Reliable measurement of intrinsically disordered proteins
A new approach allows the shape of a disordered protein to be determined in two different ways - on the same sample
proteins are essential for our bodily functions: Thousands of different proteins perform very different tasks. While some form components of our body cells, others act as enzymes to stimulate elementary metabolic processes, serve as hormones or help the immune system in its work in the form of antibodies. Put simply, proteins can be thought of as long chains of amino acids that organize themselves into various three-dimensional structures. For example, there is the alpha-helix and the beta-pleated sheet. These structures influence how the proteins interact with other proteins and what functions they perform. However, not all proteins are organized in this way: Around 30 percent exist in a disordered state. It is difficult to say to what extent these proteins cluster together or how much they stretch out in the environment - i.e. in an aqueous, cell-like solution. However, this is fundamental to their behavior: The smaller the proteins contract when they swim alone in aqueous solution, the more easily they form clumps when several proteins are present.
Verification of an intrinsically disordered protein (Re is the height, Rg is the total size).
© Miao Yu
Aggregation of proteins is the first step in the formation of plaques in the brain
The intrinsically disordered proteins can take on multiple amyloid formations. When these proteins clump together in the brain, deposits, also known as plaques, form, which increase the risk of developing Alzheimer's and other neurodegenerative diseases. Biophysicists are therefore very interested in the size of proteins in solution. "The potential of a neurodegenerative disease lies in this primal parameter, as it can be used to determine the aggregation potential. And aggregation is an essential step in the formation of plaques," said Professor Edward A. Lemke from the Institute of Molecular Physiology at Johannes Gutenberg University Mainz (JGU) and Adjunct Director at the Institute of Molecular Biology (IMB). The crux of the matter is that there are two methods for measuring this basic parameter - but they produce contradictory results. The fluorescence method can be used to measure the end-to-end distance, i.e. the distance from one end of the protein chain to the other. Small-angle X-ray scattering, on the other hand, analyzes the size of the tangle, which experts refer to as the "radius of gyration". "Although both results serve as a basis for predictions, this original parameter is still the subject of discussion due to the incompatibility of the measurement results," explains Dr. Dmitri Svergun, former group leader at EMBL Hamburg.
New scattering approach: radius of gyration and end-to-end distance on the same sample
The researchers were able to solve this dilemma using a combination of chemical biology and scattering methods. They combined a labeling method with anomalous scattering so that the size of the tangle can be measured as well as the end-to-end distance - and on the same sample. "In this way, we get two parameters from one research method and can analyze how these two variables depend on each other," explains Lemke. In 2017, the researchers were already able to measure both parameters, but two different samples were still required. Now, for the first time, the parameters can also be measured on the same sample.
Note: This article has been translated using a computer system without human intervention. LUMITOS offers these automatic translations to present a wider range of current news. Since this article has been translated with automatic translation, it is possible that it contains errors in vocabulary, syntax or grammar. The original article in German can be found here.
Original publication
Miao Yu, Andrey Yu. Gruzinov, Hao Ruan, Tom Scheidt, Aritra Chowdhury, Sabrina Giofrè, Ahmed S. A. Mohammed, Joana Caria, Paul F. Sauter, Dmitri I. Svergun, Edward A. Lemke; "A genetically encoded anomalous SAXS ruler to probe the dimensions of intrinsically disordered proteins"; Proceedings of the National Academy of Sciences, Volume 121, 2024-12-6
Gustavo Fuertes, Niccolò Banterle, Kiersten M. Ruff, Aritra Chowdhury, Davide Mercadante, Christine Koehler, Michael Kachala, Gemma Estrada Girona, Sigrid Milles, Ankur Mishra, Patrick R. Onck, Frauke Gräter, Santiago Esteban-Martín, Rohit V. Pappu, Dmitri I. Svergun, Edward A. Lemke; "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements"; Proceedings of the National Academy of Sciences, Volume 114, 2017-7-17
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Protein analytics provides a deep insight into these complex macromolecules, their structure, function and interactions. It is essential for discovering and developing biopharmaceuticals, understanding disease mechanisms, and identifying therapeutic targets. Techniques such as mass spectrometry, Western blot and immunoassays allow researchers to characterize proteins at the molecular level, determine their concentration and identify possible modifications.
Topic world Protein analytics
Protein analytics provides a deep insight into these complex macromolecules, their structure, function and interactions. It is essential for discovering and developing biopharmaceuticals, understanding disease mechanisms, and identifying therapeutic targets. Techniques such as mass spectrometry, Western blot and immunoassays allow researchers to characterize proteins at the molecular level, determine their concentration and identify possible modifications.