Thermodynamics of short alanine-based peptides.

• Main Author: Guan, Ying Li.
• Other Authors: School of Physical and Mathematical Sciences
• Format: Final Year Project
• Language: English
• Published: 2010
• Subjects: DRNTU::Science::Chemistry::Biochemistry
• Online Access: http://hdl.handle.net/10356/39941
• Institution: Nanyang Technological University

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.