1. Alanine-based peptides containing polar residues presumably favour α-helical structure entropically
- Author
-
Ichiro Yamato, Wankee Kim, and Tadashi Ando
- Subjects
Alanine ,Arginine ,Chemistry ,General Chemical Engineering ,Enthalpy ,Solvation ,General Chemistry ,Dihedral angle ,Condensed Matter Physics ,Residue (chemistry) ,Crystallography ,Modeling and Simulation ,Brownian dynamics ,General Materials Science ,Umbrella sampling ,Information Systems - Abstract
To evaluate the enthalpic and entropic contributions of polar residues in alanine-based peptides to α-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 α-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, ψ, was investigated. Arginine residue showed smaller fluctuation than alanine in elongated states. Higher α-helical propensity might originate from entropic effects. Furthermore, arginine seems to affect the α-helical propensity of alanines interacting with arginine.
- Published
- 2011