Molecular Dynamics Simulation of Folding of a Short Helical Peptide with Two Disulfide Bonds
| Autor: | 蔡宜倫 |
|---|---|
| Rok vydání: | 2005 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 93 A molecular dynamics simulation of the folding of a short helical peptide with two disulfide bonds was carried out. In 23 trajectories, 20 trajectories folded with an average time of ~10 ns. The other 3 trajectories did not fold in 100-200 ns simulations. In an additional 23 simulations, 18 trajectories folded with an average folding time of ~10 ns, giving good results in confirming statistical certainty. In all 8 non-folded trajectories, a non-local, non-native hydrogen bond (H-bond) and an additional non-native H-bond were observed in 5 trajectories. A further analysis of the other 3 non-folded trajectories indicated that, at least, 2 non-native H-bonds are needed to trap this peptide in an intermediate. An examination of the hydrophobic clustering effect shows that this effect is not significant in the folding of this peptide. To our knowledge, this is the first folding simulation for a short helical peptide with disulfide bonds. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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