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。更深入地了解这些 蛋白质将促进人类治疗剂的发展，因为许多人类疾病和病症 与转录因子的功能障碍或异常相关。调节基因转录因子 必须首先结合到它们的顺式调节元件内的功能靶标，如启动子和增强子， 基因组顺式调控元件的特异性相互作用的知识是必要的，但对我们来说是不够的。 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 尽管这些蛋白质与特定的DNA序列具有高亲和力，但这些蛋白质也与具有较弱亲和力的其他DNA序列结合。 亲和力基因组中大量的非特异性位点弥补了它们的弱亲和力， 对转录因子产生了深远的影响。转录因子的动力学和热力学效率 与其功能靶点结合的能力应受到先前与非靶位点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 转录因子借此扫描DNA，识别特定序列， 基因调控的位点。研究小组利用生物物理学、生物化学和细胞生物学方法， 本项目的第一部分将探讨以下两个问题：1）转录因子如何到达功能靶点 基因组DNA上吗2)蛋白质和DNA之间如何发生静电相互作用？基因组 包含许多转录因子的高亲和力序列，但只有一小部分位点 对基因调控有作用。这些高亲和力位点中的绝大多数作为天然诱饵， 可以将转录因子隔离在非功能区域。研究小组将测试一个假设， 天然诱饵中的螯合和改变其可接近性作为可控机制， 调节转录因子与靶DNA结合的效率。研究小组还将继续研究 推进DNA扫描过程的原子级知识，重点是侧链的行为 对DNA识别至关重要。PI的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缔合中的熵作用。研究小组将进一步研究离子的作用， 转录因子对DNA识别和扫描的动力学。研究小组表明， 分子间离子对的化学修饰可显著增强蛋白质-DNA结合亲和力。 研究小组将把这些知识应用于改进转录因子的合成诱饵。 通过这些研究，该项目将有助于改善靶向转录因子相关的治疗方法， 人类疾病和失调。

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.