Tidor B, Karplus M
Department of Chemistry, Harvard University, Cambridge, MA 02138.
J Mol Biol. 1994 May 6;238(3):405-14. doi: 10.1006/jmbi.1994.1300.
The association reaction of two molecules to form a single complex must overcome a large entropic barrier due to the loss of translational and rotational degrees of freedom; estimates of the T delta S term are of the order of 30 kcal/mol for proteins. The approach of Chandler and Pratt is used to provide a statistical mechanical formulation for the connection between the gas-phase and solution binding free energies. This makes possible a clear separation of the vibrational contribution to the gas-phase binding enthalpy and entropy from the solvation terms. Further, it suggests that the calculated gas-phase result, should be a good approximation in solution for many systems. To illustrate the formulation, a harmonic dynamics model is used to study the dimerization of insulin. The vibrational entropy increase in the dimer complex, relative to the two separate monomers, is 23 entropy units. This contributes -7.2 kcal/mol to the dimerization free energy. It is not possible to identify a small number of specific dimer modes that give rise to this entropy contribution. Instead, small alterations in the frequencies of many modes below 400 to 600 cm-1 are found to contribute. The relative importance of vibrational and other effects in macromolecule-macromolecule and macromolecule-small molecule associations is discussed.
两个分子发生缔合反应形成单一复合物时,由于平动和转动自由度的丧失,必须克服一个很大的熵垒;对于蛋白质,TΔS项的估计值约为30千卡/摩尔。采用钱德勒和普拉特的方法来提供一个统计力学公式,用于描述气相和溶液结合自由能之间的联系。这使得能够将振动对气相结合焓和熵的贡献与溶剂化项清晰地分开。此外,这表明对于许多系统,计算得到的气相结果在溶液中应该是一个很好的近似。为了说明该公式,使用一个简谐动力学模型来研究胰岛素的二聚化。相对于两个单独的单体,二聚体复合物中的振动熵增加为23个熵单位。这对二聚化自由能的贡献为 -7.2千卡/摩尔。不可能确定导致这种熵贡献的少数特定二聚体模式。相反,发现400至600厘米-1以下许多模式的频率的微小变化会产生贡献。讨论了振动和其他效应在大分子 - 大分子以及大分子 - 小分子缔合中的相对重要性。