The electrostatically driven Monte Carlo method: application to conformational analysis of decaglycine.
The Electrostatically Driven Monte Carlo (EDMC) method was applied in a study of a decamer of glycine whose conformational behavior is described by the Empirical Conformational Energy Program for Peptides (ECEPP/2) potential energy model. When free neutral end groups were used, it was found that conformations that were not alpha-helical had significantly lower potential energies than fully alpha-helical ones. However, when the N- and C-termini were blocked by acetyl and methyl amide groups, respectively, the number of unsatisfied hydrogen-bond donors and acceptors at the helix termini was diminished from 8 to 6; in this case, the possibility of forming two additional alpha-helical hydrogen bonds was an important enough factor in making the alpha-helical conformation the one with the lowest energy. The EDMC method was used as a global energy optimizer since it does not often become trapped in high-energy local minima.
Ripoll
D R
DR
Protein Engineering Section, National Research Council of Canada, Montreal, Quebec.
Vásquez
M J
MJ
Scheraga
H A
HA
D004563:Electrochemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation
D009842:Oligopeptides; D010455:Peptides; C070361:decaglycine