Cyclic beta-helical/beta-hairpin D,L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics.
A molecular dynamics (MD) simulation study of a cyclic 22 residue D,L-alpha-peptide is reported. The 154 experimental ROE distance bounds that determine a beta-helical fold in chloroform are all satisfied in MD simulations starting from the folded and from a refolded structure. Interestingly, the latter simulations generated structures of lower energy than the NMR model structures, thereby yielding a better conformational representation of the measured experimental data. The stability of the beta-helical fold, characterized by 16 beta-sheet hydrogen bonds, was investigated by varying the temperature and the solvent composition. Different metastable states were found and examined. Various strategies to fold the cyclic, highly hydrogen bonded peptide, starting from different nonfolded conformations of the peptide, were investigated. Due to the high barriers to (un)folding, a folding/unfolding equilibrium could not be established.
Meier
Katharina
K
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich ETH, 8093 Zürich, Switzerland.
van Gunsteren
Wilfred F
WF
D002725:Chloroform / Q000737:chemistry; D003198:Computer Simulation; D006358:Hot Temperature; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010456:Peptides, Cyclic / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary
D010456:Peptides, Cyclic; D002725:Chloroform