Periodic Reporting for period 2 - 3DPROTEINPUZZLES (Shape-directed protein assembly design)
Reporting period: 2019-12-01 to 2021-05-31
Current approaches for protein self-assembly design does not result in the assemblies with the required structural complexity to encode many of the sophisticated functions found in nature. Although impressive-looking protein containers have rationally been designed they have shortcomings such as large pores on the surface and lack of mechanism to assemble and disassemble the containers when loading them with molecules. Current methods also provide a very limited pool of building blocks for design of containers because the design starts from protein complexes, which are not as abundant as proteins consisting of single chains.
In this project, we propose a new protein design paradigm, shape directed protein design, in order to address shortcomings of the current methodology. The proposed method combines geometric shape matching and computational protein design. Using this approach, we will de novo design assemblies with a wide variety of structural states, including protein complexes with cyclic and dihedral symmetry as well as icosahedral protein capsids built from novel protein building blocks. The design efforts is also supported by the development of a high-throughput method to measure the stability of containers directly in cells, without having to purify them. This enables screening of thousands of protein variants and the possibility to improve designed proteins by mimicking evolution.
On the experimental side we have developed a pipeline for screening of protein variants in terms of stability inside bacterial cells. This involves developing methods for DNA library generation and bacterial cell sorting. We are now testing a first iteration of the method on simpler model system, including monomeric proteins.
A software for geometric alignment of proteins identified in with shape-matching techniques is being finalized and a manuscript will be submitted shortly about this. The graphical software, called ZEAL, will be released shortly as an open source program that can be installed on mac and pc.