Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water.
Molecular dynamics simulations of the S-peptide analogue AETAAAKFLREHMDS have been conducted in aqueous solution for 300 ps at 278 K and for 500 ps in two different runs at 358 K. The results show agreement with experimental observations in that at low temperature, 5 degrees C, the helix is stable, while unfolding is observed at 85 degrees C. In the low-temperature simulation a solvent-separated ion pair was formed between Glu-2 and Arg-10, and the side chain of His-12 reoriented toward the C-terminal end of the alpha-helix. Detailed analyses of the unfolding pathways at high temperature have also revealed that the formation or disappearance of main-chain helical hydrogen bonds occurs frequently through an alpha in equilibrium with 3(10) in equilibrium with no hydrogen bond sequence.
Tirado-Rives
J
J
Department of Chemistry, Yale University, New Haven, Connecticut 06511.
Jorgensen
W L
WL
D000595:Amino Acid Sequence; D003198:Computer Simulation; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D011487:Protein Conformation; D012259:Ribonuclease, Pancreatic / Q000737:chemistry*; D013816:Thermodynamics
D010446:Peptide Fragments; D010455:Peptides; D012259:Ribonuclease, Pancreatic