Folded state dynamics and hydration in transcriptional regulation

转录调控中的折叠态动力学和水合

• 批准号: 2028902
• 负责人: Gregory Poon
• 金额: $ 79.59万
• 依托单位: Georgia State University Research Foundation, Inc.
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2028902&HistoricalAwards=false
• 关键词: Folded; state; dynamics; hydration; transcriptional

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.

这项研究的广泛目的是了解沿着生命进化树控制基因调控的基本原理。高阶生物，例如动物，具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，高级生物体中的基因表达受到单细胞对应物中不存在的精细调节的分子机制的控制。迄今为止，这些机制的许多基本细节仍然未知。该项目的目标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属性，并且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增进我们对基因调控新兴概念的理解，而这些概念迄今为止尚未受到关注。在完成该项目的同时，PI还将开发新的计算和数据分析方法，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 Science 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。Science ATL 是一家当地非营利组织，专门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状态作为构象整体存在于动态波动中。折叠态动力学在蛋白质/DNA 相互作用的亲和力和特异性中发挥着重要作用。由于溶液中的结合还涉及水可接触表面积的重新分配，因此水合作用和动力学是蛋白质/DNA 识别中的耦合因素。与原核基因调节因子相反，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。这些复合物呈现离散结构，其结合亲和力以不连续、非连续方式变化。这种特性，我们称之为序列定向调节，是复杂真核基因组调控的核心。该项目的目标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和动力学对蛋白质/DNA 识别的贡献。 2) 联合解决核磁共振和分子动力学方法来剖析启动序列定向调节的转导途径和相关 DNA 动力学，3) 将定义驱动真核转录因子中序列定向调节进化的动态约束。该项目将使用古老的螺旋-转角-螺旋 (HTH) 基序作为模型，询问在生命王国中保守的基于 HTH 的特征基序中非连续 DNA 结合的动态要求。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学集群的支持。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients.

• DOI: 10.1084/jem.20201750
• 发表时间: 2021-07-05
• 期刊: The Journal of experimental medicine
• 作者: Le Coz C;Nguyen DN;Su C;Nolan BE;Albrecht AV;Xhani S;Sun D;Demaree B;Pillarisetti P;Khanna C;Wright F;Chen PA;Yoon S;Stiegler AL;Maurer K;Garifallou JP;Rymaszewski A;Kroft SH;Olson TS;Seif AE;Wertheim G;Grant SFA;Vo LT;Puck JM;Sullivan KE;Routes JM;Zakharova V;Shcherbina A;Mukhina A;Rudy NL;Hurst ACE;Atkinson TP;Boggon TJ;Hakonarson H;Abate AR;Hajjar J;Nicholas SK;Lupski JR;Verbsky J;Chinn IK;Gonzalez MV;Wells AD;Marson A;Poon GMK;Romberg N
• 通讯作者: Romberg N

DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method.

• DOI: 10.1016/j.ab.2021.114298
• 发表时间: 2021-09-15
• 期刊: Analytical biochemistry
• 影响因子: 2.9
• 作者: Vo TD;Schneider AL;Poon GMK;Wilson WD
• 通讯作者: Wilson WD

DNA selection by the master transcription factor PU.1.

• DOI: 10.1016/j.celrep.2023.112671
• 发表时间: 2023-07-25
• 期刊: Cell reports
• 影响因子: 8.8

Dissecting Knowledge, Guessing, and Blunder in Multiple Choice Assessments

剖析多项选择评估中的知识、猜测和错误

• DOI: 10.1080/08957347.2023.2172017
• 发表时间: 2023
• 期刊: Applied Measurement in Education
• 影响因子: 1.5
• 作者: Abu-Ghazalah, Rashid M.;Dubins, David N.;Poon, Gregory M.K.
• 通讯作者: Poon, Gregory M.K.

Salt bridge dynamics in protein/DNA recognition: a comparative analysis of Elk1 and ETV6.

• DOI: 10.1039/d1cp01568k
• 发表时间: 2021-06-23
• 期刊: Physical chemistry chemical physics : PCCP
• 作者: Vo TD;Schneider AL;Wilson WD;Poon GMK
• 通讯作者: Poon GMK