New Spectroscopy Method Could Revolutionize Study of Membrane Proteins

Researchers in Switzerland have developed a new method to study the structure of cell membrane proteins, which are a significant source of modern drug targets.

In living organisms, each cell is surrounded by a cell membrane consisting of a double layer of lipids. Proteins attached to this membrane carry various substances across the membrane and into or out of the cell. These proteins also play a crucial role in cell signaling, allowing cells to coordinate metabolic processes, development, and organization.

For these reasons, membrane proteins represent more than 60% of current drug targets, and there is considerable interest in better understanding their biophysical structure. But to characterize membrane proteins, scientists must extract them from the cell membrane and isolate them from all other proteins. Once extracted, membrane proteins cannot be studied in aqueous solutions; they have to be maintained in liquid solutions composed of detergents. They can also be inserted into artificial membranes called nanodiscs, which are made of proteins and lipids, or in pure lipidic membranes.

Such strategies, however, remove them from their physiological environment and do not allow their functioning to be finely observed in situ. Proteins outside their native environment might show different structural properties, therefore misleading drug development.

But a new method developed by a team at University of Geneva (UNIGE) in collaboration with University of Zurich (UZH) studies membrane proteins, in action and in living cells. Based on electron spin resonance spectroscopy, the method uses nanobodies.  “These are fragments of antibodies that are able to recognize and bind to a specific target, such as an antigen or in our case, a membrane transporter, in a very efficient way,’’ says Enrica Bordignon, full professor in the Department of Physical Chemistry at the UNIGE Faculty of Science.

The scientists have artificially produced specific nanobodies for a membrane transporter and use them to directly report on its structure. ‘‘Inserted into E. coli cells, two nanobodies target the desired membrane protein on the inner membrane of the cell and attach to it,’’ adds Markus A. Seeger, associate professor at the Institute for Medical Microbiology at the UZH.

Before insertion, a small magnetic probe was attached to each nanobody. ‘‘When two nanobodies bind to the transporter, we can measure the distance between the two magnetic probes in cells using our EPR methods,” says Bordignon. This electron spin resonance technique measures distance in the nanometer range. ‘‘For the first time, we have managed to obtain a clear picture of the conformation of a membrane protein in its real environment and we could follow the change induced when we modified one single amino acid into another one,” Bordignon adds.

This new strategy allows a precise determination of membrane proteins’ properties in their direct environment and may improve understanding of how these proteins transport certain substances into and out of the cell. It also could be used to better understand and therefore better target the membrane proteins that reject certain anti-cancer drugs outside the cell—thus combating multi-drug resistance.

More details  on the method can be found in a recent issue of Science Advances.