Helix folding of an alanine-based peptide in explicit water

Computer simulations using full atomic representations for both the peptide and water molecules were performed to study the folding of a 16-residue alanine-based helical peptide in aqueous solution. Using a recently developed self-guided molecular dynamics (SGMD) method, which was shown to improve the conformational searching efficiency significantly as compared to conventional MD simulation method, reversible folding (folding, unfolding and refolding) of a 16-residue alanine-based synthetic peptide in explicit water at 274 K was successfully accomplished. Consistent with experimental results, the helix was found to be the major secondary structural element in aqueous solution, and among different helix forms, the a-helix is the dominant form. Conformational analysis of our simulation results showed that turns and 3(10)-helices play an essential-role in the folding of cr-helix. Interestingly, our results showed that the propagation of a helix segment is more frequent at the C-end than at the N-end. In most helix conformations, the backbone carbonyl groups of the peptide prefer to simultaneously form intramolecular hydrogen bonds with the backbone amide groups of the peptide and intermolecular hydrogen bonds with water molecules, indicating water accessibility to the backbone carbonyl groups is crucial for helix formation in water. Therefore, the helical propensities of amino acids may be related to the water accessibility of their backbone groups in helical conformation. Water molecules also function as hydrogen bonding-bridges linking helical residue pairs (i, i + n, with n = 3, 4, 5), suggesting a role of water bridges in helix folding.