Dynamics of DNA scanning and recognition by transcription factors

DNA扫描和转录因子识别的动力学

• 批准号: 10557921
• 负责人: Junji Iwahara
• 金额: $ 47.42万
• 依托单位: UNIVERSITY OF TEXAS MED BR GALVESTON
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-02-01 至 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10557921
• 关键词: Affinity; Behavior; Binding; Biochemical; Biological; Biophysics; Cells; Chemicals; Compensation; DNA; DNA Sequence; DNA-Binding Proteins; DNA-Protein Interaction; Development; Disease; Electrostatics; Enhancers; Functional disorder; Gene Expression Regulation; Genes; Genome; Genomic DNA; Human; Ions; Kinetics; Knowledge; Modification; Nature; Play; Process; Proteins; Regulatory Element; Research; Role; Scanning; Side; Site; Testing; Therapeutic; Thermodynamics; Work; human disease; improved; interfacial; promoter; therapeutic target; transcription factor

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.

抽象的 转录因子在基因表达的调节中起着至关重要的作用。对这些的更深入的理解 蛋白质将促进人类疗法的发展，因为许多人类疾病和疾病是 与转录因子的功能障碍或异常有关。为了调节基因，转录因子 必须首先将其功能靶标与顺式调节元素（例如启动子和增强子）中的功能目标结合在一起 基因组。了解与顺式调节元素的特定相互作用是必不可少的，但对我们来说不足 完全了解转录因子的工作原理。尽管许多转录因素识别 具有高亲和力的特定DNA序列，这些蛋白还与其他DNA序列结合，较弱 亲和力。基因组中大量的非特异性位点弥补了它们的弱亲和力，使得 对转录因子的深刻总体影响。转录因子的动力学和热力学效率 与其功能目标结合应受到与非目标位点的先验相互作用的强烈影响 基因组DNA。该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，识别特定序列并定位功能很重要 调节基因的位点。研究小组使用生物物理，生化和细胞生物学方法 该项目将提出以下两个问题：1）转录因子如何达到功能目标 关于基因组DNA？ 2）如何在蛋白质和DNA之间发生静电相互作用？基因组 包含许多用于转录因子的高亲和力序列，但只有很小的位点 对于基因调控功能。这些高亲和力的绝大多数是自然诱饵 可以隔离非功能区域中的转录因子。研究团队将检验一个假设 自然诱饵中的隔离及其可访问性的改变是可控机制 调节转录因子目标DNA关联的效率。研究团队还将追求 促进对DNA扫描过程的原子级知识，重点关注侧链的行为 对于DNA识别至关重要。 PI的组最近揭示了界面离子对的高度动态性质 及其在蛋白质-DNA关联中的熵作用。研究小组将进一步研究离子的作用 DNA识别和通过转录因子扫描中的配对动力学。研究小组表明 分子间离子对的化学修饰可以显着增强蛋白-DNA结合亲和力。 研究团队将把这些知识应用于转录因子的合成诱饵。 通过这些研究，该项目将有助于改善针对与转录因子有关的治疗剂 人类疾病和疾病。