On the multiple-minima problem in the conformational analysis of polypeptides. IV. Application of the electrostatically driven monte carlo method to the 20-residue membrane-bound portion of melittin

✍ Scribed by Daniel R. Ripoll; Harold A. Scheraca

• Publisher: Wiley (John Wiley & Sons)
• Year: 1990
• Tongue: English
• Weight: 968 KB
• Volume: 30
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360300116

✦ Synopsis

T h e conformational space of the membrane-bound portion of melittin has been searched using the electrostatically driven Monte Carlo ( E D M C ) method with the E C E P P / 2 (empirical conformational energy program for peptides ) algorithm. The former 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. The algorithm produces a Monte Carlo search in the conformational hyperspace of the polypeptide using electrostatic predictions and a random sampling technique, combined with local minimization of the energy function, to locate low-energy conformations. As a result of 8 test calculations on the 20-residue membranebound portion of melittin, starting from six arbitrary and two completely random conformations, the method was able to locate a very low-energy region of the potential with a well-defined structure for the backbone. In all of the cases under study, the method found a cluster of similar low-energy conformations that agree well with the structure deduced from x-ray diffraction experiments and with one computed earlier by the build-up procedure.