### 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 α-helical coiled coil.

Original language | English (US) |
---|---|

Pages (from-to) | 2801-2811 |

Number of pages | 11 |

Journal | Biophysical journal |

Volume | 83 |

Issue number | 5 |

DOIs | |

State | Published - Nov 1 2002 |

Externally published | Yes |

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### Cite this

*Biophysical journal*,

*83*(5), 2801-2811. https://doi.org/10.1016/S0006-3495(02)75289-2

**Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper.** / Viñals, Jorge; Kolinski, Andrzej; Skolnick, Jeffrey.

Research output: Contribution to journal › Article

*Biophysical journal*, vol. 83, no. 5, pp. 2801-2811. https://doi.org/10.1016/S0006-3495(02)75289-2

}

TY - JOUR

T1 - Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper

AU - Viñals, Jorge

AU - Kolinski, Andrzej

AU - Skolnick, Jeffrey

PY - 2002/11/1

Y1 - 2002/11/1

N2 - 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 α-helical coiled coil.

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 α-helical coiled coil.

UR - http://www.scopus.com/inward/record.url?scp=0036841606&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036841606&partnerID=8YFLogxK

U2 - 10.1016/S0006-3495(02)75289-2

DO - 10.1016/S0006-3495(02)75289-2

M3 - Article

C2 - 12414712

AN - SCOPUS:0036841606

VL - 83

SP - 2801

EP - 2811

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 5

ER -