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Proteins in glass
CHALMERS, Sweden—As explained by Martin Andersson, professor at the Department of Chemistry and Chemical Engineering at Chalmers University of Technology in Sweden, “Proteins consist of long chains of amino acids that fold in different ways to activate different functions. To understand a protein’s function, these 3D structures are investigated, but if you remove a protein from its membrane environment, it alters its shape. Therefore, it is useful to be able to image and analyze membrane proteins in their normal environment.”
Along those lines, researchers at Chalmers have developed an innovative method for studying proteins that could open new doors for medicinal research. By capturing proteins in a nano-capsule made of glass, the researchers have created a unique model of proteins in natural environments. The researchers published their results in the scientific journal Small.
Because proteins are target-seeking and carry out many different tasks necessary to cells’ survival and functions, they are interesting for the development of new medicines, according to Andersson. This is especially true of proteins in the cellular membrane that govern which molecules can enter the cell and which cannot. Understanding the structure of such proteins and how they work is a critical challenge in developing more advanced medicines, but such proteins are very complex. While several different methods are used for imaging proteins, no method offers a full solution to the challenge of studying individual membrane proteins in their natural environment.
Protein structures are usually unveiled experimentally by X-ray crystallography or NMR spectroscopy—and more recently, by cryo-electron microscopy. Andersson and his colleagues have developed a method for structural analysis of individual proteins on the sub-nanometer scale using atom probe tomography, which had previously been used for analyzing metals and other hard materials. This technique offers a combination of high-resolution analysis of biomolecules in 3D and the chemical sensitivity of mass spectrometry.
As Andersson explained, “It was in connection with a study of contact surfaces between the skeleton and implants when we discovered we could distinguish organic materials in the bone with this technique. That gave us the idea to develop the method further for proteins.”
The well-characterized antibody IgG is used as a model protein. IgG is encapsulated in an amorphous solid silica matrix using a sol-gel process to provide support for atom probe analysis. The silica synthesis is tuned to resemble physiological conditions.
According to Andersson and his colleagues, the 3D reconstructions show good agreement with the protein databank IgG crystal structure. They believe that the silica-embedding strategy can open the field of atom probe tomography to the analysis of biological molecules. The technique may provide high-resolution structural information, as well as chemical information on the atomic scale using isotopic labeling. The team hopes that this method can provide a useful supplement to existing tools in structural biology, especially to examine proteins that have low propensity for crystallization.
To cope with the challenge of keeping the proteins intact in their natural environment, the researchers encapsulated the protein in a very thin piece of glass, only around 50 nanometers in diameter. By slicing off the outermost layer of the glass using an electrical field, they freed the protein atom by atom and recreated it in 3D on a computer. They then verified the results of the study through comparison with existing 3D models of known proteins. In the future, the researchers will refine the method to improve the speed and accuracy.
“The method is groundbreaking in several ways,” says Andersson. “In addition to modeling the three-dimensional structure, it simultaneously reveals the proteins’ chemical composition. Our method offers a lot of good solutions and can be a strong complement to existing methods. It will be possible to study how proteins are built at an atomic level.”
Gustav Sundell, a researcher in Andersson’s research group, added, “With this method, potentially all proteins can be studied, something that is currently not possible. Today, only around 1 percent of membrane proteins have been structurally analyzed successfully. We can study individual proteins, not just study a large number of proteins and create an average value.”
“With atom probe tomography, information on an atom’s mass can also be derived,” Mats Hulander, another researcher in Andersson’s group, remarked. “Because we collect information on atoms’ masses in our method, we can measure the weight. We can then create tests combining medicinal molecules with different isotopes—giving them different masses—which makes them distinguishable in a study. It should contribute to expediting processes for constructing and testing new medicines.”