Proton first : rationalizing a proton transfer in a protein-fragment complex

Abstract

A combination of experimental and theoretical approaches is used to decipher the molecular recognition event of benzoic acid complexed with protein kinase A. The publicly known crystal structure suggests the protonated form of benzoic acid to be complexed with Protein Kinase A. Such a protonation pattern of is unlikely for benzoic acid in aqueous environment and must be induced by complexation to protein kinase A. Unfortunately, isothermal titration calorimetry does not reveal any binding event, which may be due to low affinity. However, Poisson–Boltzmann calculations and molecular dynamics simulations strengthen the initial hypothesis of a protonated benzoic acid binding to protein kinase A.