TY - JOUR
T1 - Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper
JF - Biophysical Journal
Y1 - 2002
A1 - Jorge Viñals
A1 - Andrzej Koliński
A1 - Jeffrey Skolnick
KW - Biophysical Phenomena
KW - Biophysics
KW - Databases as Topic
KW - Dimerization
KW - DNA-Binding Proteins
KW - DNA-Binding Proteins: chemistry
KW - Entropy
KW - Hot Temperature
KW - Leucine Zippers
KW - Models
KW - Monte Carlo Method
KW - Protein Folding
KW - Protein Kinases
KW - Protein Kinases: chemistry
KW - Saccharomyces cerevisiae Proteins
KW - Saccharomyces cerevisiae Proteins: chemistry
KW - Temperature
KW - Theoretical
KW - Thermodynamics
AB - A lattice-based model of a protein and the Monte Carlo simulation method are used to calculate the entropy loss of dimerization of the GCN4 leucine zipper. In the representation used, a protein is a sequence of interaction centers arranged on a cubic lattice, with effective interaction potentials that are both of physical and statistical nature. The Monte Carlo simulation method is then used to sample the partition functions of both the monomer and dimer forms as a function of temperature. A method is described to estimate the entropy loss upon dimerization, a quantity that enters the free energy difference between monomer and dimer, and the corresponding dimerization reaction constant. As expected, but contrary to previous numerical studies, we find that the entropy loss of dimerization is a strong function of energy (or temperature), except in the limit of large energies in which the motion of the two dimer chains becomes largely uncorrelated. At the monomer-dimer transition temperature we find that the entropy loss of dimerization is approximately five times smaller than the value that would result from ideal gas statistics, a result that is qualitatively consistent with a recent experimental determination of the entropy loss of dimerization of a synthetic peptide that also forms a two-stranded alpha-helical coiled coil.
VL - 83
UR - http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302364&tool=pmcentrez&rendertype=abstract
ER -