RUI: Characterization and modulation of SH3 domain binding pathway biophysics

RUI：SH3 结构域结合途径生物物理学的表征和调节

• 批准号: 1852677
• 负责人: K Aurelia Ball
• 金额: $ 36.44万
• 依托单位: Skidmore College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1852677&HistoricalAwards=false
• 关键词: RUI; Characterization; modulation; SH3; domain

The goal of this research is to understand how common protein binding interactions can be tuned in small ways to perform specialized functions in different cellular contexts. The communication within cells that allows cellular processes to occur is mediated by interactions between proteins. Understanding the details of these interactions, including their strength and specificity, will allow researchers to predict and modify the many types of cell behavior. Results will provide deeper insights into how protein binding interactions function in different cellular contexts and help explain how a common interaction can specialize to perform many different cellular functions. Undergraduate students working on this project will have the opportunity to learn both computational and experimental biophysics skills, including how both computational and experimental data can contribute to a project to form a more complete model of protein interactions. Students will also work closely with scientists at Texas Tech University (Mike Latham) and the University of Liverpool (Elliott Stollar) and experience first-hand the importance of collaboration to the modern scientific process. To allow a larger number of students to have an experience with undergraduate research, a research-based lab course will expose students to techniques in computational biophysics and molecular dynamics simulations. In this course, students develop and carryout a research project contributing to the larger project goals. This project also includes the development of a one-credit course for science majors on women and underrepresented groups in science. This course will be geared toward all natural science majors, and will encourage students navigating a major where women are traditionally underrepresented to consider and grapple with ideas about identity in science. Topics will include the challenges that women and minorities may face regarding identifying as scientists, stereotype threat, and impostor syndrome. The course will prepare students to be leaders on the topic of underrepresented groups in science and include a service-learning project.Cellular signaling interactions often involve binding of intrinsically disordered protein regions to small domains, but the binding pathways for these interactions are often not well understood. Full understanding of how these disordered folding and binding interactions contribute to function requires knowing how the binding pathway can be tuned in different contexts by adjusting the disordered sequence, domain sequence, or solvent environment of the interaction. This project will address this question using an SH3 domain-peptide interaction (Abp1p SH3 domain binding to the ArkA peptide) as a model system and employing a combination of molecular dynamics simulations and NMR spectroscopy. SH3 domains are ubiquitous across eukaryotes, but the SH3 domain family contains many variations that impact function. These variations can influence the binding pathway, which in turn will affect biophysical properties such as binding affinity and association rates. This research will investigate how different aspects of the SH3-peptide interaction contribute to the binding pathway and biophysical properties of binding, ultimately defining a set of "rules" that help predict the ways that this interaction can be modulated with different functional consequences. Binding is hypothesized to begin with an initial encounter between ArkA and the SH3 domain, followed by fast initial binding of ArkA segment 1, and then slower, more specific binding of segment 2. Aim 1 of the research will confirm the role of the two ArkA segments in the binding pathway and determine how each affects affinity, specificity, and kinetics. Aim 2 will focus on the role of electrostatics in binding, and how it affects initial steering to the binding site as well its importance for specifically binding the correct peptide sequence. Aim 3 will focus on the importance of proline residues in the peptide sequence. Proline can uniquely affect conformation by switching between cis and trans conformational states and adopting a rigid poly-proline II helix structure. The project will help to advance our understanding of how disordered protein regions bind SH3 domains and how diversity between different SH3 domains and partners contributes to their functional differentiation. Understanding how these biophysical properties are tuned will not only impact the field of SH3 signaling, but also the wider field of disordered peptide binding, as similar mechanisms may exist for other recognition domains.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.

这项研究的目的是了解如何以少量方式调整常见的蛋白质结合相互作用，以在不同的细胞环境中执行专业功能。细胞内允许细胞过程发生的通信是由蛋白质之间的相互作用介导的。了解这些相互作用的细节，包括它们的强度和特异性，将使研究人员能够预测和修改许多类型的细胞行为。结果将为蛋白质结合相互作用如何在不同的细胞环境中起作用，并有助于解释共同相互作用如何专门执行许多不同的细胞功能。从事该项目的本科生将有机会学习计算和实验性生物物理学技能，包括计算和实验数据如何有助于形成更完整的蛋白质相互作用模型。学生还将与德克萨斯理工大学（Mike Latham）和利物浦大学（Elliott Stollar）的科学家紧密合作，并亲身体验合作对现代科学过程的重要性。为了允许更多的学生在本科研究方面具有经验，基于研究的实验室课程将使学生了解计算生物物理学和分子动力学模拟中的技术。在本课程中，学生开发并进行了一个研究项目，为更大的项目目标做出了贡献。该项目还包括开发针对女性科学专业和科学不足群体的一门学科课程。本课程将针对所有自然科学专业的专业，并将鼓励学生在少校中浏览妇女传统上代表性不足而无法考虑并努力探讨有关科学身份的想法。主题将包括妇女和少数民族在认同科学家，刻板印象威胁和冒名顶替综合症方面面临的挑战。该课程将使学生成为科学中代表性不足的群体主题的领导者，并包括一个服务学习项目。细胞信号传导相互作用通常涉及与小领域的内在无序蛋白质区域的结合，但是这些相互作用的结合途径通常不太了解。对这些无序的折叠和结合相互作用如何有助于功能的充分理解，需要通过调整相互作用的无序序列，域序列或溶剂环境来了解如何在不同情况下调整结合途径。该项目将使用SH3域肽相互作用（ABP1P SH3结构域与ARKA肽结合）作为模型系统来解决这个问题，并采用了分子动力学模拟和NMR光谱的组合。 SH3域在整个真核生物中无处不在，但是SH3域家族包含许多影响功能的变化。这些变化会影响结合途径，这反过来会影响生物物理特性，例如结合亲和力和关联速率。这项研究将研究SH3肽相互作用的不同方面如何有助于结合结合的结合途径和生物物理特性，最终定义一组“规则”，这些“规则”有助于预测这种相互作用可以通过不同功能后果调节的方式。假设结合是从ARKA和SH3结构域之间的初始相遇开始的，然后是ARKA段1的快速初始结合，然后较慢，更慢，对段2的更具体的结合。研究的目标1将证实两个ARKA段在结合途径中的作用，并确定每种影响如何影响亲和力，特异性，特异性和动力学。 AIM 2将集中于静电在结合中的作用，以及它如何影响对结合位点的初始转向，以及其对于专门结合正确肽序列的重要性。 AIM 3将集中于肽序列中脯氨酸残基的重要性。脯氨酸可以通过在顺式和反式构象状态之间切换并采用刚性多丙烯II螺旋结构来唯一影响构象。该项目将有助于提高我们对无序蛋白质区域如何结合SH3领域的理解，以及不同SH3领域与伴侣之间的多样性如何促进其功能分化。了解这些生物物理特性如何调整不仅会影响SH3信号传导领域，而且还会影响肽结合无序的范围更广泛的领域，因为其他识别域可能存在相似的机制。该奖项反映了NSF的法定任务，并通过使用该基金会的智力优点和更广泛的影响来评估Criteria criteria criteria criteria criteria criteria criteria criteria criteria均被视为值得的。