Proteins are the fundamental building blocks of life. Every animal, every plant and every microorganism is made up of proteins and only ‘works’ on the basis of countless complex processes that are controlled by the interplay of different proteins. It is therefore no wonder that science has a keen interest in a better understanding of these biochemical all-rounders.
The problem is that we cannot simply measure them with a ruler. Researchers thus have to resort to a whole toolbox full of different investigative methods in order to arrive at an accurate picture of what proteins look like, how they behave and how they work.
In a large-scale comparative study involving 19 laboratories around the globe, a team working with LMU scientists Professor Thorben Cordes and Professor Don C. Lamb, alongside Professor Claus Seidel and Dr Anders Barth of the HHU-institute for Physical Chemistry, has now tested an optical method of measuring the precise dimensions and comparability of biomolecules. The work at HHU took place, among others, within the framework of the Collaborative Research Center SFB 1208 "Identity and Dynamics of Membrane Systems – from Molecules to Cellular Functions".
How do you measure moving protein structures?
The FRET analysis of single molecules is especially well suited for this purpose. It makes use of what is known as Förster resonance energy transfer (FRET), where energy from an excited chromophore is non-radiatively transferred to a second chromophore in a distance dependent manner and fluorescence of both dyes is registered. For this optical ruler, synthetic dye molecules are introduced into the biomolecules of interest in order to specifically measure very small distances in the nanometer range (one nanometer corresponds to a billionth of a meter).
This approach already works quite well to measure distances between different molecules. The structure of rigid DNA strands can likewise be examined reliably. Compared to DNA, however, performing similar operations with proteins is considerably trickier. Proteins are more varied and, above all, more mobile, which makes them much more difficult to analyze.
Notwithstanding, the researchers conducting the study have now been able to establish the process for movable proteins too – successfully enough to achieve precise and reproducible results. For example, they were able to measure not only tiny distances within the protein complexes but also to observe structural differences as proteins changed their shape.
The laboratories taking part in the study were able to measure such structural changes to within one nanometer, and that on time scales of less than a millisecond. This astonishing precision shows that even dynamic protein systems can be reproducibly resolved with FRET.
“Until now, many of our fellow structural biologists were sceptical about whether using FRET to analyze proteins could yield reproducible results, and about how to interpret the FRET data when proteins move,” say the authors. “We have now been able to dispel these doubts and to demonstrate the precision of FRET. At the same time, it also shows us the resolution limit, i.e., how tiny and fast protein movements can be, so that we can still observe and quantify them with FRET."
The authors are convinced that another versatile and reliable instrument has now been added to structural biologists’ toolbox. Their hope is that the resultant data will also improve the accuracy of AI-based predictions and thereby further advance our attention for and understanding of dynamic processes in proteins.
Agam, G., Gebhardt, C., Popara, M., ... , Barth, A., Seidel, C. A. M., Lamb, D. C. and Cordes, T., Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nat Methods (2023).