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，代表了合成生物学所有分支至关重要的基本功能单位。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（主要是基因和功能性蛋白质结构域），但合成生物学的巨大挑战不仅是结合现有的自然结构，而且是组装自然界中看不见的新分子结构，这些结构可以体现新功能，并为不同的应用可持续地生产。为了实现这一挑战，我们需要开发基本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。本建议的主要目标是发展对这些基本过程和应用它的工具的理解。我们将集中于最通用的生物分子，多肽，这也是最难控制的。我们将测试和演示新的多肽和核酸-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，它们的可持续大规模生产也具有相当大的潜力。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精湛范例，这些纳米结构具有任何人造材料无法达到的多功能，包括催化、分子识别、细胞支架组装和许多其他功能。然而，我们重新设计天然蛋白质样结构和功能的能力虽然有所提高，但仍然有限。相比之下，近几十年来，生物工程师对DNA进行了惊人的改造，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，形成几乎任何二维或三维纳米级结构，从盒子到球体，具有几纳米的特征分辨率。尽管基于工程核酸的纳米结构已经通过化学修饰实现了功能化，但与蛋白质相比，它们的功能范围非常有限。本方案旨在结合多肽体系和核酸体系的优点，规避两者的局限性。我们现在已经达到了合成生物学相当大的进步的门槛，以收获基于多肽的纳米级结构设计的潜力。为了实现这一目标，本项目旨在结合结构生物学、DNA纳米技术、数学和大规模基因合成的方法，在合成生物学的不同子领域之间转化概念和技术。BioOrigami联盟由七个小组组成，他们是基于核酸、多肽和蛋白质的分子合成生物学的先驱。我们计划推进蛋白质结构的设计，超越自然界中存在的褶皱，并弥合优雅但很大程度上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能力的支持。

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.