Protein Crystallization Programmed with DNA

用 DNA 编程的蛋白质结晶

基本信息

批准号：
2104353
负责人：
Chad Mirkin
金额：
$ 52.5万
依托单位：
Northwestern University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2021
资助国家：
美国
起止时间：
2021-06-01 至 2024-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2104353&HistoricalAwards=false
关键词：
Protein Crystallization Programmed DNA

项目摘要

PART 1: NON-TECHNICAL SUMMARYProteins are natural, tiny molecular machines – often 10,000 times smaller than the width of a human hair – that play crucial roles in biology. Since their discovery almost 200 years ago, understanding their structures and functions has enabled scientists to learn about the processes that underpin life and solve scientific problems facing humanity. However, their tiny size makes them incredibly difficult to characterize and understand. One powerful way to determine the structures and functions of proteins is protein crystallography, a technique where X-rays interact with a highly ordered assembly of proteins, known as a single crystal. Unfortunately, obtaining protein single crystals represents a major bottleneck in this process because proteins can interact with each other in many ways that prevent them from forming highly ordered assemblies. This project aims to overcome this challenge using DNA – the genetic code of life – as a blueprint to define the interactions between proteins and thus control how they arrange into single crystals. Importantly, these single crystals will not only provide insight into the tiny world of proteins but will function as new, synthetic materials in their own right, useful as sustainable catalysts or energy conversion materials. Using DNA to control protein interactions and arrangement will allow crystals to be assembled by design. This work will help transform protein crystallography from an experiment of chance to an experiment of purpose to solve pressing societal needs in energy, sustainability, and medicine. Researchers at various stages of their careers (from undergraduate students to postdoctoral researchers) will benefit from the training provided by this project, and will disseminate their knowledge and skills in publications, presentations, and by engagement with students from typically underrepresented and marginalized groups through synergistic outreach activities.PART 2: TECHNICAL SUMMARYProtein single crystals provide valuable, angstrom-level resolution and structural insight into the macromolecules that engender the infrastructure of life and represent a promising class of biomaterials with cooperative properties and concerted functions. This project seeks to understand the interactions that drive crystallization and discover a means to disrupt, reprogram, and redefine those interactions, using the programmability of DNA. This challenge will be approached from four complementary perspectives, each of which will yield valuable fundamental insight into protein crystallization: increasing the role of DNA in protein-DNA crystals; investigating how symmetry and valency affect crystallization; defining specific protein interfaces within crystals; and manipulating the conformations of flexible proteins so that they can be controlled and, ultimately, harnessed. These findings will result in design principles that will allow one to exploit the many distinct attributes of DNA, including its specific hybridization, tunable length, inherent flexibility, and tailorable interaction strength, to program the assembly of proteins. Therefore, achieving these objectives will not only render challenging proteins amenable to crystallographic analysis but also, importantly, open a new class of tailorable, programmed crystalline materials that can harness the intrinsic functionality of proteins. This project will generate new fundamental knowledge of how to control the interplay between DNA-DNA and protein-protein interactions, thereby empowering researchers with tools to engineer the structural outcomes of protein crystallization towards the creation of novel functional biomaterials.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.

第 1 部分：非技术概要蛋白质是天然的微小分子机器，通常比人类头发的宽度小 10,000 倍，自近 200 年前被发现以来，它们在生物学中发挥着至关重要的作用，了解它们的结构和功能使科学家能够了解它们的结构和功能。了解支撑生命的过程并解决人类面临的科学问题。然而，它们的微小尺寸使得它们难以表征和理解，这是一种确定蛋白质结构和功能的强大方法。 X射线与高度有序的蛋白质组装体（称为单晶体）相互作用，不幸的是，获得蛋白质单晶体是这一过程的主要瓶颈，因为蛋白质可以通过多种方式相互作用，从而阻止它们形成有序的组装体。该项目旨在克服这一挑战，利用 DNA（生命的遗传密码）作为蓝图来定义蛋白质之间的相互作用，从而控制它们如何形成单晶体。重要的是，这些单晶体不仅可以提供对蛋白质微小世界的洞察。但会像新的一样使用，合成材料本身可用作可持续催化剂或能量转换材料，利用 DNA 控制蛋白质相互作用和排列将允许通过设计组装晶体，这项工作将有助于将蛋白质晶体学从偶然实验转变为有目的实验。为了解决能源、可持续发展和医学方面紧迫的社会需求，处于职业生涯各个阶段的研究人员（从本科生到博士后研究人员）将受益于该项目提供的培训，并将通过出版物、演示文稿、并通过与来自典型的学生的接触第 2 部分：技术摘要蛋白质单晶为大分子提供了有价值的埃级分辨率和结构洞察力，这些大分子构成了生命的基础设施，并代表了一类具有合作特性和协同功能的有前途的生物材料。旨在了解驱动结晶的相互作用，并发现一种利用 DNA 的可编程性来破坏、重新编程和重新定义这些相互作用的方法。四个互补的观点，每个观点都会对蛋白质结晶产生有价值的基本见解：增加DNA在蛋白质-DNA晶体中的作用；研究对称性和化合价如何影响结晶；定义晶体内的特定蛋白质界面并操纵柔性蛋白质的构象；这些发现将产生设计原则，使人们能够利用 DNA 的许多独特属性，包括其特定的杂交、可调长度、固有的灵活性和可定制的相互作用强度，来对 DNA 进行编程。因此，实现这些目标不仅使具有挑战性的蛋白质能够进行晶体学分析，而且重要的是，开辟了一种新的可定制、编程的晶体材料，可以利用蛋白质的内在功能。该项目将产生新的基础知识。研究如何控制 DNA-DNA 和蛋白质-蛋白质相互作用之间的相互作用，从而为研究人员提供工具来设计蛋白质结晶的结构结果，从而创造新型功能性生物材料。该奖项反映了 NSF 的法定使命，并被认为值得支持通过评估利用基金会的智力优势和更广泛的影响审查标准。

项目成果

期刊论文数量（3）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Spherical Nucleic Acids: Integrating Nanotechnology Concepts into General Chemistry Curricula

球形核酸：将纳米技术概念融入普通化学课程

DOI：
10.1021/acs.jchemed.1c00441
发表时间：
2021-10
期刊：
Journal of Chemical Education
影响因子：
3
作者：
Petrosko, Sarah Hurst;Coleman, Benjamin D.;Drout, Riki J.;Schultz, Jonathan D.;Mirkin, Chad A.
通讯作者：
Mirkin, Chad A.

Modular nucleic acid scaffolds for synthesizing monodisperse and sequence-encoded antibody oligomers

用于合成单分散和序列编码抗体寡聚物的模块化核酸支架

DOI：
10.1016/j.chempr.2022.07.003
发表时间：
2022-11-10
期刊：
Chem
影响因子：
23.5
作者：
Winegar, Peter H.;Figg, C. Adrian;Teplensky, Michelle H.;Ramani, Namrata;Mirkin, Chad A.
通讯作者：
Mirkin, Chad A.

Redefining Protein Interfaces within Protein Single Crystals with DNA

用 DNA 重新定义蛋白质单晶内的蛋白质界面