Description
Protein origami is an exciting emerging field, inspired by the success of DNA origami. Proteins however, unlike DNA, have a large number of weak long range interactions which are very difficult to predict and even more to design. This problem can be elegantly solved by using modular components with exactly defined binding partners of which coiled coils are an excellent example (Kočar et al., WIREs, 2014). The topology of where the interacting building blocks are located in the sequence determines the final three dimensional shape of such TOPOFOLD proteins. As an example, a topofold tetrahedron has recently been constructed out of six coiled coil pairs (Gradišar et al., NatChemBiol 2013).
The folding pathway is often critical for the correct structure and function of proteins. In contrast to natural proteins, topofold proteins do not possess a compact hydrophobic core and the folding pathway is therefore determined by the topology of building blocks and the order in which these building blocks assemble.
Here we present a short overview of the methodology used to design arbitrary protein polyhedra. The folding pathway of a topofold protein tetrahedron is presented in detail. In particular we have examined the folding using all-atom structure based (Go) simulations. We are using these simulations to test how different arrangements of building blocks in the protein sequence affect its folding pathway. This allows us to design optimized versions of topofold proteins with smooth folding pathways in order to avoid misfolding and aggregation.
We have also examined the folding pathways using stop-flow techniques. The chevron plot shows a weak dependence on denaturant concentration, which is compatible with multistate folding pathways observed in Go simulations.
