CAREER: Leaving the Fold: Leveraging Mass Spectrometry Proteomics to Shift the Paradigm on Protein Folding
职业:离开折叠:利用质谱蛋白质组学改变蛋白质折叠的范式
基本信息
- 批准号:2045844
- 负责人:
- 金额:$ 84.71万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Continuing Grant
- 财政年份:2021
- 资助国家:美国
- 起止时间:2021-01-01 至 2025-12-31
- 项目状态:未结题
- 来源:
- 关键词:
项目摘要
Proteins must fold themselves up into specific three-dimensional shapes to perform tasks required by the cell. On the other hand, when proteins fold into the wrong shape, they can disrupt the normal functioning of the cell, and are associated with a wide range of maladies including Alzheimer's and Parkinson's diseases. How is it that proteins ‘know’ how to fold into the correct structures (at least, most of the time)? Simple proteins typically have the property that after being disassembled in a test tube, they can spontaneously refold back into their native structures. This implies that their native states are also their most stable forms, and therefore thermodynamics naturally favor their formation. However, most studies of protein folding to date focus on a small number of simple model systems and leave out the fact that cells have thousands of different proteins, many of which are bigger and more complicated than the ones that are typically amenable for biophysical characterization. The purpose of this project is to apply modern mass spectrometry (MS) proteomics methods – which can routinely characterize thousands of proteins in complex mixtures – to problems in protein folding. These tools will enable the exploration of many classes of proteins whose folding has never been interrogated. Moreover, since the majority of the concepts and theories about protein folding have been based on a heretofore “privileged” subset of model proteins, the expectation is that this research will “leave the fold” and shift current paradigms on protein folding. The project will also provide opportunities to engage individuals that are underrepresented in the scientific community and workforce. One of these activities targets first-generation undergraduates and integrates closely with the research plan. The second activity is designed to meet a pressing need in the Baltimore area to introduce more STEM career development resources to low-income communities. A web database aimed at increasing the accessibility of proteomic data generated by this research project to the biophysical community will be developed. Over time, this database could take on the role as the authoritative resource of protein folding due to the ability of proteomics experiments to quantify folding for large numbers of proteins under uniform conditions. Specifically, this project utilizes and expands two emerging approaches in structural proteomics and seeks to address two far-reaching questions about protein folding. Methodologically, the project employs limited proteolysis and crosslinking in order to encode structural information about proteins (as well as their folding intermediates and their misfolded forms following failed attempts at refolding) into cleavage sites and crosslinks, which can be sequenced en masse by mass spectrometry. With these methods, this project will explore the limits of thermodynamic refolding. In particular, proteins from thermophilic organisms and ancient proteins might be expected to be more refoldable than their mesophilic and extant peers. Moreover, chaperones are expected to help rescue the refolding of proteins that could not refold on their own. Experiments conducted as part of this project will explicitly test these hypotheses by using limited proteolysis mass spectrometry to examine the refoldability of a wide range of proteins and with the assistance of a range of several chaperone systems. Secondly, this research aims to uncover the biophysical basis of non-refoldability. When a protein fails to refold, what structure does it assume and what intermediates lead it down that ill-fated path? Experiments will address these questions by using crosslinking mass spectrometry to probe the structural dynamics of refolding proteomes. The results will provide new insight into the topologies of protein free energy landscapes and enable the characterization of kinetically-trapped misfolded species.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.
蛋白质必须将自身折叠成特定的三维形状才能执行细胞所需的任务。 另一方面,当蛋白质折叠成错误的形状时,它们会破坏细胞的正常功能,并与包括阿尔茨海默病和帕金森病在内的多种疾病有关。 蛋白质是如何“知道”如何折叠成正确的结构(至少在大多数时候)? 简单蛋白质通常具有这样的特性:在试管中被分解后,它们可以自发地重新折叠回其天然结构。 这意味着它们的原生状态也是它们最稳定的形式,因此热力学自然有利于它们的形成。 然而,迄今为止,大多数蛋白质折叠研究都集中在少数简单的模型系统上,而忽略了细胞具有数千种不同蛋白质的事实,其中许多蛋白质比通常适合生物物理表征的蛋白质更大、更复杂。 该项目的目的是将现代质谱 (MS) 蛋白质组学方法(可以常规地表征复杂混合物中的数千种蛋白质)应用于解决蛋白质折叠问题。 这些工具将使人们能够探索许多类别的蛋白质,这些蛋白质的折叠从未受到质疑。 此外,由于大多数有关蛋白质折叠的概念和理论都基于迄今为止“特权”的模型蛋白质子集,因此预计这项研究将“离开折叠”并改变当前蛋白质折叠的范式。该项目还将提供机会让科学界和劳动力中代表性不足的个人参与进来。其中一项活动针对第一代本科生,并与研究计划紧密结合。第二项活动旨在满足巴尔的摩地区向低收入社区引入更多STEM职业发展资源的迫切需求。将开发一个网络数据库,旨在提高生物物理学界对本研究项目生成的蛋白质组数据的可访问性。随着时间的推移,由于蛋白质组学实验能够在统一条件下量化大量蛋白质的折叠,因此该数据库可能会成为蛋白质折叠的权威资源。具体来说,该项目利用并扩展了结构蛋白质组学中的两种新兴方法,并寻求解决有关蛋白质折叠的两个影响深远的问题。 从方法上讲,该项目采用有限的蛋白水解和交联,以便将蛋白质的结构信息(以及它们的折叠中间体和重折叠失败后的错误折叠形式)编码成切割位点和交联,这些信息可以通过质谱法进行整体测序。 通过这些方法,该项目将探索热力学重折叠的极限。 特别是,来自嗜热生物体的蛋白质和古代蛋白质可能比嗜温生物和现存的同类蛋白质更容易重折叠。 此外,分子伴侣有望帮助挽救无法自行重折叠的蛋白质的重折叠。 作为该项目的一部分进行的实验将通过使用有限的蛋白水解质谱法来检查各种蛋白质的可重折叠性并在一系列几个分子伴侣系统的帮助下明确测试这些假设。 其次,本研究旨在揭示不可重折叠性的生物物理基础。 当蛋白质无法重折叠时,它会呈现出什么样的结构以及哪些中间体会导致它走上这条不幸的道路? 实验将通过使用交联质谱来探测重折叠蛋白质组的结构动力学来解决这些问题。 研究结果将为蛋白质自由能景观的拓扑提供新的见解,并能够表征动力学捕获的错误折叠物种。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
期刊论文数量(10)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo
- DOI:10.1021/acs.analchem.3c01369
- 发表时间:2023-06-21
- 期刊:
- 影响因子:7.4
- 作者:Faustino,Anneliese M. M.;Sharma,Piyoosh;Fried,Stephen D. D.
- 通讯作者:Fried,Stephen D. D.
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
Stephen Fried其他文献
Stephen Fried的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
相似海外基金
A comparative effectiveness trial of sublingual versus extended-release buprenorphine with individuals leaving a carceral setting
舌下含服与缓释丁丙诺啡对离开监狱环境的个体的有效性比较试验
- 批准号:
10718889 - 财政年份:2023
- 资助金额:
$ 84.71万 - 项目类别:
Community reentry for older adults leaving prison with and without health limitations
有或没有健康限制的出狱老年人重返社区
- 批准号:
10741029 - 财政年份:2023
- 资助金额:
$ 84.71万 - 项目类别:
CAS: Tuning Deoxyfluorination Reactivity and Selectivity by Coherently Modulating Fluoride-pi Interaction Strength, SNAr Kinetics, and Leaving Group Ability
CAS:通过连贯调节氟化物-π 相互作用强度、SNAr 动力学和离去基团能力来调节脱氧氟化反应性和选择性
- 批准号:
2247635 - 财政年份:2023
- 资助金额:
$ 84.71万 - 项目类别:
Standard Grant
Leaving Earth: de novo soil ecology and the Anthropocene.
离开地球:从头土壤生态学和人类世。
- 批准号:
2893669 - 财政年份:2023
- 资助金额:
$ 84.71万 - 项目类别:
Studentship
After leaving a home country: Social determinants of health among refugees and migrants in Japan
离开祖国后:日本难民和移民健康的社会决定因素
- 批准号:
23H03616 - 财政年份:2023
- 资助金额:
$ 84.71万 - 项目类别:
Grant-in-Aid for Scientific Research (B)
Development of a Nursing Management Database to Prevent Nurses from Leaving the Workforce and Motivate Nurses to Work
开发护理管理数据库以防止护士离开劳动力并激励护士工作
- 批准号:
23H03179 - 财政年份:2023
- 资助金额:
$ 84.71万 - 项目类别:
Grant-in-Aid for Scientific Research (B)
Exploring the `Harperian' paradox: Leaving descendants in a crowded plant world
探索“哈珀”悖论:将后代留在拥挤的植物世界中
- 批准号:
RGPIN-2019-04688 - 财政年份:2022
- 资助金额:
$ 84.71万 - 项目类别:
Discovery Grants Program - Individual
Divergent synthesis of unsymmetrical polysulfides by the selective activation of sulfur-bonded leaving groups
通过硫键离去基团的选择性活化不对称多硫化物的发散合成
- 批准号:
22K14687 - 财政年份:2022
- 资助金额:
$ 84.71万 - 项目类别:
Grant-in-Aid for Early-Career Scientists
Collaborative Research: United States University CLOUD (Cosmics Leaving OUtdoor Droplets) Consortium Membership
合作研究:美国大学 CLOUD(宇宙留下户外水滴)联盟成员
- 批准号:
2215489 - 财政年份:2022
- 资助金额:
$ 84.71万 - 项目类别:
Standard Grant
Collaborative Research: United States University CLOUD (Cosmics Leaving OUtdoor Droplets) Consortium Membership
合作研究:美国大学 CLOUD(宇宙留下户外水滴)联盟成员
- 批准号:
2215527 - 财政年份:2022
- 资助金额:
$ 84.71万 - 项目类别:
Standard Grant