Periodic Reporting for period 3 - 3DPROTEINPUZZLES (Shape-directed protein assembly design)
Reporting period: 2021-06-01 to 2022-11-30
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, bacterial cell sorting and next generation sequencing. We have demonstrated that our in vivo assay, consisting of two fluorescent outputs, is able to distinguish stable from unstable proteins. Then we expanded the method to enable comparison of lots of protein variants within the same experiments by combining the stability assay with cell sorting and DNA sequencing, and showed that the approach can be used to select for more stable proteins.
The experimental and computational methodology developed so far in this project can be of great value to researchers outside this project, and to find applications in the industrial setting as well.