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The Electrostatically Driven Monte Carlo method: Application to conformational analysis of decaglycine
Author(s) -
Ripoll Daniel R.,
Vásquez Max J.,
Scheraga Harold A.
Publication year - 1991
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360310306
Subject(s) - chemistry , monte carlo method , maxima and minima , hydrogen bond , helix (gastropod) , amide , crystallography , computational chemistry , molecule , organic chemistry , mathematical analysis , ecology , statistics , mathematics , snail , biology
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 α‐helical had significantly lower potential energies than fully α‐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 α‐helical hydrogen bonds was an important enough factor in making the α‐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.