Molecules in full gallop
An interdisciplinary team of scientists investigates how exactly individual biomolecules move around. One of the tricks the researchers use involves tiny pores that only allow one molecule to slip through at a time.
“Proteins are the workhorses of our body,” says Sonja Schmid. They transmit messages, assemble cells, transport energy, and much more. Performing these tasks requires the proteins to be in constant motion — folding open and shut, bending and twisting, forming temporary partnerships, trapping atoms, and letting them go again.
These dynamic processes occur on the scale of millionths of a millimeter. Indeed, researchers are unable to observe the exact sequence of such movements with conventional methods. “Typical experiments look at millions of molecules at the same time, but only their mean value can be measured. The individual movements fall by the wayside,” says Schmid.
Similarly, a single high-resolution image created with an electron microscope, for example, only provides a snapshot of what’s going on. Schmid, who has led a research group as an assistant professor at the Department of Chemistry of the University of Basel since early 2024, wants to change that and instead directly watch single molecules at work.
Video instead of stills.
Schmid compares this to the sequence of a horse’s gallop, which couldn’t be deciphered until the advent of film. The exact movements only became clear when images of a single horse were captured in quick succession.
“If we look at the dynamics of individual molecules in a similar way, it allows us to understand many biological processes for the first time.” This can be protein malfunction in cancer cells or elsewhere.
Unfortunately, the technical capabilities for tracking these “protein gallops” are still limited. With that in mind, Schmid’s team is developing various methods for shedding light on the matter with single-molecule precision — for example, using a special fluorescence method (FRET) that can resolve movements on the scale of just a nanometer.
Experiments involving “nanopores” also provide valuable information. At the heart of this measurement setup are two small fluid chambers. The chambers are separated from one another by a thin membrane that contains a nanopore — a tiny hole measuring just about a nanometer across, to fit the size of the molecule under study. After placing the sample solution in one of the chambers, the researchers apply an electric voltage that drives the molecules through the nanopore into the neighboring chamber one after another.
For the molecules, this is probably a bit like when people have to squeeze through a small hatch: It’s easier for a small woman than for a man with broad shoulders. Other factors, such as wearing a large backpack, also affect how fast the hatch can be passed.
It’s the same with the molecules: Their passage through the nanopore will be more or less straightforward depending on how they’re currently folded or what additional modifications they exhibit. “When a molecule briefly gets stuck in the pore, there’s a characteristic reduction in current flow,” explains Schmid. Using machine learning, the researchers can recognize significant patterns in tiny current blockages and derive conclusions regarding each individual molecule’s size, shape, and charge.
Tailored design on the nanoscale.
“The exciting challenge is to find the right pore and experiment for a given molecule and question at hand,” says Schmid. “That takes a lot of creativity.” Schmid’s team uses naturally occurring pore proteins, such as a bacterial toxin that perforates cell membranes. This method recently helped them gain a better understanding of the “immune system” of bacteria. Specifically, bacteria need to protect themselves against special viruses known as phages. In the event of a phage attack, the bacterial defense system raises the alarm and produces specific signaling substances.
For the first time, researchers working with Schmid have demonstrated that these messenger molecules usually come in 3-fold or 4-fold symmetry. The nanoscientist says that, in the future, the findings could also help with the diagnosis of infections in human medicine. To this end, the machinery of the bacterial immune system could be reprogrammed so that it was triggered by contact with pathogens in human blood or saliva — rather than by contact with phages. Messenger molecules formed in response could then be detected using nanopores.
Here, the key thing is that the measuring device would be portable and cheap to produce — and could therefore be used even in remote regions or regions with limited healthcare provision. In other experiments, Schmid also uses synthetic materials such as solid-state chips with an extremely thin silicon nitride membrane.
With these, she builds unique protein traps in order to observe individual molecules more precisely and for a longer period of time. Schmid fabricates these chips in collaboration with the Swiss Nanoscience Institute: “With our measurements, we aim to break new ground. To do this, we need top-quality material — and we’re lucky to have the necessary expertise right here in Basel.”
From: UNI NOVA - Das Wissenschaftsmagazin der Universität Basel (Text: Yvonne Vahlensieck)
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