Allosteric Effects of DNA on Bacteriophage 434 Repressor Function

蛋白质结合的DNA序列可以深刻地影响蛋白质-DNA复合体参与基因调控过程的能力。因此，DNA不仅仅是蛋白质组装的被动平台，它还可以作为蛋白质功能的变构效应器发挥积极的第二作用。DNA的变构效应是最近发现的一种现象。因此，了解DNA如何影响转录调节蛋白的形式和功能的目标代表了DNA结合蛋白功能工作的前沿。噬菌体434的抑制子似乎经历了两个构象变化，一个是在非特异性DNA存在下发生二聚，另一个是当抑制子二聚体与特定的DNA结合位点结合时。434阻遏物-DNA复合体的结构和功能可能会随着其结合的DNA序列的同一性而变化。在其他变化中，这些不同的结构形式在形成更高阶低聚化合物的能力上有所不同。这些复合体之间的构象差异影响1)抑制物的序列识别；2)DNA结合抑制物之间的协同作用；3)抑制物与RecA的相互作用。根据这些发现，将确定DNA对抑制物功能的变构效应的基础。在确定了DNA变构的本质之后，这些信息将被用来探索DNA对阻遏物四聚体形成的变构作用，以深入了解DNA依赖的阻遏物协同结合的机制。此外，这些信息将指导旨在提供对各种寡聚形式的阻遏物的分布如何通过与宿主细胞中的其他蛋白质和DNA的相互作用来调节的理解的实验。从这些结果中获得的见解将进一步了解这些和其他序列特异的蛋白质-DNA复合体中功能的关键决定因素。除了作为一个原型系统，可以研究DNA序列对功能的影响，Lambdoid噬菌体还提供了一个概念上和实践上可访问的系统，在其中研究蛋白质-蛋白质相互作用在基因调控中的作用。这些功能使所有级别的学生，包括高中级别的学生，对这个系统的观察和理解做出了重大贡献。通过在这个系统中工作，研究生、本科生和高中学生学会了如何提出重要的生物学问题，并利用他们的观察为理解基因调控机制做出了重要贡献。该系统优雅的简单性确保了其他人也会这么做。

The DNA sequence to which a protein binds can profoundly affect the ability of the protein-DNA complex to participate in gene regulatory processes. Hence, DNA is more than a passive platform onto which proteins assemble, it can play an active, second role as an allosteric effector of protein function. The allosteric effect of DNA is a recently discovered phenomenon. Thus, the goal of understanding how DNA influences the form and function of the transcriptional regulatory protein represents the leading edge of the work on the function of DNA binding proteins. The repressor of bacteriophage 434 appears to undergo two conformational changes, one as it dimerizes in the presence of nonspecific DNA and another as the repressor dimer binds to a specific DNA binding site. The structure and function of the 434 repressor-DNA complex may vary with the identity of the DNA sequence to which it binds. Among other changes these distinct structural forms vary in their abilities to form higher order oligomeric complexes. The conformational differences between these complexes influence 1) sequence recognition by the repressors; 2) cooperative interactions between DNA bound repressors and 3) the interaction of the repressor with RecA. In light of these findings, the basis for the allosteric effect of DNA on repressor function will be determined. Having established the nature of DNA allostery, this information will then be used to probe the allosteric effect of DNA on repressor tetramer formation to provide insight into the mechanism of DNA-dependent cooperative binding of repressor. In addition, this information will guide experiments aimed at providing an understanding of how the distribution of the various oligomeric forms of repressor can be regulated by interaction with other proteins and DNA in the host cell. Insights gained from these results will further the understanding of the critical determinants of function in these and other sequence-specific protein-DNA complexes. In addition to being an archetypal system in which the effect of DNA sequence on function can be investigated, the lambdoid bacteriophages provide a conceptually and practically accessible system in which to study the role of protein-protein interactions in gene regulation. These features have allowed students at all levels, including those at the high school level, to significantly contribute to the battery of observations and understanding in this system. By working in this system, students at the graduate, undergraduate and high school levels, have learned how to ask important biological questions, and used their observations to make important contributions to the understanding of gene regulatory mechanisms. The elegant simplicity of the system ensures that others will do the same.