title: Conformational Sampling of a Biomolecular Rugged Energy Landscape.
abstract: The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field. The effectiveness of the search was assessed using a variety of methods. The robustness of sampling was checked by the energy yield function which measures quantitatively the number of the peptide decoys residing in an energetic funnel. Furthermore, the potential energy-dependent Pareto fronts were calculated to elucidate dissimilarities between peptide conformations and the native state as observed by x-ray crystallography. Our results showed that the probed potential energy landscape of [Leu]Enkephalin is self-similar on different metric scales and that the local potential energy minima of the peptide decoys are metastable, thus they can be refined to conformations whose potential energy is decreased by approximately 250 kJ/mol.
authors.forename: Jakub
authors.initials: J
authors.lastname: Rydzewski
authors.forename: Rafal
authors.initials: R
authors.lastname: Jakubowski
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Nicosia
authors.forename: Wieslaw
authors.initials: W
authors.lastname: Nowak
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins