14-ERASynBio: BioMolecular Origami

合成生物学的总体目标是使生物系统的工程更容易、更可预测，并最终适用于现实生活中的应用。由生物聚合物组成的分子结构，如蛋白质和核酸，代表着对合成生物学的所有分支至关重要的基本功能单元。虽然该领域的许多方法使用即插即用策略来设计自然进化的生物部分(主要是基因和功能蛋白质结构域)，但合成生物学的重大挑战不仅是结合现有的自然结构，而且是组装自然界中未见的从头开始的分子结构，这些结构可以体现新的功能，并可持续地生产用于不同的应用。为了实现这一挑战，我们需要开发基本的工具来编程核酸和多肽序列，以控制自组装成定义的三维(3D)纳米结构。这项提案的主要目标是了解这些基本程序和应用这些程序的工具。我们将专注于用途最广的生物分子，多肽，这也是最难控制的。我们将测试和演示用于设计和设计新的多肽和核酸-多肽杂交系统的工具。这将为对基于生物分子的纳米结构和材料的构建和应用进行前所未有的控制铺平道路。生物聚合物可以自组装成纳米尺度上定义的复杂结构。它们在电池工厂的可持续大规模生产也有相当大的潜力。这两种特性使它们非常适合不同的技术应用。更具体地说，蛋白质提供了复杂的自组装纳米结构的精湛例子，这些纳米结构具有任何人造材料所达不到的多功能，包括催化、分子识别、细胞支架组装等[1]。然而，我们从头开始设计天然蛋白质样结构和功能的能力，尽管有所改进，但仍然有限。相比之下，近几十年来，生物工程师惊人地改变了DNA的用途，形成了基于互补碱基配对的设计结构。现在，我们可以设计核苷酸序列来形成几乎任何2D或3D纳米级结构，从盒子到球体，特征分辨率只有几个纳米。尽管基于核酸的工程纳米结构已经通过化学修饰实现了功能化[2]，但与蛋白质相比，它们的功能范围极其有限。这项提议旨在结合多肽和核酸系统的优点，并绕过两者的限制。我们现在已经达到了在合成生物学方面取得重大进展的门槛，以挖掘基于多肽的纳米结构设计的潜力。为了实现这一目标，该项目旨在将结构生物学、DNA纳米技术、数学和大规模基因合成的方法结合起来，在合成生物学的不同子领域之间转换概念和技术。BioOrigami联盟由七个小组组成，它们是基于核酸、多肽和蛋白质的分子合成生物学的先驱。我们计划使蛋白质结构的设计超越自然界中存在的折叠，并弥合优雅但主要无功能的自组装核酸纳米结构与蛋白质组装的精致功能和可扩展性之间的差距。该项目得到了大规模基因合成和筛选的力量的支持。

The overall objective of synthetic biology is to make the engineering of biological systems easier, more predictable, and, ultimately, applicable to real-life applications. Molecular structures assembled from biopolymers, such as proteins and nucleic acids represent the basic functional units crucial for all branches of synthetic biology. Whilst, many approaches in this field use "plug-and-play" strategies to engineer naturally evolved biological parts (primarily genes and functional protein domains), the grand challenge of synthetic biology is not only to combine the existing natural structures but to assemble de novo molecular structures unseen in nature that could embody new functions and be produced sustainably for different applications. To realize this challenge we need to develop the fundamental tools to program the sequences of nucleic acids and polypeptides to to control self-assembly into defined three-dimensional (3D) nanostructures. The primary objectives of this proposal are to develop an understanding of these basic processes and tools to apply it. We will concentrate on the most versatile biomolecules, polypeptides, which are also the most difficult to control. We will test and demonstrate tools for the design and engineering of new polypeptide and nucleic acid-polypeptide hybrid systems. This will pave the way to unprecedented control over the construction of, and applications for, biomolecule-based nanostructures and materials.Biopolymers can self-assemble into complex structures defined at the nanometer scale. There is also a considerable potential for their sustainable large-scale production in cell factories. Both properties make them highly desirable for diverse technological applications. More specifically, proteins provide masterful examples of complex self-assembling nanostructures that have versatile functionalities beyond the reach of any manmade materials, including catalysis, molecular recognition, assembly of cellular scaffolds and many others[1]. However, our ability to engineer native protein-like structure and function de novo, although improving, is limited. In contrast, in recent decades, DNA has been spectacularly repurposed by bioengineers to form designed structures based on complementary base pairing. Now, we can design nucleotide sequences to form almost any 2D or 3D nanoscale structures, from boxes to spheres, with a feature resolution of few nanometers. Although engineered nucleic acid-based nanostructures have been functionalized via chemical modifications,[2] compared to proteins their range of functionalities is extremely limited. This proposal aims to combine the advantages of polypeptide and nucleic-acid systems and circumvent the limits of both. We have now reached the threshold of considerable advances in synthetic biology to harvest the potentials of polypeptide-based design of nano-scale structures. In order to achieve this goal, this project aims to translate concepts and technologies between different subfields of synthetic biology, combining methods of structural biology, DNA nanotechnology, mathematics and large scale gene synthesis.The BioOrigami consortium comprises seven groups that are pioneers in molecular synthetic biology based on nucleic acids, peptides and proteins. We plan to progress the design of protein structures beyond folds present in nature and bridge the gap between the elegant, but largely non-functional self-assembled nucleic-acid nanostructures and the exquisite functionality and scalability of protein assemblies. This project is supported by the power of large-scale gene synthesis and screening.