Thermodynamics of short alanine-based peptides.
Short alanine-based peptide forms approximately 80% helix content when formed under optimal conditions. Factors such as solvent concentration, pH, temperature and pressure play a part in determining the formation and stability of the helix content. The effect of temperature on protein folding is exa...
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| Format: | Final Year Project |
| Language: | English |
| Published: |
2010
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| Online Access: | http://hdl.handle.net/10356/39941 |
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| Institution: | Nanyang Technological University |
| Language: | English |
| Summary: | Short alanine-based peptide forms approximately 80% helix content when formed under optimal conditions. Factors such as solvent concentration, pH, temperature and pressure play a part in determining the formation and stability of the helix content. The effect of temperature on protein folding is examined by performing a molecular dynamics simulation using AMBER force field, ff03, on 3K(I); acetyl-AAAAKAAAAKAAAAKA-amide at various temperatures to mimic an experimental study. The results are then characterized using root-mean-square deviation (RMSD), snapshots of the folding process, potential mean force (PMF) energy diagrams and secondary structure prediction using DSSP. |
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