'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介导蛋白质与DNA的序列特异性结合产生了一般性的理解。 然而，DNA结构和动力学的细微差异往往在介导蛋白质-DNA相互作用中发挥关键作用，这些相互作用通过独立于蛋白质-DNA直接接触的机制调节许多细胞过程。利用这种间接控制机制的调节系统是乳头瘤病毒E2蛋白的序列特异性DNA结合。 E2蛋白在复制和基因转录之间保持良好的平衡，这对病毒的生命周期至关重要;一些人乳头瘤病毒株的感染与宫颈癌直接相关。 乳头瘤病毒复制和病毒基因转录的调节依赖于E2蛋白与病毒基因组内一系列位点的结合。 位于E2蛋白结合位点内的DNA的结构和动力学是蛋白结合亲和力的主要决定因素。拟议的研究使用E2蛋白-DNA相互作用作为模型系统来确定局部DNA结构和动态调节序列特异性结合的机制。 拟议的热力学和结构研究的基础是原子分辨率结构的自由蛋白质，游离DNA和蛋白质-DNA复合物的进化相关的蛋白质，不同的DNA结构和动力学的敏感性E2家族的合奏。 这些结构的可用性提供了一个独特的机会，开发定量的结构-功能相关性的DNA构象倾向蛋白结合后的间接影响的上下文中，直接蛋白质-DNA相互作用保持不变。

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.