A new building block links proteins to other molecules, thereby enabling the creation of complex three-dimensional shapes: a so-called foldamer. Researchers led by Professor Ivan Huc from the Department of Chemistry and Pharmacy at Ludwig-Maximilians-Universität (LMU), in collaboration with colleagues from Berlin, Bordeaux, and Nantes, have developed an artificial protein-foldamer pair.
Proteins form complex three-dimensional shapes and can assemble into larger structures. Researchers at LMU aim to harness these properties for artificial materials. Arranging proteins and synthetic molecules together with high structural precision has proven challenging. This is due, in part, to the lack of large, clearly defined contact surfaces between the two components.
“A specifically selected protein recognizes a synthetic molecule and binds to it with high affinity,” Huc summarizes. “The structurally well-defined contact surface makes it possible to use the complex as a modular building block for larger molecular architectures.” The team has now published its findings in the journal Nature Chemistry.
The research focuses on what is known as a “foldamer.” This is an artificial molecule that folds into a stable structure—in this case, a helix—much like a protein. The researchers sought a protein that would fit this foldamer precisely. To do so, they used ribosome display, a biochemical method for identifying protein-protein interactions that allows for the testing of numerous protein variants. After four rounds of selection, the team identified variant C10 of a protein scaffold known as nanofitin.
The right-handed P-helix of the foldamer binds to the C10 protein, whereas no binding was detected for the left-handed M-helix. The protein and foldamer come into contact over a large, clearly defined surface area. Earlier protein-foldamer complexes were less stable or required flexible linkers. The team investigated how the protein and foldamer fit together spatially using, among other methods, nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. The researchers also analyzed larger complexes using mass spectrometry.
They then used these binding pairs to build more complex structures. A foldamer designed for this purpose was able to bind two proteins while keeping them spatially separated. Conversely, protein dimers could be engineered to bind two foldamers.
In addition, ring-shaped structures and a one-dimensional, zigzag-shaped network formed in the crystals. The arrangement can be influenced by the geometry of the building blocks. For example, the length of the foldamer determines the distance between and the spatial orientation of the bound proteins. Computer-aided analyses of the crystal lattice reveal high porosity. The largest cavities could theoretically accommodate spheres with a diameter of about five nanometers.
“Our results show that artificial foldamers can be used as precise connecting elements for protein architectures,” said Huc. “Since their length and chemical composition can be modified, they could play a role in the future in the construction of porous three-dimensional materials, thereby introducing additional functional groups into such structures.”
Another avenue for future research is the targeted arrangement of naturally occurring proteins. If these proteins are equipped with foldamer-binding domains, foldamers could bring them together or keep them at a defined distance from one another, thereby potentially influencing their biological function.