14-ERASynBio BioOrigami

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，并最终适用于实际应用。由生物聚合物（如蛋白质和核酸）组装的分子结构代表了合成生物学所有分支的基本功能单元。虽然该领域的许多方法使用“即插即用”策略来工程化自然进化的生物部分（主要是基因和功能蛋白质结构域），但合成生物学的巨大挑战不仅是将现有的天然结构联合收割机组合，而且是重新组装自然界中看不见的分子结构，这些分子结构可以体现新的功能并可持续地产生以用于不同的应用。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的序列，以控制自组装成定义的三维（3D）纳米结构。本提案的主要目标是发展对这些基本过程的理解和应用工具。我们将专注于最通用的生物分子，多肽，这也是最难控制的。我们将测试和展示新的多肽和核酸-多肽杂交系统的设计和工程工具。这将为前所未有地控制基于生物分子的纳米结构和材料的构建和应用铺平道路。生物聚合物可以自组装成纳米尺度的复杂结构。在细胞工厂中进行可持续的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各种技术应用。更具体地说，蛋白质提供了复杂的自组装纳米结构的巧妙例子，这些纳米结构具有超出任何人造材料的多功能性，包括催化，分子识别，细胞支架组装等。然而，我们从头设计天然蛋白质样结构和功能的能力虽然有所改善，但仍然有限。相比之下，近几十年来，DNA已经被生物工程师重新利用，以形成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纳米结构，从盒子到球体，具有几纳米的特征分辨率。尽管工程化的基于核酸的纳米结构已经通过化学修饰而功能化，但与蛋白质相比，它们的功能范围极其有限。该建议旨在联合收割机结合多肽和核酸系统的优点并规避两者的限制。我们现在已经达到了在合成生物学的相当大的进步收获的潜力，基于多肽的纳米级结构的设计的门槛。为了实现这一目标，该项目旨在将合成生物学的不同子领域之间的概念和技术转化，结合结构生物学，DNA纳米技术，数学和大规模基因合成的方法。BioOrigami联盟由七个小组组成，他们是基于核酸，肽和蛋白质的分子合成生物学的先驱。我们计划将蛋白质结构的设计进展到自然界中存在的折叠之外，并弥合优雅但基本上无功能的自组装核酸纳米结构与蛋白质组装体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. 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, 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.