Analysis of protein and DNA-mediated contributions to cooperative assembly of protein-DNA complexes.
Analysis of protein and DNA-mediated contributions to cooperative assembly of protein-DNA complexes.
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分析蛋白质和 DNA 介导的蛋白质-DNA 复合物协同组装的贡献。
DOI：
10.1006/meth.1998.0641
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发表时间：
1998
期刊：
影响因子：
--
通讯作者：
Laue,TM
中科院分区：
文献类型：
--
作者：
Senear,DF;Ross,JB;Laue,TM
蛋白质-DNA复合物的协同组装是一种普遍现象，对转录调控具有特别重要的意义。这些复合物的组装由大分子相互作用的化学控制。从这个意义上说，转录调控是一个化学问题。本文的目的是提出一种分析方法，旨在从化学的角度来理解这一规定。通过研究分子、蛋白质-蛋白质、蛋白质-配体和蛋白质-DNA的所有组合之间的溶液相互作用以及它们之间的相互作用，可以确定调节复合物的不同构型的相对自由能。这决定了它们的分布，从而控制了生物活性。为了说明这种方法，我们将解决噬菌体λ中协同性的分子基础，溶原性裂解开关机制，一个长期以来一直作为基因调控范例的系统。基因调控复合物组装中协同性的驱动力通常被认为是由直接的蛋白质-蛋白质相互作用提供的。然而，蛋白质和DNA介导的其他相互作用也参与其中，并且可能对调节机制至关重要。我们将回顾过去几年来在应用生物物理化学方法研究蛋白质-蛋白质和蛋白质-DNA相互作用方面的进展。这些应用中的许多都是首次用于λ系统。除了描述的物理基础的方法，我们将集中在独特的信息，可以获得和如何联合收割机从几种技术获得的信息，以开发一个全面的观点的关键监管相互作用。
The cooperative assembly of protein–DNA complexes is a widespread phenomenon that is of particular significance to transcriptional regulation. Assembly of these complexes is controlled by the chemistry of the macromolecular interactions. In this sense, transcriptional regulation is a chemical issue. The purpose of this review is to present an analytical approach designed to understand this regulation from a chemical perspective. By investigating the solution interactions between all combinations of molecules, protein–protein, protein–ligand, and protein–DNA, and the interplay between them, it is possible to determine the relative free energies of the different configurations of the regulatory complex. This governs their distribution and thereby controls the biological activity. To illustrate the approach, we will address the molecular basis for cooperativity in the bacteriophage λ, lysogenic–lytic switch mechanism, a system that has long served as a paradigm for gene regulation. The driving force for cooperativity in the assembly of gene regulatory complexes is generally thought to be provided by direct protein–protein interactions. However, other interactions mediated by both proteins and DNA are also involved and may be critical to the regulatory mechanism. We will review advances over the past several years in the application of biophysical chemical methods to investigate protein–protein and protein–DNA interactions. Many of these applications were first employed for the λ system. In addition to describing the physical basis for the methods, we will focus on the unique information that can be gained and how to combine the information obtained from several techniques to develop a comprehensive view of the critical regulatory interactions.