image: The supermicroscope’s interior. The Cryo-TEM is four meters tall and extremely sensitive. © Charité | Wiebke Peitz
Credit: © Charité | Wiebke Peitz
Ribosomes are miniature factories of life. A detailed understanding of their mechanical mastery lays the foundations for all manner of applications – from manufacturing vaccines to developing new antibiotics. This is why Prof. Christian Spahn, a biophysicist at Charité – Universitätsmedizin Berlin, wants to see these nanofactories in action. And that’s no mean feat: it requires ultra-cold temperatures and a four-meter-tall microscope that has to be handled as carefully as a raw egg. However, it will enable him to observe ribosomes at higher temporal resolution than ever before. Spahn’s project has now secured an ERC Advanced Grant – one of Europe’s most prestigious research funding awards.
All living cells need ribosomes. Measuring just 25 nanometers, these molecular factories decrypt genetic code and use the instructions to produce proteins that serve as structural elements, messenger substances and other molecular tools in cells. Ribosomes operate like an assembly line, turning hundreds of components into protein products at a rapid pace.
“To date, we’ve only been able to capture momentary snapshots of this exceptionally complex process,” says Christian Spahn, Director of the Institute of Medical Physics and Biophysics at Charité. “Now, we want to take a closer look and make the ultra-fast intermediate steps visible.” His DeepRibosome project impressed the European Research Council (ERC), which has awarded Spahn an Advanced Grant of roughly €2.5 million for the next five years.
Higher resolutions means greater effort
Together with his team, Christian Spahn hopes to decipher exactly how ribosomes change shape as they function and how temperature, ions and antibiotics influence ribosomal processes. But this is easier said than done – and calls for cutting-edge technology. A whole range of scientific institutions in Berlin have worked for years to acquire the necessary technical infrastructure, with support from state and federal governments.
Before Spahn’s team can capture images of ribosomes in action, they must first remove the ribosomes from the cell and stimulate them to function outside of their usual environment. The researchers have developed a novel method to achieve this. The reactivated ribosomes are then flash-frozen in liquid ethane at ultra-low temperatures (–150°C), so that, instead of ice crystals forming, crystal-clear ice surrounds the molecules in their natural form. Wafer-thin slices of the sample – just 300 nm thick – are then placed under an extraordinary high-performance microscope: the cryogenic transmission electron microscope (Cryo-TEM).
The supermicroscope: A colossal device more sensitive than a raw egg
What makes this €5 million device so special? It’s capable of visualizing even the tiniest cell structures in their natural, aqueous environment in three dimensions – and at almost atomic resolution, to less than a millionth of a millimeter. Earlier electron microscopes required chemical sample preparation, which meant they did not necessarily reflect the molecules’ original structure. The development of cryogenic electron microscopy, in which samples are not chemically modified, was rewarded with the 2017 Nobel Prize in Chemistry. One of the Nobel laureates, Joachim Frank, taught Christian Spahn the intricacies of this imaging method.
The Cryo-TEM equipment not only takes up a great deal of space – with the microscope alone measuring some four meters – but is also highly sensitive. It cannot tolerate temperature fluctuations, elevated moisture levels or vibrations. As a result, the Cryo-TEM system is housed in a dedicated building. Its double-walled “house-in-house” design features a 1.25-meter-thick concrete floor that offsets vibrations along with an efficient ventilation system.
Complex analysis of hundreds of thousands of images
Despite this, the individual images produced by the microscope are relatively noisy. The final step in creating a 3D model of the ribosome is modern digital image processing software – and computing power. “We analyze hundreds of thousands of images with advanced computing technology to sort and classify them automatically,” explains Christian Spahn. “The computations can take weeks or even months. But this also allows us to visualize very rare, short-lived intermediate states of ribosomes in the millisecond range, which until now have remained hidden.”
Spahn compares the process to analyzing a horse’s gait. “Let’s say we’re photographing a herd of identical horses galloping across a field, countless times, from different angles. We capture each horse at a slightly different point in its sequence of movement. Then, we take all of these individual snapshots and combine them to create a three-dimensional film that depicts their gait in all its detail.”
All this effort is worthwhile: a better understanding of the mechanics behind these protein factories not only clarifies a fundamental principle of life but could also be relevant for biotechnological and medical applications. “These insights could be used to optimize artificial protein manufacturing – including for the production of medicines, vaccines and artificial cells,” says Spahn. “As ribosomes are the primary target for antibiotics, a better understanding of how they function could also support the development of more effective medicines to fight resistant bacteria.”
About the Cryo-TEM
The cryogenic transmission electron microscope is operated by the Core Facility for Cryo-electron Microscopy (CFcryo-EM), which Charité maintains in conjunction with the Max Delbrück Center and the Leibniz Research Institute for Molecular Pharmacology (FMP). The microscope’s purchase was supported by the German Research Foundation (DFG), the Federal State of Berlin, Charité and Freie Universität Berlin. The Max Delbrück Center financed the building’s construction on the Buch campus in Berlin. A ceremony was held in 2023 to celebrate the opening of the building and its microscopy infrastructure. The CFcryo-EM at Charité is part of the Alliance Center Electron Microscopy (ACEM) of the Berlin University Alliance (BUA), a jointly supported virtual and interdisciplinary electron microscopy equipment center of Freie Universität Berlin, Humboldt-Universität zu Berlin, Technische Universität Berlin and Charité.
ERC Advanced Grants
Advanced Grants are one of five research funding programs currently offered by the European Research Council (ERC). They support established elite researchers with an outstanding scientific track record in opening up new fields of research. The project has been awarded funding of €2.5 million for a five-year term.