A quick, purification-free method was developed by researchers at Institute of Science Tokyo, to capture the detailed 3D structures of flexible sugar molecules. By growing crystals of galectin-10 protein using a cell-free crystallization process and soaking them in sugar solution, the researchers were able to trap and analyze the molecular arrangement of sugars and their interactions with the protein. This offers a powerful tool to accelerate research in drug discovery and molecular biology.
Sugars, or saccharides, do much more than sweeten food. In living organisms, these molecules decorate the surfaces of cell and also act as vital messengers in processes such as infection control and tissue repair. Understanding how these sugar molecules fold, move, and interact with proteins is important for interpreting their roles. But structural complexity and flexibility make them difficult to study using conventional techniques.
To overcome this challenge, a research team at Institute of Science Tokyo（Science Tokyo）, Japan, led by Professor Takafumi Ueno from the School of Life Science and Technology developed a rapid, purification-free method for structural analysis of sugars. Their study was published in the journal Small Structures on October 23, 2025.
Using an innovative cell-free protein crystallization (CFPC) system, the team synthesized crystals of a sugar-binding protein called galectin-10 (Gal-10). This process simply involved crystallization within a test-tube without the need of a cell culture. Within just a day, these protein crystals formed molecular structures that could trap sugar molecules.
"We developed scaffold-like crystals of Gal-10 that hold sugar molecules within their network, allowing us to visualize the precise conformations of sugars at the atomic level using X-ray techniques," explains Ueno.
Once the Gal-10 crystals were developed, the team incorporated several natural sugars into these crystals by soaking in sugar solutions. In this way, the team successfully captured the detailed 3D structures of five different sugars including the first ever atomic-resolution image of melezitose, a complex sugar previously too flexible to study in detail. They also mapped raffinose, a prebiotic sugar which is known to be beneficial for gut bacteria.
Furthermore, the researchers also analyzed the effect of protein mutation on the change in binding of sugar. Replacing a single amino acid (E33A) in the Gal-10 protein allowed the sugar molecules to fit more snugly within the crystal, revealing how small protein modifications influence sugar binding.
"Being able to visualize these sugars so rapidly gives us an entirely new way to explore their behavior," says Ueno. "We can now observe directly how sugar molecules move and interact with proteins which is the key to understanding many biological processes."
To gain a deeper insight into the molecular behavior of the sugars, the team combined X-ray crystallography technique with molecular dynamics simulations. This allowed them to track how the sugars moved over time. The analyses revealed that the crystal gently restricts sugar motion, thus stabilizing them for detailed imaging. Additionally, the approach also showed how tiny shifts in the molecular shapes of sugars affect binding strength, providing details that could aid design of new drugs and biomolecules.
According to the researchers, this CFPC–Gal-10 platform opens the door to faster, more precise analysis of complex carbohydrates. "With our system, researchers could screen hundreds of sugars and small molecules within a short time span, accelerating discoveries in glycobiology, drug development and biomaterials," concludes Ueno.
About Institute of Science Tokyo (Science Tokyo)
Institute of Science Tokyo (Science Tokyo) was established on October 1, 2024, following the merger between Tokyo Medical and Dental University (TMDU) and Tokyo Institute of Technology (Tokyo Tech), with the mission of "Advancing science and human wellbeing to create value for and with society."
Ueno Lab.
https://www.ueno.bio.titech.ac.jp/en/
