| Protein folding is one of the most challenging problems in the field of biochemistry. Despite the presence of the thousands of experimentally determined protein structures, and decades of experimental and theoretical study, the folding mechanism is still unclear for the vast majority of proteins. Computer simulation represents a powerful tool for the discovery of the underlining physics behind the folding mechanism as they can provide atomic detail of folding intermediates not available by experiment. Here, we investigate the folding and stability of a 10-residue 3:5 β-hairpin forming peptide (YITNSNGTWT) by computer simulation in explicit solvent. This peptide provides a model for the initial steps in β-sheet formation, a key step in protein folding, and was chosen as experimental studies show it forms a highly populated (80%) hairpin structure in water. The hairpin was successfully folded and remained stable. The folding mechanism was investigated by isolating intermediates from the simulations, and a folding pathway is proposed. Nine possible native contacts were suggested to be responsible for the folding and stability of the peptide. Further studies of a known unstable mutation (T3S) resulted in hairpin unfolding. Examination of the wild type and mutant simulations suggested the major differences in their stabilities related to the presence of residual structure in the denatured state. Finally, a systematic study of all possible alanine mutations was performed to determine the effects of each residue on the stability of the hairpin. It was observed that one of the main factors responsible for the folding pathway contributed little to the stability of the hairpin structure, emphasizing differences in kinetic and thermodynamic effects. |
