Folded state dynamics and hydration in transcriptional regulation

这项研究的主要目的是了解沿着生命进化之树控制遗传调控的基本原理。高等生物，如动物，有复杂的身体结构和明确的发育阶段。为了满足这些复杂的生理需求，高阶生物中的基因表达是由精细调节的分子机制控制的，这在单细胞中是不存在的。迄今为止，这些机制的许多基本细节仍然未知。该项目的目的是阐明动力学在基因调控中的作用。动力学代表了生物分子的基本特性，并与它们与充满水的环境的相互作用密切相关。从这个项目中获得的知识将促进我们对迄今为止很少受到关注的基因调控新兴概念的理解。在完成这个项目的同时，PI还将开发新的计算和数据分析方法，这些方法将适用于解决其他科学问题，从而使更广泛的研究界受益。该项目将通过科学ATL的协调努力，向年轻学生介绍物理科学领域的主题和职业。科学ATL是一个当地的非营利组织，负责举办活动和社区建设活动，以增加获得STEM机会的机会。蛋白质、核酸及其复合物的折叠态在动态涨落中以构象集合的形式存在。折叠态动力学在蛋白质/DNA相互作用的亲和力和特异性中起着重要作用。由于溶液中的结合还涉及到水可及表面积的重新分配，水合作用和动力学是蛋白质/DNA识别的耦合贡献者。与原核基因调控因子相比，真核转录因子与同源DNA序列形成不同的复合物，从而引发不同的生物学结果。这些配合物具有离散的结构，以不连续的、非连续的方式随结合亲和力变化。这种特性，我们称之为序列定向调谐，是复杂真核生物基因组调控的核心。这个项目的目的是揭示动态和水合作用对序列定向调谐的贡献。为了实现这一目标，1)该项目将建立一个体积框架来分析水合作用和动力学对蛋白质/DNA识别的贡献。2)联合溶液核磁共振和分子动力学方法来剖析启动序列定向调谐的转导途径和相关的DNA动力学；3)将定义真核转录因子中驱动序列定向调谐进化的动态约束。使用古老的螺旋-转-螺旋（HTH）基序作为模型，该项目将查询非连续体DNA结合的动态要求，这些非连续体DNA结合是在生命王国中保守的特征HTH基序。该项目得到了生物科学理事会分子和细胞生物科学部分子生物物理集群的支持。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This research is aimed broadly at understanding fundamental principles that govern genetic regulation along the evolutionary tree of life. Higher-order organisms, such as animals, have complex body plans and well-defined developmental stages. To meet these complicated physiologic demands, gene expression in high order organisms is controlled by finely tuned molecular mechanisms that are absent in single-cell counterparts. To date, many basic details of these mechanisms remain unknown. The objective of this project is to elucidate the role of dynamics in gene regulation. Dynamics represent a fundamental property of biological molecules and are intimately related to their interactions with their water-filled environment. The knowledge gained from this project will advance our understanding of emerging concepts in gene regulation that have thus far received little attention. While completing this project, the PI will also develop novel methods of computation and data analysis that will apply to tackling other scientific problems, thus benefiting the wider research community. This project will introduce young students to topics and careers in the physical sciences by a coordinated effort through Science ATL, a local nonprofit organization that produces events and community-building activities that enhance access to STEM opportunities. The folded states of proteins, nucleic acids and their complexes exist as conformational ensembles in dynamic fluctuation. Folded state dynamics play a major role in the affinity and specificity of protein/DNA interactions. As binding in solution also involves a redistribution of water-accessible surface area, hydration and dynamics are coupled contributors in protein/DNA recognition. In contrast with prokaryotic gene regulators, eukaryotic transcription factors form distinct complexes with cognate DNA sequences that invoke divergent biological outcomes. These complexes assume discrete structures that vary in a discontinuous, non-continuum manner with binding affinity. This property, which we term sequence-directed tuning, is central to the regulation of complex eukaryotic genomes. The objective of this project is to unveil the dynamic and hydration contributions to sequence-directed tuning. To achieve this objective, 1) the project will establish a volumetric framework to analyze the hydration and dynamics contributions to protein/DNA recognition. 2) A joint solution NMR and molecular dynamics approach to dissect the transduction pathways and the relevant DNA dynamics that initiate sequence-directed tuning, 3) the dynamic constraints that drive the evolution of sequence-directed tuning in eukaryotic transcription factors will be defined. Using ancient helix-turn-helix (HTH) motifs as models, the project will query the dynamic requirements for non-continuum DNA binding in characteristic HTH-based motifs that are conserved across the kingdoms of life. This project is supported by the Molecular Biophysics Cluster of the Molecular and Cellular Biosciences Division in the Biological Sciences Directorate.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.