Viñals Jorge, Kolinski Andrzej, Skolnick Jeffrey
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
Biophys J. 2002 Nov;83(5):2801-11. doi: 10.1016/S0006-3495(02)75289-2.
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.
利用基于晶格的蛋白质模型和蒙特卡罗模拟方法来计算GCN4亮氨酸拉链二聚化的熵损失。在所采用的表示方法中，蛋白质是排列在立方晶格上的相互作用中心序列，具有物理和统计性质的有效相互作用势。然后使用蒙特卡罗模拟方法来采样单体和二聚体形式的配分函数作为温度的函数。描述了一种估计二聚化时熵损失的方法，该量进入单体和二聚体之间的自由能差以及相应的二聚化反应常数。正如预期的那样，但与先前的数值研究相反，我们发现二聚化的熵损失是能量（或温度）的强函数，除了在大能量极限下，此时两条二聚体链的运动变得基本不相关。在单体 - 二聚体转变温度下，我们发现二聚化的熵损失大约比理想气体统计所得到的值小五倍，这一结果在定性上与最近对也形成双链α - 螺旋卷曲螺旋的合成肽二聚化熵损失的实验测定一致。
