Härd T, Lundbäck T
Dept. of Biochemistry and Biotechnology, Royal Institute of Technology, Center for Structural Biochemistry, NOVUM, 14157 Huddinge, Sweden.
Biophys Chem. 1996 Nov 29;62(1-3):121-39. doi: 10.1016/s0301-4622(96)02197-7.
The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics. Many molecular mechanisms act in concert to form the specific interface. These include conformational changes in DNA and protein, dehydration of surfaces, reorganization of ion atmospheres, and changes in dynamics. Here we review the current understanding of how different mechanisms contribute to the thermodynamics of the binding equilibrium and the stabilizing effect of the different types of noncovalent interactions found in protein-DNA complexes. The relation to the thermodynamics of small molecule-DNA binding and protein folding is also briefly discussed.
序列特异性蛋白质-DNA相互作用中的分子识别过程十分复杂。所有序列特异性蛋白质-DNA结构共有的唯一特征是一个大的相互作用界面，该界面在形状、极性和静电方面表现出高度的互补性。许多分子机制协同作用以形成特定界面。这些机制包括DNA和蛋白质的构象变化、表面脱水、离子氛围的重组以及动力学变化。在这里，我们综述了目前对于不同机制如何对结合平衡的热力学以及蛋白质-DNA复合物中发现的不同类型非共价相互作用的稳定作用产生影响的理解。还简要讨论了与小分子-DNA结合和蛋白质折叠的热力学之间的关系。
