Intrinsic Relative Stabilities of the Neutral Tautomers of Arginine Side-Chain Models.

The specific protonation state of amino acids is crucial for the physicochemical properties of proteins and their biological functions. These protonation states influence, for instance, properties related to hydrogen bonding, solubility, and folding. pKa calculations for proteins are, therefore, important and require, in principle, a specification of the most stable protonated and deprotonated forms of each titratable group. This is complicated by the existence of multiple tautomers, like the five neutral tautomers of the guanidine moiety in arginine. In this study, the compounds N-methyl-guanidine and N-ethyl-guanidine were used to model the charged and all neutral protonation states of the arginine side chain. The relative stabilities of all five neutral tautomers were investigated systematically for the first time, using quantum-mechanical calculations. These relative stabilities were obtained in vacuo, water and chloroform, by combining the quantum-mechanical calculations with a continuum solvation model. The water model was used to represent arginines exposed to an aqueous solution, whereas the chloroform model has a polarity representative of a protein core or a membrane. This allowed determining the relative pKa's associated with each neutral tautomer in these environments. A key result is that significant differences in stability are found between the neutral tautomers, in both water and chloroform. Some tautomers are consistently found to be the most stable. These findings will be helpful to refine pKa calculations in proteins.