The team successfully tested and validated a new method for measuring the exact dimensions and comparability of biomolecules

Accurate measurement of biomolecules can play an important role in improving our understanding of basic life processes. In a large-scale comparative study involving 19 laboratories around the world, a team working with LMU scientists Professor Thorben Cordes and Professor Don C. Lamb, together with Professor Klaus Seidel from HHU Düsseldorf and Dr Anders Barth from Delft University of Technology, conducted the study. Now test a method for measuring the exact dimensions and comparability of biomolecules.

Their findings have been published in nature ways.

Proteins are the basic building blocks of life. Every animal, every plant, and every living organism is made of proteins and only “functions” on the basis of a myriad of complex processes that are controlled by the interaction of different proteins. It is therefore no wonder that science has a keen interest in better understanding these overall biochemical elements.

The problem is that we can’t simply measure it with a ruler. So researchers have to turn to an entire toolkit full of different investigative methods in order to get an accurate picture of what proteins look like, how they behave and how they function.

How do you measure moving protein structures?

Single-molecule FRET analysis is particularly well suited for this purpose. It uses what is known as Forster resonance energy transfer (FRET), in which energy is transferred from a non-radiatively excited chromophore to a second photosensitive molecule. By artificially introducing color molecules (chromophores) into the biomolecules under investigation, it becomes possible to measure extremely small distances in the nanometer range.

This approach already works well for measuring the distances between different molecules. The structure of DNA strands can also be examined fairly reliably. Compared with DNA, it is much more difficult to perform similar operations with proteins. Proteins are more diverse and, above all, more mobile, which makes them more difficult to analyze.

Now though, the researchers behind the study have now been able to create the process for moving proteins as well — with enough success to yield accurate and reproducible results. For example, they were able to measure not only small distances within the protein complexes but also note structural differences as the proteins changed shape.

On time scales of less than a millisecond, the labs involved in the study were able to measure such structural changes to within one nanometer. This impressive accuracy shows that even dynamic protein systems can be measured repeatedly with FRET.

“Until now, many of our colleagues in structural biology have been skeptical about whether using FRET to analyze proteins can yield any reproducible results at all, and about how to interpret the results when proteins are in motion,” says Thorbin Cordes. “We have now been able to dispel these doubts. But in doing so, we have also shown how small and fast the proteins’ movements can be so that we can monitor and quantify them using FRET.”

The researchers are convinced: Another versatile and reliable tool has been added to the toolkit of structural biologists. They hope that the resulting data will also improve the accuracy of AI-based predictions and thus advance our understanding of dynamic processes in proteins.