Alanine-based peptides containing polar residues presumably favour α-helical structure entropically

To evaluate the enthalpic and entropic contributions of polar residues in alanine-based peptides to alpha-helical propensities of peptides, we applied a Brownian dynamics simulation, together with the umbrella sampling, to two alanine-based 21-residue peptides: one composed of alanine only (AAA), the other composed of 18 alanines and 3 arginines (ARA). Higher alpha-helical propensity of ARA than that of AAA was obtained. However, they showed similar conformational stability in enthalpy, considering the contribution of the solvation energy and the potential energy. As an evaluation of entropic effects, the fluctuation of a dihedral angle, psi, was investigated. Arginine residue showed smaller fluctuation than alanine in elongated states. Higher alpha-helical propensity might originate from entropic effects. Furthermore, arginine seems to affect the a-helical propensity of alanines interacting with arginine.