of proteins.