'Indirect Readout' Mediation of Protein-DNA Interactions

蛋白质识别和结合特定DNA序列的能力是细胞功能和调节的关键部分。广泛的结构和热力学研究已经对直接接触如何调节蛋白质与DNA的序列特异性结合产生了大致的理解。然而，DNA结构和动力学上的细微差异往往在调节蛋白质-DNA相互作用方面发挥关键作用，这种相互作用是通过独立于蛋白质-DNA直接接触的机制来调节许多细胞过程的。利用这种间接控制机制的调节系统是由乳头瘤病毒E2蛋白结合的序列特异性DNA。E2蛋白在复制和基因转录之间保持着良好的平衡，这对病毒的生命周期是必不可少的；一些人类乳头瘤病毒株的感染直接与宫颈癌有关。乳头瘤病毒复制和病毒基因转录的调节依赖于E2蛋白与病毒基因组中一系列位置的结合。位于E2蛋白结合部位的DNA的结构和动力学是蛋白质结合亲和力的主要决定因素。本研究以E2蛋白-DNA相互作用为模型系统，确定局部DNA结构和动力学调控序列特异性结合的机制。热力学和结构研究的基础是进化相关的E2家族蛋白质的游离蛋白质、游离DNA和蛋白质-DNA复合体的原子分辨结构的集合，这些蛋白质对DNA结构和动力学的敏感性不同。这些结构的可获得性为在蛋白质-DNA直接相互作用保持不变的情况下，发展关于DNA构象倾向对蛋白质结合的间接影响的定量结构-功能相关性提供了独特的机会。

The ability of proteins to recognize and bind specific sequences of DNA is a critical part of cellular function and regulation. Extensive structural and thermodynamic studies have yielded a general understanding of how direct contacts mediate the sequence-specific binding of proteins to DNA. However, subtle differences in DNA structure and dynamics often play critical roles in mediating the protein-DNA interactions that regulate many cellular processes by mechanisms independent of direct protein-DNA contacts. A regulatory system utilizing such an indirect control mechanism is the sequence-specific DNA binding by the papillomavirus E2 proteins. The E2 protein maintains a fine balance between replication and gene transcription that is essential for the viral life cycle; infection by some human papillomavirus strains is directly linked to cervical cancer. The regulation of papillomavirus replication and viral gene transcription is dependent upon E2 protein binding to an array of sites within viral genomes. The structure and dynamics of the DNA located within E2 protein binding sites is a principal determinant of protein binding affinity. The proposed studies use the E2 protein-DNA interaction as a model system to determine the mechanism by which local DNA structure and dynamics regulates sequence-specific binding. The foundation for the proposed thermodynamic and structural studies is the ensemble of atomic resolution structures of free protein, free DNA and protein-DNA complexes for the E2 family of evolutionarily related proteins that differ in their sensitivity to DNA structure and dynamics. The availability of these structures provides a unique opportunity to develop quantitative structure-function correlations regarding the indirect effect of conformational propensities of DNA upon protein binding in a context where direct protein-DNA interactions are kept constant.