How optimization of potential functions affects protein folding.
The relationship between the optimization of the potential function and the foldability of theoretical protein models is studied based on investigations of a 27-mer cubic-lattice protein model and a more realistic lattice model for the protein crambin. In both the simple and the more complicated systems, optimization of the energy parameters achieves significant improvements in the statistical-mechanical characteristics of the systems and leads to foldable protein models in simulation experiments. The foldability of the protein models is characterized by their statistical-mechanical properties--e.g., by the density of states and by Monte Carlo folding simulations of the models. With optimized energy parameters, a high level of consistency exists among different interactions in the native structures of the protein models, as revealed by a correlation function between the optimized energy parameters and the native structure of the model proteins. The results of this work are relevant to the design of a general potential function for folding proteins by theoretical simulations.
Hao
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MH
Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, USA.
Scheraga
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HA
D055592:Biophysical Phenomena; D001703:Biophysics; D016208:Databases, Factual; D008956:Models, Chemical; D009010:Monte Carlo Method; D010940:Plant Proteins / Q000737:chemistry / Q000502:physiology; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000502:physiology*; D013816:Thermodynamics
D010940:Plant Proteins; D011506:Proteins; C024934:crambin protein, Crambe abyssinica