De novo design of structural and functional extensions of the SynRFR beta-solenoid scaffold

蛋白质设计是一个快速发展的领域，可能会给人类带来巨大的未来利益。从头开始的蛋白质设计提供了一个机会来测试和提高我们对基本蛋白质生物物理和生物化学的理解，例如蛋白质折叠和序列-结构-功能关系，同时产生有用的催化剂、疫苗和自然界中找不到的纳米材料。为了扩展人造蛋白质组，必须通过计算探索新的结构和功能。由于Rosetta等软件包性能的提高，以及计算能力的增加，使新设计的常规生产成为可能，使更多的研究人员能够加入蛋白质设计工作。由Murray集团(MacDonald等人，2016)设计的贝塔螺线管支架SynRFR是基于五肽重复蛋白质家族的。SynRFR可以支持环路和全域插入，使功能组件的设计更容易，而重复结构理论上允许在单个支架上合并多个这样的组件。SynRFR脚手架的长度也可以改变，从而控制可以容纳的功能模块的数量。该项目将由3部分组成：1。结构插入的从头设计，以产生一个小蛋白核心。迷你蛋白是指小于40个氨基酸但具有有序和稳定的三维结构的多肽链。已经成功地设计了SynRFR支架的Beta发夹延伸(MacDonald等人，2016)，这增加了使用两个或更多这样的插入组装微小蛋白样延伸的可能性。例如，理论上，贝塔发夹可以通过设计相邻的贝塔发夹扩展成一个最小的贝塔三明治，然后再扩展成一个三个发夹的贝塔三明治，这在自然界中是没有观察到的。另一个有趣的扩展是螺旋状的发夹。改进型SynRFR脚手架的合理设计将通过引入SpyCatcher/SpyTag系统的元素来设计可功能化的SynRFR支架(Zakeri等人，2012年)。此外，SynRFR24.1变种将被拆分成两个自组装组件。最后，如果成功，这两种设计将被组合成可功能化的自组装构件。3.对贝塔螺旋结构进行生物信息学分析，以了解贝塔螺线管的“极限”。对PDB的β-螺旋结构的比较分析可以为在SynRFR支架的结构中引入偏离理想性的偏差提供一般设计原则，例如弯曲或用不同的二级结构元素替换部分β-螺线管。

Protein design is a rapidly developing field, with potentially substantial future benefits for humanity. De novo protein design provides an opportunity to test and improve our understanding of fundamental protein biophysics and biochemistry, such as protein folding and the sequence-structure-function relationship, whilst generating useful catalysts, vaccines and nanomaterials not found in nature. Both novel structures and functions must be computationally explored to expand the man-made proteome. The routine production of novel designs has been made possible by the improved performance of software packages, such as Rosetta, and an increase in computing power, enabling more researchers to join the protein design effort. The beta-solenoid scaffold SynRFR, designed in the Murray group (MacDonald et al, 2016) is based on the pentapeptide repeat family of proteins. SynRFR can support both loop and whole-domain insertions, enabling easier design of functional components, whilst the repeating structure theoretically allows the incorporation of multiple such components on a single scaffold. The length of the SynRFR scaffold can also be altered, providing control over the number of functional modules that can be accommodated. The project will consist of 3 parts: 1. De novo design of structural insertions to generate a miniprotein core. Miniproteins are defined as polypeptide chains smaller than 40 amino acids but with ordered and stable 3D structures. A beta-hairpin extension of the SynRFR scaffold has already been successfully designed (MacDonald et al, 2016), raising the possibility of assembling miniprotein-like extensions using two or more such insertions. For example, the beta hairpin could theoretically be expanded into a minimal beta sandwich through the design of an adjacent beta-hairpin, and then into a triple-hairpin beta-sandwich, not observed in nature. A further extension of interest is a helical hairpin.2. Rational design of modified SynRFR scaffolds. Functionalisable SynRFR scaffolds will be designed through introduction of elements of the SpyCatcher/SpyTag system (Zakeri et al, 2012). In addition, the SynRFR24.1 variant will be split into two self-assembling components. Finally, if successful, the two designs will be combined into functionalisable self-assembling building blocks. 3. Bioinformatic analysis of beta-helical structures to inform an exploration of the 'limits' of the beta-solenoid. Comparative analysis of beta-helical structures from the PDB could provide general design principles for introducing deviations from ideality into the structure of the SynRFR scaffold such as a bend or the replacement of parts of the beta-solenoid with different secondary structure elements.