NEW OPTIMIZATION METHOD AND ITS APPLICATION TO COLLAGEN PACKING

Cornell University Ithaca, Ithaca NY

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Abstract

(a) Computational study of packing a collagen-like molecule: The lateral packing of a collagen-like molecule has been examined by energy minimization with the ECEPP/3 force field. Two current packing models, the Smith collagen microfibril twisted equilateral pentagon model and the quasi-hexagonal packing model, have been extensively investigated. The quasi-hexagonal packing structure is found to be energetically more favorable than the Smith microfibril by as much as 31.2 kcal/mol of five triple helices. (b) New optimization method for conformational energy calculations on polypeptides: Conformational space annealing: A new optimization method is presented to search for the global minimum-energy conformations of polypeptides. It combines essential aspects of the build-up procedure and the genetic algorithm, and it introduces the important concept of conformational space annealing. When tested on Met-enkephalin, a 24-dihedral angle problem, the accepted global minimum-energy conformation is obtained for all 100 independent runs after about 2600 local minimizations on average. The algorithm is ideally suited for parallel computations, and the parallelization of the algorithm is in progress, which would make it possible to investigate larger polypeptides.