title: De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.
abstract: Entropy Sampling Monte Carlo (ESMC) simulations were carried out to study the thermodynamics of the folding transition in the GCN4 leucine zipper (GCN4-lz) in the context of a reduced model. Using the calculated partition functions for the monomer and dimer, and taking into account the equilibrium between the monomer and dimer, the average helix content of the GCN4-lz was computed over a range of temperatures and chain concentrations. The predicted helix contents for the native and denatured states of GCN4-lz agree with the experimental values. Similar to experimental results, our helix content versus temperature curves show a small linear decline in helix content with an increase in temperature in the native region. This is followed by a sharp transition to the denatured state. van't Hoff analysis of the helix content versus temperature curves indicates that the folding transition can be described using a two-state model. This indicates that knowledge-based potentials can be used to describe the properties of the folded and unfolded states of proteins.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: D
authors.initials: D
authors.lastname: Mohanty
authors.forename: A
authors.initials: A
authors.lastname: Kolinski
authors.forename: J
authors.initials: J
authors.lastname: Skolnick
mesh_terms: D003198:Computer Simulation; D004268:DNA-Binding Proteins; D019281:Dimerization; D005656:Fungal Proteins / Q000737:chemistry*; D016350:Leucine Zippers; D009010:Monte Carlo Method; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011494:Protein Kinases / Q000737:chemistry*; D017433:Protein Structure, Secondary; D029701:Saccharomyces cerevisiae Proteins; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases