title: Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper.
abstract: 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.
authors.affiliation: Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA. jvinals@danforthcenter.org
authors.forename: Jorge
authors.initials: J
authors.lastname: Viñals
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Skolnick
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D004268:DNA-Binding Proteins / Q000737:chemistry*; D019992:Databases as Topic; D019281:Dimerization; D019277:Entropy; D006358:Hot Temperature; D016350:Leucine Zippers; D008962:Models, Theoretical; D009010:Monte Carlo Method; D017510:Protein Folding; D011494:Protein Kinases / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases