Scientists at the University of Konstanz and Umeå University in Sweden have ar-rived at a structural model of the enzyme adenylate kinase in its closed state
The adenylate kinase enzyme is crucial to managing the energy budget of cells, accelerating the biochemical process whereby energy is stored or released. The enzyme continuously changes between open and closed states. In its closed form, adenylate kinase is particularly active biochemically and thus able to accelerate the chemical reaction of “docked” molecules that it has encased like a clam.
These are called ligands. Researchers at the Universities of Konstanz (Germany) and Umeå (Sweden) have managed to generate a structural model of the atomic make-up of the enzyme in its closed state, including an embedded ligand. Using nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, structural information about the enzyme in its closed state was won – information, that is, about the precise moment that the enzyme is biochemically particularly active.
A particular trick was necessary to facilitate the structural analysis of the enzyme’s closed state in the first place. The research findings, which provide important information about the biochemical mechanisms that govern the energy budgets of cells, were published in the Journal Pro-ceedings of the National Academy of Sciences (PNAS).
The adenylate kinase enzyme opens and closes like a clam: it opens to receive a ligand and closes in order to “process” it biochemically. Afterwards, it opens once again to release it and admit the next ligand. This happens 340 times per second – much too fast to map the individual stages of the process via structural analysis.
For structural biologists, gaining information about the closed state of the enzyme at the precise point in the process where biochemical activity peaks is of immense value. Professor Michael Kovermann, junior professor of magnetic resonance spectroscopy at the University of Konstanz, found a way to make this possible.
He introduced a disulphide bond as a “chemical thread” of sorts in order to force the enzyme to take on its closed form and trap it in this state. The enzyme remains in exactly this position, allowing the researchers to analyse it using NMR spectroscopy and X-ray crystallography. Kovermann was able for the very first time to generate images of the precise moment that the enzyme processes the ligand biochemically.
Two years earlier, he had already managed to take structural images of the enzyme in its open state and with the ligand already in place. “The beauty of it is that, now, we are able to image both liminal states and to make the structural data publicly available”, Kovermann says.
His trick of trapping the enzyme in its closed state can now be used in further inquiries. The state of the enzyme can be controlled by linking or removing the disulphide bond. Kovermann’s analyses had already shown that the enzyme’s affinity for reaction – the chemical pull between the enzyme and its ligand – increases many times over in its closed state, whereas its productive turnover decreases at the same rate. In other words: Chemical activity between ligand and enzyme is particularly high during the closed state. But turnover decreases because the ligand cannot escape the closed “clamshell”, which means fewer ligands in total pass through the enzyme.
Kovermann was also able to prove that adenylate kinase’s structural dynamic strongly depends upon the interaction between enzyme and ligand – i.e. upon the presence or absence of a ligand. To do so, he compared the enzyme’s closed state for both variations, with and without a trapped ligand. If there is no ligand, the closed enzyme’s dynamic remains unchanged as compared to its open state. However, once a ligand is present, marked changes can be observed. “This behaviour is counter-intuitive, it’s not what one would expect”, explains Michael Kovermann. “It is only thanks to NMR spectroscopy that we were able to document this surprising result”.
“Structural basis for ligand binding to an enzyme by a conformational selection pathway”.
M. Kovermann, C. Grundström, E.A. Sauer-Eriksson, U.H. Sauer, M. Wolf-Watz, Proceedings of the National Academy of Sciences 114(24):6298-6303, 2017.
- Direct project funding from: German Research Foundation (DFG), 2013-2015
- Research collaboration with: Umeå University (Sweden)
- The research conducted by Junior Professor Michael Kovermann at the University of Kon-stanz is funded by the Baden-Württemberg Foundation, the Collaborative Research Centre CRC 969 “Chemical and Biological Principles of Cellular Proteostasis” as well as the Kon-stanz Research School Chemical Biology (KoRS-CB).
- Prior publication: “Structural basis for catalytically restrictive dynamics of a high-energy enzyme state”. M. Kovermann, J. Ådén, C. Grundström, E.A. Sauer-Eriksson, U.H. Sauer, M. Wolf-Watz M. Nature Communications, 6:7644, 2015. DOI: 10.1038/ncomms8644.
Note to the editors:
Please click here to download an image:
Caption: Representation of electron density at the disulphide bond (yellow, between C56 and C163) and in its close vicinity.
University of Konstanz
Communications and Marketing
Phone: + 49 7531 88 -3603
Julia Wandt | idw - Informationsdienst Wissenschaft
One step closer to reality
20.04.2018 | Max-Planck-Institut für Entwicklungsbiologie
The dark side of cichlid fish: from cannibal to caregiver
20.04.2018 | Veterinärmedizinische Universität Wien
University of Connecticut researchers have created a biodegradable composite made of silk fibers that can be used to repair broken load-bearing bones without the complications sometimes presented by other materials.
Repairing major load-bearing bones such as those in the leg can be a long and uncomfortable process.
Study published in the journal ACS Applied Materials & Interfaces is the outcome of an international effort that included teams from Dresden and Berlin in Germany, and the US.
Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) together with colleagues from the Helmholtz-Zentrum Berlin (HZB) and the University of Virginia...
Novel highly efficient and brilliant gamma-ray source: Based on model calculations, physicists of the Max PIanck Institute for Nuclear Physics in Heidelberg propose a novel method for an efficient high-brilliance gamma-ray source. A giant collimated gamma-ray pulse is generated from the interaction of a dense ultra-relativistic electron beam with a thin solid conductor. Energetic gamma-rays are copiously produced as the electron beam splits into filaments while propagating across the conductor. The resulting gamma-ray energy and flux enable novel experiments in nuclear and fundamental physics.
The typical wavelength of light interacting with an object of the microcosm scales with the size of this object. For atoms, this ranges from visible light to...
Stable joint cartilage can be produced from adult stem cells originating from bone marrow. This is made possible by inducing specific molecular processes occurring during embryonic cartilage formation, as researchers from the University and University Hospital of Basel report in the scientific journal PNAS.
Certain mesenchymal stem/stromal cells from the bone marrow of adults are considered extremely promising for skeletal tissue regeneration. These adult stem...
In the fight against cancer, scientists are developing new drugs to hit tumor cells at so far unused weak points. Such a “sore spot” is the protein complex...
13.04.2018 | Event News
12.04.2018 | Event News
09.04.2018 | Event News
20.04.2018 | Physics and Astronomy
20.04.2018 | Interdisciplinary Research
20.04.2018 | Physics and Astronomy