Understanding beta-hairpin formation by molecular dynamics simulations of unfolding.
We have studied the mechanism of formation of a 16-residue beta-hairpin from the protein GB1 using molecular dynamics simulations in an aqueous environment. The analysis of unfolding trajectories at high temperatures suggests a refolding pathway consisting of several transient intermediates. The changes in the interaction energies of residues are related with the structural changes during the unfolding of the hairpin. The electrostatic energies of the residues in the turn region are found to be responsible for the transition between the folded state and the hydrophobic core state. The van der Waals interaction energies of the residues in the hydrophobic core reflect the behavior of the radius of gyration of the core region. We have examined the opposing influences of the protein-protein (PP) energy, which favors the native state, and the protein-solvent (PS) energy, which favors unfolding, in the formation of the beta-hairpin structure. It is found that the behavior of the electrostatic components of PP and PS energies reflects the structural changes associated with the loss of backbone hydrogen bonding. Relative changes in the PP and PS van der Waals interactions are related with the disruption of the hydrophobic core of a protein. The results of the simulations support the hydrophobic collapse mechanism of beta-hairpin folding.
Lee
J
J
School of Chemistry and Molecular Engineering, Seoul National University, Seoul 151-747, Korea.
Shin
S
S
D000818:Animals; D001426:Bacterial Proteins; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012260:Ribonucleases / Q000737:chemistry; D055672:Static Electricity; D013816:Thermodynamics
D001426:Bacterial Proteins; C029152:G-substrate; D009419:Nerve Tissue Proteins; D010446:Peptide Fragments; D010455:Peptides; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; C030526:tendamistate