PROTONATION EFFECTS ON THE EQUILIBRIUM AND DYNAMICAL PROPERTIES OF THE ALANINE TETRAPEPTIDE

The effect of terminal group charge on the structure and dynamics of t he alanine tetrapeptide has been investigated using molecular dynamics simulations. Neutral and positive N-termini, together with neutral an d negative C-termini, were studied, resulting in a total of four 10 ns simulations with different terminal group charge combinations. Analys is of these simulations indicates that the terminal group charge has o nly a minor effect on the conformations sampled for the central dihedr als, but a significant effect on the population distribution of the di hedrals close to the terminal groups. The conformational distribution at the C-terminus (psi 3) was also found to depend on the charge at th e N-terminus. Here, the differences result from the formation of trans ient ion pairs (salt bridges) in the zwitterion case. However, equilib rium sampling of these intramolecular ion pairs was still not fully co nverged even after 10 ns.