Designed Expanded Co-Crystals for Guest Structure Determination

设计用于客体结构测定的膨胀共晶

基本信息

  • 批准号:
    2003748
  • 负责人:
  • 金额:
    $ 42.29万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    2020
  • 资助国家:
    美国
  • 起止时间:
    2020-07-15 至 2024-06-30
  • 项目状态:
    已结题

项目摘要

Nontechnical DescriptionTo understand biology and to design medical interventions, it is essential to observe the structure adopted by large biological molecules. One of the main methods for determining those structures is to coax the molecules into arranging themselves into a crystal, and then to collect the diffraction pattern that results when these crystals are exposed to an X-ray beam. This conventional process has a high failure rate. Researchers have therefore long sought to develop scaffold crystals that can organize guest molecules.This project will produce a new class of candidate scaffold crystals. Technically, these new crystalline superstructures are co-crystals, since they are composed of both protein and DNA building blocks. To identify the most promising materials in this family, the team will use computational design and all-atom simulations to evaluate candidates for experimental validation. These new crystal materials will feature a modular design where “DNA struts” with any desired sequence are exposed to open channels that are large enough to permit the movement of guest proteins. The research team will grow crystals in which these DNA struts have sequences that are specifically recognized by certain DNA-binding proteins. When these guest proteins latch onto their target DNA they will join the crystal lattice and become observable via X-ray diffraction. This approach circumvents the haphazard crystal growth process that is the basis for conventional crystallography. The resulting materials may therefore provide a transformative method for scientists to routinely and easily observe atomic details for the complexes between DNA and DNA-binding proteins, complexes that drive critically important life processes such as transcription and regulation.Broader Impacts: Precise control of the 3-D position of functional molecules within a scaffold crystal opens the door for materials with unprecedented performance for diverse additional applications including biosensing, catalysis, energy conversion, biomedicine, and biotechnology. To partially explore these alternative applications, the team will provide mentorship and funding for 3 years of undergraduate-led biomolecular design teams (2020, 2021, and 2022), with each project culminating in the international BIOMOD competition. Inspiring and training the next generation of students to innovate at the biomaterials design frontier will directly accelerate the pace of discovery, to the benefit of the scientific community and the nation.Technical DescriptionThe team will use atomistic modeling and simulation to design “expandable” protein:DNA co-crystal structures. The approach is pragmatic: re-engineering protein-DNA systems that are already known to form co-crystals. Inserted DNA struts will be tuned to preserve existing crystallographic contacts and symmetry. Co-crystals will be grown, optimized, and stabilized using crosslinking and ligation chemistry. Critically, large solvent channels in the resulting co-crystals will permit post-crystallization additive molecular assembly, using the inserted DNA struts with the appropriate sequence for site-specific capture of cognate DNA-binding molecules. This approach circumvents the haphazard nucleation and growth that underlies conventional crystallography. The team will determine if DNA-binding molecules captured by the scaffold crystal become visible via X-ray diffraction. Goal 1. Design candidate engineered co-crystals. Use all-atom simulations to prioritize variants for experimental validation.Goal 2. Express, purify, and crystallize novel designed crystals composed of engineered protein and DNA building blocks. Optimize crystal growth by varying the length and sequence of the DNA blocks.Goal 3. Stabilize designed co-crystals using chemical crosslinking. Capture a guest protein that binds specifically to the DNA sequences that were inserted into the struts.The proposed materials have unique aspects that warrant investigation as a potential platform technology. [1] The design and experimental validation of highly porous protein:DNA co-crystals as scaffolds is unknown, as is [2] the subsequent site-specific capture of DNA-binding proteins therein. Unlike conventional biomolecular crystals, the proposed scaffold crystals [3] have pore sizes that may be expanded by changing the number of base pairs present within DNA struts, and [4] have topologies that are amenable to modular incorporation of arbitrary DNA sequences. This project will focus on the structural biology application of these materials, but side applications (e.g. biosensing or catalysis) may be the focus of the 3 annual undergraduate BIOMOD biomolecular design teams for whom the project will provide mentorship and funding.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.
为了理解生物学和设计医疗干预措施,观察大生物分子的结构是必不可少的。确定这些结构的主要方法之一是诱导分子排列成晶体,然后收集这些晶体暴露于X射线束时产生的衍射图案。这种传统的工艺具有很高的失败率。因此,研究人员长期以来一直在寻求开发能够组织客体分子的支架晶体。该项目将产生一类新的候选支架晶体。从技术上讲,这些新的晶体超结构是共晶体,因为它们由蛋白质和DNA构建块组成。为了确定这个家族中最有前途的材料,该团队将使用计算设计和全原子模拟来评估实验验证的候选材料。这些新的晶体材料将采用模块化设计,其中具有任何所需序列的“DNA支柱”暴露于足够大以允许客体蛋白质移动的开放通道。研究小组将培养晶体,其中这些DNA支柱具有被某些DNA结合蛋白特异性识别的序列。当这些客体蛋白质锁定在它们的靶DNA上时,它们将加入晶格,并通过X射线衍射变得可观察。这种方法避免了作为传统晶体学基础的随机晶体生长过程。因此,所产生的材料可能为科学家提供一种变革性的方法,使他们能够常规、轻松地观察DNA和DNA结合蛋白之间复合物的原子细节,这些复合物驱动着至关重要的生命过程,如转录和调节。精确控制3-功能分子在支架晶体中的三维位置为具有前所未有的性能的材料打开了大门,应用包括生物传感、催化、能量转换、生物医学和生物技术。为了部分探索这些替代应用,该团队将为3年的本科生领导的生物分子设计团队(2020年,2021年和2022年)提供指导和资金,每个项目都将在国际BIOMOD竞赛中达到高潮。培养和培养下一代学生在生物材料设计前沿进行创新,将直接加快发现的步伐,造福科学界和国家。技术描述该团队将使用原子建模和模拟来设计“可扩展”蛋白质:DNA共晶结构。这种方法是实用的:重新设计已知可以形成共晶体的蛋白质-DNA系统。插入的DNA支柱将被调整以保持现有的晶体学接触和对称性。共晶体将使用交联和连接化学进行生长、优化和稳定。关键的是,所得共晶体中的大溶剂通道将允许结晶后加成分子组装,使用具有适当序列的插入DNA支柱用于同源DNA结合分子的位点特异性捕获。这种方法避免了传统晶体学中的随机成核和生长。研究小组将确定支架晶体捕获的DNA结合分子是否通过X射线衍射变得可见。目标1. 设计候选工程共晶。使用全原子模拟对变体进行优先级排序,以便进行实验验证。目标2. 表达、纯化和结晶由工程蛋白质和DNA构建块组成的新型设计晶体。通过改变DNA块的长度和序列来优化晶体生长。目标3. 使用化学交联稳定设计的共晶。捕获一种客体蛋白质,该蛋白质特异性地结合到插入到支柱中的DNA序列上。所提出的材料具有独特的方面,值得作为一种潜在的平台技术进行研究。[1]高度多孔的蛋白质:DNA共晶体作为支架的设计和实验验证是未知的,因为[2]随后的DNA结合蛋白的位点特异性捕获。与传统的生物分子晶体不同,所提出的支架晶体[3]具有可以通过改变DNA支柱内存在的碱基对的数量来扩大的孔径,并且[4]具有适合于任意DNA序列的模块化并入的拓扑结构。该项目将重点关注这些材料的结构生物学应用,但副应用(例如生物传感或催化)可能是3个年度本科生BIOMOD生物分子设计团队的重点,该项目将为他们提供指导和资金。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(1)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Stabilizing DNA–Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA
通过 DNA 的晶内化学连接稳定 DNA 与蛋白质共晶
  • DOI:
    10.3390/cryst12010049
  • 发表时间:
    2022
  • 期刊:
  • 影响因子:
    2.7
  • 作者:
    Ward, Abigail R.;Dmytriw, Sara;Vajapayajula, Ananya;Snow, Christopher D.
  • 通讯作者:
    Snow, Christopher 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 }}

Christopher Snow其他文献

Christopher Snow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 }}

{{ truncateString('Christopher Snow', 18)}}的其他基金

Self-Assembly and Dynamic Reconstruction of Expanded Biomolecular Co-Crystals
膨胀生物分子共晶的自组装和动态重建
  • 批准号:
    2310574
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Standard Grant
EAGER: Coherent Guest Protein Organization Inside Host Protein Crystals
EAGER:宿主蛋白晶体内一致的客体蛋白组织
  • 批准号:
    1645015
  • 财政年份:
    2016
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Standard Grant
Programmed Assembly of Conductive Protein Crystals
导电蛋白晶体的程序组装
  • 批准号:
    1506219
  • 财政年份:
    2015
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Continuing Grant
Highly Parallel Synthesis of Nanostructures Inside Crystalline Protein Scaffolds
晶体蛋白支架内纳米结构的高度并行合成
  • 批准号:
    1434786
  • 财政年份:
    2014
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Standard Grant

相似海外基金

Combining structural biology and genetics to understand the function of a multi-gene family expanded in neglected human malaria parasites
结合结构生物学和遗传学来了解在被忽视的人类疟疾寄生虫中扩展的多基因家族的功能
  • 批准号:
    MR/Y012895/1
  • 财政年份:
    2024
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Research Grant
Scalable Production of Precisely Engineered Proteins Using an Expanded Genetic Code
使用扩展的遗传密码大规模生产精确工程蛋白质
  • 批准号:
    BB/Y00812X/1
  • 财政年份:
    2024
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Research Grant
Auditioning the Sonosphere: Live Audio Streaming as Expanded Geo-Practice
试听 Sonosphere:实时音频流作为扩展的地理实践
  • 批准号:
    2887383
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Studentship
MRI RI-Track 2: Development of the Expanded Owens Valley Solar Array (EOVSA)-15--Major Upgrade of a Community Facility for Solar and Space Weather Physics
MRI RI-轨道 2:扩展欧文斯谷太阳能电池阵列 (EOVSA)-15 的开发——太阳能和空间天气物理社区设施的重大升级
  • 批准号:
    2320478
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Standard Grant
Beyond the Visual: Blindness and Expanded Sculpture
超越视觉:失明与扩展的雕塑
  • 批准号:
    AH/Y005856/1
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Research Grant
An expanded 75-color panel of Pdots for spectral multiplexing
用于光谱复用的扩展 75 色 Pdot 面板
  • 批准号:
    10761598
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
Self-Assembly and Dynamic Reconstruction of Expanded Biomolecular Co-Crystals
膨胀生物分子共晶的自组装和动态重建
  • 批准号:
    2310574
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Standard Grant
NSF INCLUDES Network Connector: Expanded Network for Broader Participation in Aerospace Engineering through Education, Mentoring, and Workforce Development
NSF 包括网络连接器:通过教育、指导和劳动力发展扩大网络以更广泛地参与航空航天工程
  • 批准号:
    2304456
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Continuing Grant
Intermediate-sized Expanded Access Protocol for CNM-Au8 in Amyotrophic Lateral Sclerosis (ALS).
CNM-Au8 在肌萎缩侧索硬化症 (ALS) 中的中等规模扩展访问协议。
  • 批准号:
    10835565
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
Cross-disciplinary Research on Expanded Cinema and Intermedia in Japan
日本扩展电影和多媒体的跨学科研究
  • 批准号:
    23K00202
  • 财政年份:
    2023
  • 资助金额:
    $ 42.29万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
{{ showInfoDetail.title }}

作者:{{ showInfoDetail.author }}

知道了