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首页> 美国卫生研究院文献>Nucleic Acids Research >Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components
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Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components

机译：解释蛋白质/ DNA相互作用：区分特异性和非特异性以及静电和非静电成分

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We discuss the effectiveness of existing methods for understanding the forces driving the formation of specific protein–DNA complexes. Theoretical approaches using the Poisson–Boltzmann (PB) equation to analyse interactions between these highly charged macromolecules to form known structures are contrasted with an empirical approach that analyses the effects of salt on the stability of these complexes and assumes that release of counter-ions associated with the free DNA plays the dominant role in their formation. According to this counter-ion condensation (CC) concept, the salt-dependent part of the Gibbs energy of binding, which is defined as the electrostatic component, is fully entropic and its dependence on the salt concentration represents the number of ionic contacts present in the complex. It is shown that although this electrostatic component provides the majority of the Gibbs energy of complex formation and does not depend on the DNA sequence, the salt-independent part of the Gibbs energy—usually regarded as non-electrostatic—is sequence specific. The CC approach thus has considerable practical value for studying protein/DNA complexes, while practical applications of PB analysis have yet to demonstrate their merit.
机译：我们讨论了现有方法对理解驱动特定蛋白质-DNA复合物形成的作用力的有效性。使用泊松-玻耳兹曼（PB）方程分析这些高电荷大分子之间相互作用以形成已知结构的理论方法与分析盐对这些络合物稳定性的影响并假设释放抗衡离子的经验方法形成对比。游离DNA起着主导作用。根据此抗衡离子缩合（CC）概念，吉布斯结合能的盐依赖性部分（定义为静电成分）是完全熵的，其对盐浓度的依赖性表示存在于离子中的离子接触数复杂。结果表明，尽管这种静电成分提供了大部分复合物形成的吉布斯能量，并且不依赖于DNA序列，但吉布斯能量的不依赖盐的部分（通常被认为是非静电的）是特定于序列的。因此，CC方法对于研究蛋白质/ DNA复合物具有相当大的实用价值，而PB分析的实际应用尚未证明其优点。

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