Protonation effects on the equilibrium and dynamical properties of the alanine tetrapeptide

The effect of terminal group charge on the structure and dynamics of the alanine tetrapeptide has been investigated using molecular dynamics simulations. Neutral and positive N-termini, together with neutral and negative C-termini, were studied, resulting in a total of four 10 ns simulations with different terminal group charge combinations. Analysis of these simulations indicates that the terminal group charge has only a minor effect on the conformations sampled for the central dihedrals, but a significant effect on the population distribution of the dihedrals close to the terminal groups. The conformational distribution at the C-terminus (ψ₃) was also found to depend on the charge at the N-terminus. Here, the differences result from the formation of transient ion pairs (salt bridges) in the zwitterion case. However, equilibrium sampling of these intramolecular ion pairs was still not fully converged even after 10 ns.