Secondary structure provides a template for the folding of nearby polypeptides

Although protein structures are primarily encoded by their sequences, they are also critically dependent on environmental factors such as solvents and interactions with other molecules. Here we investigate how the folding-energy landscape of a short peptide is altered by interactions with another peptide, by performing atomistic replica-exchange molecular dynamics simulations of polyalanines in various environments. We analyzed the free-energy landscapes of Ala7 and Ala8 in isolation, near an alpha-helix template, and near a beta-strand template. The isolated Ala7 and Ala8 at 270 K were mainly in polyproline II helix conformations and in equilibrium between the alpha-helix and polyproline II helix, respectively, in harmony with the experiment. Interestingly, we found remarkably strong secondary-structure "templating"; namely, the alpha-helix template enhanced alpha-helix conformation and the beta-strand template induced beta-strand conformation in the simulated Ala8. The alpha-helix template lowered the nearby dielectric constant, which strengthened hydrogen bonds in the simulated Ala8, leading to alpha-helix stabilization. The beta-strand template provided hydrogen bond positions to the simulated Ala8, sharply inducing beta-strand structure. With or without templates, the energy landscape of Ala8 is always funnel-like and centered at the alpha-helix conformation, whereas entropic contribution disfavors the alpha-helix, leading to subtle competition. Secondary-structure templating may play a critical role in protein conformation dynamics in the cellular environment.