The impact of interchain hydrogen bonding on ß-hairpin stability is readily predicted by molecular dynamics simulation.

ABSTRACT

Peptides are frequently used model systems for protein folding. They are also gaining increased importance as therapeutics. Here, the ability of molecular dynamics (MD) simulation for describing the structure and dynamics of ß-hairpin peptides was investigated, with special attention given to the impact of a single interstrand sidechain to sidechain interaction. The MD trajectories were compared to structural information gained from solution NMR. By assigning frames from restraint-free MD simulations to an intuitive hydrogen bond on/off pattern, folding ratios and folding pathways were predicted. The computed molecular model successfully reproduces the folding ratios determined by NMR, indicating that MD simulation may be straightforwardly used as a screening tool in ß-hairpin design.