De novo simulations of the folding thermodynamics of the GCN4 leucine zipper

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Title: De novo simulations of the folding thermodynamics of the GCN4 leucine zipper
Author: Mohanty, Debasisa ; Kolinski, Andrzej ; Skolnick, Jeffrey
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.
Description: © 1999 by the Biophysical Society
Type: Article
ISSN: 0006-3495
Citation: Mohanty, D, Kolinski A, Skolnick J. 1999. De novo simulations of the folding thermodynamics of the GCN4 leucine zipper. Biophysical journal. 77(1):54-69.
Date: 1999-07
Contributor: Uniwersytet Warszawski. Wydział Chemii
Scripps Research Institute. Dept. of Molecular Biology
Publisher: Georgia Institute of Technology
Biophysical Society
Subject: Entropy sampling Monte Carlo simulation
Leucine zippers
Two-state model
Coiled coils
Folding transition

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