Study of conformational switching in polyalanine at solid surfaces using molecular simulation

Abstract

We report a numerical study of the change in the conformation of polyalanine on a rigid, smooth uncharged solid surface as a function of the peptide size and surface energy. It is shown that the polyalanine molecule switches between distinct conformations at specific surface energies rather than undergoing gradual changes with surface energy. It appears that this behavior arises out of the ability of the molecule to sustain intramolecular hydrogen bonding and, we hypothesize, its symmetry. Two conformational switches are observed: (1) α helix → 3.1₁₀ helix, and (2) 3.1₁₀ 0 helix → 2₇ helix. The surface energy associated with the first switch is lower than that of the second. Both switching surface energies change in a complex manner with the size of the peptide. The switches are also accompanied by significant strains along the peptide axis. The conformational and length changes could be exploited technologically (e.g., molecular switches) and could possibly be of relevance to the activity and function of natural proteins when near solid surfaces.