The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin.
The three-dimensional conformation of Met-enkephalin, corresponding to the lowest minimum of the empirical potential energy function ECEPP/2 (empirical conformational energy program for peptides), has been determined using a new algorithm, viz. the Electrostatically Driven Monte Carlo Method. This methodology assumes that a polypeptide or protein molecule is driven toward the native structure by the combined action of electrostatic interactions and stochastic conformational changes associated with thermal movements. These features are included in the algorithm that produces a Monte Carlo search in the conformational hyperspace of the polypeptide, using electrostatic predictions and a random sampling technique to locate low-energy conformations. In addition, we have incorporated an alternative mechanism that allows the structure to escape from some conformational regions representing metastable local energy minima and even from regions of the conformational space with great stability. In 33 test calculations on Met-enkephalin, starting from arbitrary or completely random conformations, the structure corresponding to the global energy minimum was found in all the cases analyzed, with a relatively small search of the conformational space. Some of these starting conformations were right or left-handed alpha-helices, characterized by good electrostatic interactions involving their backbone peptide dipoles; nevertheless, the procedure was able to convert such locally stable structures to the global-minimum conformation.
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Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301.
Scheraga
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D004563:Electrochemistry / Q000379:methods; D004744:Enkephalin, Methionine; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides; D011487:Protein Conformation; D013816:Thermodynamics
D010455:Peptides; D004744:Enkephalin, Methionine