Concurrent interactions contribute to the raised pKa of His18 in Barnase

To understand the source of the stability due to a charged His side-chain located at the C terminus of an alpha-helix in barnase, we computed the stabilization free energy, upon ionization of the His side-chain, in the native protein, the Leu94 mutant, and a "pseudo-native" protein, using free energy molecular dynamics simulations. We show that there are a number of interactions that can individually stabilize the native protein. These interactions cannot be portrayed satisfactorily by a unique model such as: (1) the helix dipole model, in which there is a strong interaction between His+ and the helix dipole; or (2) the H-bond model, in which His+ acts as a donor to either a carbonyl group at the C terminus of the helix or to the aromatic moiety of the neighbouring Trp94 residue. The protonated form of His18 in the native protein is computed to be more stable than the neutral form, in accord with the experimental observation. Part of this stabilization is due to the last turn of the alpha-helix. In the simulation of the folded proteins, the persistence of a H-bond between the His18 side-chain and a carbonyl group at the C terminus of the helix sustains the H-bond model. However, it is difficult to perceive whether this helix-stabilizing interaction is stronger when the His side-chain is charged. It is shown, in agreement with experiment, that the Trp94 side-chain, in the vicinity of the charged His residue, stabilizes the protein. Water molecules hydrogen-bonded to His18 have longer residence times ( > 100 ps) in the native protein than in the Leu94 mutant ( < 50 ps). This observation might be indicative of the capacity of Trp94, by a mechanism not evident, for trapping water molecules in the vicinity of His18 and making the exchange of a water molecule, bound to His18, with bulk water more difficult. A conformational analysis of the native and Leu94 mutant proteins shows that the simulations reproduce fairly well features of the crystal and NMR structures of these proteins.