Folding or Misfolding: The Choice of β‑Hairpin

Proteins fold through complex inter-residue interactions which are mutually supportive and cooperatively lead to thermodynamically favorable native structures. Competing (misfolded) structures, however, could exist, which might affect the thermodynamic and kinetic properties of folded structure. Running long-time REMD simulations on two β-structured polypeptides, the present study identifies the folded and (less populated) competing misfolded states of β-hairpins. Of particular interest is a one-residue shifted misfolded state which has been often seen in previous reports. The folding and misfolding pathways are then energetically characterized by free energy landscape analysis, indicating that the folding and misfolding of β-hairpin are parallel pathways and a protein’s selection of following which pathway is a consequence of the competition between the formation of alterable turn configurations and cross-strand hydrophobic interactions. Proteins possessing high percentage of hydrophobic residues introduce strong cross-strand hydrophobic interactions which stabilize the native structural elements in the folding pathway, leading to low possibility of misfolding. The present study provides novel insights into the origin of sequence-dependent β-hairpin misfolding “hidden” behind experimentally detectable β-hairpin folding, suggesting the direction for the structure design of β-structured protein