The life of a cell relies heavily on the continuous production of proteins. This task is assigned to tiny intracellular machines—ribosomes. First, a messenger RNA molecule delivers a genetic instruction copied from DNA to the ribosome, and the ribosome, like a reading device, translates this text into the language of amino acids by linking them into long chains of future proteins. This process is called translation, and it is so crucial that it has become a primary target for antibiotics. These drugs enter a bacterium and disrupt some stage of protein assembly, leading to the microbe’s death. However, bacteria can defend themselves: they slightly alter the shape of their molecular components, and the medicine no longer recognizes them. To develop new antibiotics and enhance existing ones, a detailed understanding of all molecular interactions during translation is necessary. Older research methods are either too cumbersome and require hazardous radioactive substances, or they fail to provide the needed precision.
A group of scientists from the St. Petersburg Institute of Nuclear Physics (part of the Kurchatov Institute), along with their colleagues from Peru and Germany, found a simple and elegant solution. They created a test platform based on the physical phenomenon of microthermophoresis. The essence of the method is straightforward. A researcher labels the molecule of interest with a special fluorescent dye and introduces it into an ultra-thin glass capillary. Then, an infrared laser is directed at this capillary, creating a temperature gradient inside—from a warm zone to a cold one. Under this gradient, the labeled molecule begins to move in a specific direction. The speed and direction of its movement depend on the molecule’s size, electric charge, and surface coating. If any partner molecule binds to this fluorescent molecule, its travel speed through the capillary changes. By measuring this change, scientists can precisely determine the occurrence of the interaction and even gauge the binding strength between the molecules.
Previously, this method was poorly suited for studying translation because it was difficult to select labels that wouldn’t interfere with ribosome function, and the entire protein assembly system is highly complex, consisting of many components. The authors of this study managed to identify suitable harmless dyes, chemically attach them to the necessary substances, and develop a gentle technique for labeling the ribosomes themselves. Afterward, they focused on investigating the very first and most intricate stage of protein synthesis—initiation. During this phase, the ribosome assembles into a working machine, attaches to messenger RNA, and recruits auxiliary proteins known as initiation factors, forming a large multicomponent complex.
In their experiments, the scientists observed an interesting phenomenon: the auxiliary proteins assist each other in attaching to the ribosome and amplify each other’s effects. Moreover, they were able to clarify the specific role of each of these proteins at the start of assembly. Through this, the researchers demonstrated that their model platform is well-suited for fast, affordable, and controlled study of even the most bulky molecular structures.
Next, the scientists put the new technology to the test. They examined how various substances that inhibit protein synthesis work: DNA fragments (aptamers), natural antimicrobial peptides, and classic antibiotics. The platform allowed them to quickly assess how strongly each substance binds to its target. This type of information is essential in the early stages of drug development to weed out weak candidates and avoid wasting time on them.
The project supervisor, supported by an RSF grant, is Daria Vinogradova. Source: Daria Vinogradova / B.P. Konstantinov St. Petersburg Institute of Nuclear Physics, NRC “Kurchatov Institute”
According to Daria Vinogradova, a Candidate of Physical and Mathematical Sciences and a research fellow at the institute, this method is already ready for use in pharmaceuticals:
“The method we have proposed represents a ready-made tool for the pharmaceutical industry, allowing for rapid and precise testing of the potential and mechanisms of action of new antimicrobial compounds, which is extremely important given the growing resistance of microorganisms to drugs. In the future, we also plan to apply this platform to study the fundamental principles of translation, including the role of regulatory elements in mRNA, which is key to developing mRNA vaccines against viral infections and oncological diseases.”
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