Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most
biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino
acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to
7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged
residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions,
including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the
influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP.
Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of
commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated
His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part,
to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is
predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the
peptide – HLA-DP protein complex.