Enhanced molecular dynamics simulation of the transformation between α-helix and β-hairpin structures for peptide

Abstract

ABSTRACTHere, we investigated the secondary structure transformation for a design peptide, which has both the α-helix (PDB ID code 2DX3) and β-hairpin (PDB ID code 2DX4) structures in aqueous solution. We show that the transformation between α-helix and β-hairpin structures can be sampled efficiently using the enhanced sampling method based on integrated tempering without the definition of reaction coordinates. The reliable and smooth two-dimensional potential of mean force surfaces of the conformation space can be obtained efficiently, which has been used to propose the probable pathways for the transformation of the α-helix and β-hairpin structures. Our simulation results revealed the efficiency, and further suggested the general applicability of integrated tempering sampling method into complex biomolecule processes without prior structure knowledge.