Biophysicists have elucidated why unexpected structures can sometimes arise during protein design.

Artificially designed proteins are usually based on building blocks that obey strict rules of symmetry. As such, their structure can generally be predicted using computer simulations. But there are exceptions: Some proteins designed on computers exhibit surprising new structures or properties that could be useful. An international team led by Professor Alena Khmelinskaia from the Department of Chemistry at LMU and Professor Neil King from the University of Washington has now discovered why this is the case: Some proteins contain flexible components and can take on more than one structure. These findings could open up new avenues for the development of customized proteins.

In their study, the researchers analyzed three designer proteins which exhibited significantly different structures in experiments than predicted. These proteins are synthetized as follows: First, two or three of the starting materials react with each other and form so-called dimers or trimers. By means of self-assembly, these dimers and trimers are then supposed to produce highly symmetrical structures such as icosahedra or octahedra. However, this did not always occur: In addition to the pre-calculated structures, the researchers also found quite a number of particles that were substantially larger or had even formed completely different architectures.

Deviating proteins investigated in detail

“To understand the cause of these deviations, we characterized these three reactions in detail,” says Khmelinskaia. With various investigation methods such as cryo-electron microscopy and mass spectrometry as well as mathematical, AI-supported computing methods and simulations, the researchers uncovered the principal cause of their observation.

As the scientists demonstrate, there are small local areas in the investigated proteins that are structurally flexible and do not behave in a completely rigid manner. “Remarkably, this flexibility produces not just an undefined polymorphism of structures, but only a small defined number of possible structures – that is to say, oligomorphism,” explains Khmelinskaia.

The three proteins thus behave similarly to the natural proteins that form the shells of viruses or support the formation of vesicles, taking on very different sizes and shapes. “The oligomorphism we observed opens up interesting prospects for the development of adaptable proteins tailored to specific applications,” says Khmelinskaia. “The design principles presented here could decisively advance the development of customized protein nanomaterials.”