title: Energy landscape and global optimization for a frustrated model protein.
abstract: The three-color (BLN) 69-residue model protein was designed to exhibit frustrated folding. We investigate the energy landscape of this protein using disconnectivity graphs and compare it to a Gō model, which is designed to reduce the frustration by removing all non-native attractive interactions. Finding the global minimum on a frustrated energy landscape is a good test of global optimization techniques, and we present calculations evaluating the performance of basin-hopping and genetic algorithms for this system. Comparisons are made with the widely studied 46-residue BLN protein. We show that the energy landscape of the 69-residue BLN protein contains several deep funnels, each of which corresponds to a different β-barrel structure.
authors.affiliation: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
authors.forename: Mark T
authors.initials: MT
authors.lastname: Oakley
authors.forename: David J
authors.initials: DJ
authors.lastname: Wales
authors.forename: Roy L
authors.initials: RL
authors.lastname: Johnston
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D011506:Proteins