Dynamics of DNA scanning and recognition by transcription factors

摘要 转录因子在基因表达调控中起着至关重要的作用。对这些问题有更深的认识 蛋白质将促进人类治疗的发展，因为许多人类疾病和障碍 与转录因子的功能障碍或异常有关。来调节基因、转录因子 必须首先与顺式调控元件中的功能靶点结合，例如 基因组。了解与顺式调控元件的具体相互作用是必要的，但对我们来说还不够。 来完全理解转录因子是如何工作的。尽管许多转录因子识别 特定的DNA序列具有高亲和力，这些蛋白质也与其他DNA序列结合较弱 亲和力。基因组中大量的非特异性位点补偿了它们弱的亲和力，使 对转录因子产生深远的整体影响。转录因子的动力学和热力学效率 与其功能靶点的结合应受到先前与非靶点的相互作用的强烈影响 基因组DNA。这个项目的总体目标是加深我们对动态过程的理解 转录因子扫描DNA，识别特定的序列，并定位重要的功能 基因调控的位置。利用生物物理、生化和细胞生物学的方法，研究小组 1)转录因子是如何达到功能靶点的 在基因组DNA上？2)蛋白质和DNA之间如何发生静电作用？基因组 包含许多转录因子的高亲和力序列，但只有很小一部分位点 具有基因调控的功能。这些高亲和力网站中的绝大多数都是天然的诱饵 可以将转录因子隔离在非功能区。研究小组将测试一种假设，即 对天然诱饵的隔离和改变其可获得性是一种可控的机制， 调节转录因子的靶DNA结合效率。研究小组还将继续 推进DNA扫描过程的原子级知识，重点关注侧链的行为 对DNA识别至关重要。Pi的研究小组最近揭示了界面离子对的高度动态性质 以及它们在蛋白质-DNA结合中的熵作用。研究小组将进一步研究离子的作用- 转录因子识别和扫描DNA的配对动力学。研究小组表明， 分子间离子对的化学修饰可以显著提高蛋白质与DNA的结合亲和力。 研究小组将把这一知识应用于改进转录因子的合成诱饵。 通过这些研究，该项目将有助于改进针对转录因子的治疗方法。 人类的疾病和紊乱。

Abstract Transcription factors play crucial roles in regulation of gene expression. A deeper understanding of these proteins will facilitate development of human therapeutics because many human diseases and disorders are associated with dysfunction or abnormality of transcription factors. To regulate genes, transcription factors must first bind to their functional targets within cis-regulatory elements such as promoters and enhancers in the genome. Knowledge of the specific interactions with cis-regulatory elements is essential, but insufficient for us to completely understand how transcription factors work. Although many transcription factors recognize particular DNA sequences with high affinity, these proteins also bind to other DNA sequences with weaker affinity. The vast quantity of nonspecific sites in the genome compensates for their weak affinity, making profound overall impacts on transcription factors. Kinetic and thermodynamic efficiency for transcription factors to bind to their functional targets should be influenced strongly by prior interactions with non-target sites on genomic DNA. The overall objective in this project is to deepen our understanding of dynamic processes whereby transcription factors scan DNA, recognize particular sequences, and locate functionally important sites for regulation of genes. Using biophysical, biochemical, and cell-biological approaches, the research team of this project will pursue the following two questions: 1) How do transcription factors reach functional targets on genomic DNA? 2) How do electrostatic interactions occur between proteins and DNA? The genome contains numerous high-affinity sequences for transcription factors, but only a very small fraction of the sites are functional for gene regulation. The vast majority of these high-affinity sites serve as natural decoys that could sequester the transcription factors in nonfunctional regions. The research team will test a hypothesis that sequestration in natural decoys and alteration of their accessibility serve as controllable mechanisms that regulate efficiency in target DNA association of transcription factors. The research team will also pursue advancing the atomic-level knowledge of the DNA scanning process, focusing on the behavior of side chains crucial for DNA recognition. The PI's group recently revealed the highly dynamic nature of interfacial ion pairs and their entropic roles in protein-DNA association. The research team will further study the roles of the ion- pair dynamics in DNA recognition and scanning by transcription factors. The research team showed that chemical modifications of the intermolecular ion pairs could significantly enhance protein-DNA binding affinity. The research team will apply this knowledge toward improving synthetic decoys for transcription factors. Through these studies, this project will help improve therapeutics targeting transcription factors relevant to human diseases and disorders.