The smallest ‘ruler’ ever measures distances as small as the width of an atom

The smallest ‘ruler’ ever is so precise that it can measure the width of a single atom within a protein.

Proteins and other large molecules, or macromolecules, sometimes fold into the wrong shape, and this can affect the way they function. Some structural changes even play a role in conditions such as Alzheimer’s disease. To understand this process, it is important to determine the exact distance between atoms – and clusters of atoms – within these macromolecules, says Steffen Sahl of the Max Planck Institute for Multidisciplinary Sciences in Germany.

“We wanted to go from a microscope that maps the positions of macromolecules relative to each other to the bold step of going inside the macromolecule,” he says.

To construct their intramolecular “ruler,” Sahl and his colleagues used fluorescence, or the fact that some molecules glow when illuminated. They attached two fluorescent molecules at two different points on a larger protein molecule and then used a laser beam to illuminate them. Based on the light released by the glowing molecules, the researchers were able to measure the distance between them.

They used this method to measure distances between the molecules of several well-understood proteins. The smallest of those distances was just 0.1 nanometers – the width of a typical atom. The fluorescent ruler also provided accurate measurements down to about 12 nanometers, giving it a wider measuring range than is possible with many traditional methods.

In one example, the researchers looked at two different shapes of the same protein and found that they could distinguish between these two points because the same two points were 1 nanometer apart for one shape and 4 nanometers apart for the other. In another experiment, they measured small distances in a human bone cancer cell.

Sahl says the team achieved this precision by taking advantage of several recent technological advances, such as better microscopes and fluorescent molecules that don’t flicker or produce a glow that could be confused with another effect.

“I don’t know how they got their microscopes so stable. The new technology is definitely a technical advance,” says Jonas Ries of the University of Vienna in Austria. But future studies will need to determine for which exact molecules it will prove most useful as a source of information for biologists, he says.

“While the new method has impressive accuracy, it does not necessarily achieve the same level of detail or resolution when applied to more complex biological systems,” says Kirti Prakash of the Royal Marsden NHS Foundation Trust and the Institute of Cancer Research in Britain . . Moreover, he says that several other new techniques are already becoming competitive in terms of measuring increasingly smaller distances.

Sahl says his team will now work on two tracks: further refining the method and expanding their ideas about which macromolecules they can now look inside.