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X-ray structure analysis shows how MHC I molecules are prepared for peptide loading
For an adequate immune response, it is essential that T lymphocytes recognise infected or degenerated cells. They do so by means of antigenic peptides, which these cells present with the help of specialised surface molecules (MHC I molecules). Using X-ray structure analysis, a research team from Frankfurt has now been able to show how the MHC I molecules are loaded with peptides and how suitable peptides are selected for this purpose.
FRANKFURT. As task forces of the adaptive immune system, T lymphocytes are responsible for attacking and killing infected or cancerous cells. Such cells, like almost all cells in the human body, present on their surface fragments of all the proteins they produce inside. If these include peptides that a T lymphocyte recognises as foreign, the lymphocyte is activated and kills the cell in question. It is therefore important for a robust T-cell response that suitable protein fragments are presented to the T lymphocyte. The research team led by Simon Trowitzsch and Robert Tampé from the Institute of Biochemistry at Goethe University Frankfurt has now shed light on how the cell selects these protein fragments or peptides.
Peptide presentation takes place on so-called major histocompatibility complex class I molecules (MHC I). MHC I molecules are a group of very diverse surface proteins that can bind myriads of different peptides. They are anchored in the cell membrane and form a peptide-binding pocket with their outward-facing part. Like all surface proteins, MHC I molecules take the so-called secretory pathway: they are synthesised into the cell's cavity system (endoplasmic reticulum (ER) and Golgi apparatus) and folded there. Small vesicles then bud off from the cavity system, migrate to the cell membrane and fuse with it.
The maturation process of the MHC I molecules is very strictly controlled: in the ER, proteins known as “chaperones" help them fold. The chaperone tapasin is essential for peptide loading in this process. “When an MHC I molecule has bound a peptide, tapasin checks how tight the binding is," says Trowitzsch, explaining the chaperone's task. “If the bond is unstable, the peptide is removed and replaced by a tightly binding one." However, it has not yet been possible to clarify how exactly tapasin performs this task – especially because the loading process is extremely fast.
The biochemists and structural biologists from Goethe University Frankfurt have now succeeded for the first time in visualising the short-lived interaction between chaperone and MHC I molecule by means of X-ray structure analysis. To do this, they produced variants of the two interaction partners that were no longer embedded in the membrane, purified them and brought them together. A trick helped to capture the loading complex in action for crystallisation: first, the research team loaded the MHC I molecule with a high-affinity peptide so that a stable complex was created. A light signal triggered cleavage of the peptide, which greatly reduced its ability to bind the MHC I molecule. Immediately, tapasin entered the scene and remained bound to the MHC I molecule that lacks its peptide. “The photo-induced cleavage of the peptide was pivotal to the success of our experiment," says Tampé. “With the help of this optochemical biology, we can now systematically reproduce complex cellular processes one by one."
X-ray structure analysis of the crystals revealed how tapasin widens the peptide-binding pocket of the MHC I molecule, thereby testing the strength of the peptide bond. For this purpose, the interaction partners form a large contact area; for stabilisation, a loop of tapasin sits on top of the widened binding pocket. “This is the first time we have shown the process of loading at high resolution," Tampé is pleased to report. The images also reveal how a single chaperone can interact with the enormous diversity of MHC I molecules, says the biochemist: “Tapasin binds precisely the non-variable regions of the MHC I molecules." However, the new structure not only improves our understanding of the complex processes involved in loading MHC I molecules. It should also help select suitable candidates for vaccine development.
Publication: Ines Katharina Müller, Christian Winter, Christoph Thomas, Robbert M. Spaapen, Simon Trowitzsch, Robert Tampé. Structure of an MHC I–tapasin–ERp57 editing complex defines chaperone promiscuity. Nature Communications (2022) https://www.nature.com/articles/s41467-022-32841-9
Professor Robert Tampé / Dr Simon Trowitzsch
CRC 1507 – Protein Assemblies and Machineries in Cell Membranes
Institute of Biochemistry, Biocenter
Goethe University Frankfurt
Tel.: +49 69 798-29475
International research team with a member from Goethe University analyses inclusions in diamonds
Correction In the first paragraph it should read: ...analysed a rare diamond formed 660 kilometres below the Earth's surface... (not "metres")
The transition zone between the Earth's upper and lower mantle contains considerable quantities of water, according to an international study involving the Institute for Geosciences at Goethe University in Frankfurt. The German-Italian-American research team analysed a rare diamond formed 660 kilometres below the Earth's surface using techniques including Raman spectroscopy and FTIR spectrometry. The study confirmed something that for a long time was only a theory, namely that ocean water accompanies subducting slabs and thus enters the transition zone. This means that our planet's water cycle includes the Earth's interior. (Nature Geoscience, DOI 10.1038/s41561-022-01024-y)
FRANKFURT. The transition zone (TZ) is the name given to the boundary layer that separates the Earth's upper mantle and the lower mantle. It is located at a depth of 410 to 660 kilometres. The immense pressure of up to 23,000 bar in the TZ causes the olive-green mineral olivine, which constitutes around 70 percent of the Earth's upper mantle and is also called peridot, to alter its crystalline structure. At the upper boundary of the transition zone, at a depth of about 410 kilometres, it is converted into denser wadsleyite; at 520 kilometres it then metamorphoses into even denser ringwoodite.
“These mineral transformations greatly hinder the movements of rock in the mantle," explains Prof. Frank Brenker from the Institute for Geosciences at Goethe University in Frankfurt. For example, mantle plumes – rising columns of hot rock from the deep mantle – sometimes stop directly below the transition zone. The movement of mass in the opposite direction also comes to standstill. Brenker says, “Subducting plates often have difficulty in breaking through the entire transition zone. So there is a whole graveyard of such plates in this zone underneath Europe."
However, until now it was not known what the long-term effects of “sucking" material into the transition zone were on its geochemical composition and whether larger quantities of water existed there. Brenker explains: “The subducting slabs also carry deep-sea sediments piggy-back into the Earth's interior. These sediments can hold large quantities of water and CO2. But until now it was unclear just how much enters the transition zone in the form of more stable, hydrous minerals and carbonates – and it was therefore also unclear whether large quantities of water really are stored there."
The prevailing conditions would certainly be conducive to that. The dense minerals wadsleyite and ringwoodite can (unlike the olivine at lesser depths) store large quantities of water– in fact so large that the transition zone would theoretically be able to absorb six times the amount of water in our oceans. “So we knew that the boundary layer has an enormous capacity for storing water," Brenker says. “However, we didn't know whether it actually did so."
An international study in which the Frankfurt geoscientist was involved has now supplied the answer. The research team analysed a diamond from Botswana, Africa. It was formed at a depth of 660 kilometres, right at the interface between the transition zone and the lower mantle, where ringwoodite is the prevailing mineral. Diamonds from this region are very rare, even among the rare diamonds of super-deep origin, which account for only one percent of diamonds. The analyses revealed that the stone contains numerous ringwoodite inclusions – which exhibit a high water content. Furthermore, the research group was able to determine the chemical composition of the stone. It was almost exactly the same as that of virtually every fragment of mantle rock found in basalts anywhere in the world. This showed that the diamond definitely came from a normal piece of the Earth's mantle. “In this study we have demonstrated that the transition zone is not a dry sponge, but holds considerable quantities of water," Brenker says, adding: “This also brings us one step closer to Jules Verne's idea of an ocean inside the Earth." The difference is that there is no ocean down there, but hydrous rock which, according to Brenker, would neither feel wet nor drip water.
Hydrous ringwoodite was first detected in a diamond from the transition zone as early as 2014. Brenker was involved in that study, too. However, it was not possible to determine the precise chemical composition of the stone because it was too small. It therefore remained unclear how representative the first study was of the mantle in general, as the water content of that diamond could also have resulted from an exotic chemical environment. By contrast, the inclusions in the 1.5 centimetre diamond from Botswana, which the research team investigated in the present study, were large enough to allow the precise chemical composition to be determined, and this supplied final confirmation of the preliminary results from 2014.
The transition zone's high water content has far-reaching consequences for the dynamic situation inside the Earth. What this leads to can be seen, for example, in the hot mantle plumes coming from below, which get stuck in the transition zone. There, they heat up the water-rich transition zone, which in turn leads to the formation of new smaller mantle plumes that absorb the water stored in the transition zone. If these smaller water-rich mantle plumes now migrate further upwards and break through the boundary to the upper mantle, the following happens: The water contained in the mantle plumes is released, which lowers the melting point of the emerging material. It therefore melts immediately and not just before it reaches the surface, as usually happens. As a result, the rock masses in this part of the Earth's mantle are no longer as tough overall, which gives the mass movements more dynamism. The transition zone, which otherwise acts as a barrier to the dynamics there, suddenly becomes a driver of the global material circulation.
Publication: Tingting Gu, Martha G. Pamato, Davide Novella, Matteo Alvaro, John Fournelle, Frank E. Brenker, Wuyi Wang, Fabrizio Nestola: Hydrous peridotitic fragments of Earth's mantle 660 km discontinuity sampled by a diamond. Nature Geoscience (https://www.nature.com/articles/s41561-022-01024-y)
Picture download: https://www.uni-frankfurt.de/125674824
Caption: The diamond from Botswana revealed to the scientists that considerable amounts of water are stored in the rock at a depth of more than 600 kilometres. Photo: Tingting Gu, Gemological Institute of America, New York, NY, USA
Professor Frank Brenker
Department of Geoscience Mineralogy
Phone: +49 (0)69 798-40134
Mobile: +49 (0)151 68109472
Laureates raised knowledge of the development of the immune system to a new level
Immunologists Frederick W. Alt (73) of Harvard Medical School and David G. Schatz (64) of Yale School of Medicine are to receive the 2023 Paul Ehrlich and Ludwig Darmstaedter Prize, as the Scientific Council of the Paul Ehrlich Foundation announced today. The two researchers are being acknowledged for their discovery of molecules and mechanisms that enable our immune system to perform the astounding feat of recognizing billions of different antigens on first contact.
FRANKFURT. Both the antibodies produced by B cells and structures on the surface of T cells are able to capture antigens. Collectively, they are referred to as antigen receptors. In the first instance, their tremendous variety is thanks to different gene fragments combining at random to form functional genes. Almost 50 years ago, this principle was first demonstrated for the production of antibodies. However, the finer details of this somatic recombination remained largely in the dark until Alt and Schatz increasingly shed light on the subject. “The picture we have today of the diversification of antigen receptors in the immune system of vertebrates is above all thanks to the two prize winners," says Professor Thomas Boehm, Chairman of the Scientific Council of the Paul Ehrlich Foundation. “They have raised our knowledge of the development of the immune system to a new level."
Antigen receptors are proteins consisting of constant and variable parts. In each antibody, for example, two heavy and two light chains are joined together in a Y-shape. Which antigen an antibody can recognize depends on the variable parts in the arms of the Y. In each of our B cells, an antibody with different claws matures during its development in the bone marrow. In total, our body can build approximately ten billion different antibodies, although it has only about 20,000 protein blueprints in the form of genes. It achieves this by means of an extraordinarily daring procedure that makes cutting up and re-assembling the genetic information DNA on certain chromosomes of maturing lymphocytes the norm.
The enzyme complex RAG1/2 discovered by David Schatz and colleagues conducts these cuts at pre-designated sites. For the formation of the variable portions of heavy antibody chains, for example, these sites are located on chromosome 14. There, they flank relatively widely spaced segments in three different regions called V (for variable), D (for diversity), and J (for joining). RAG1/2 conducts cuts at a randomly selected segment from each of these regions for each antibody. Subsequently, DNA repair enzymes assemble a VDJ gene to encode a heavy chain variable region. Frederick Alt discovered the repair enzymes that work together to join the ends of the cut-out segments. In the next step of B cell maturation, the light chains are formed in a similar way, but only a VJ recombination occurs there in this case.
The RAG enzymes do not, however, wander aimlessly through the cell nucleus of immature lymphocytes. On the contrary, they draw the chromatin filaments together, in which the DNA is coiled up in a space-saving way, temporarily and again and again to form V(D)J recombination centers. There, they perform chromatin scanning. In this process, a chromatin loop, which can be more than one million DNA letters long, passes through the recombination center so that widely separated sections of text can be reliably linked together. The loop extrusion mechanism of V(D)J recombination elucidated by Frederick Alt elegantly explains how these loops are created and pulled through the recombination center.
Frederick Alt made further decisive contributions to the understanding of antigen receptor diversity. For example, he succeeded in showing that combinatorial diversity is increased many-fold by the enzymatic insertion of very short random DNA sequences, called N-nucleotides, at the interfaces of the gene segments to be joined. In B cells, antibody diversity is further potentiated by the phenomenon of somatic hypermutation. In this process, the normal rate of mutations affecting only one DNA letter is increased millions of times in the regions of the V segments by an enzyme. Alt, Schatz, and others showed how this enzyme performs its work with pinpoint accuracy. They thus provided a framework for solving the question of how B cells can take advantage of the enormous mutational capacity of AID for antibody maturation without running the risk of suffering tumor-inducing mutations.
Without the recombination-activating enzyme complex RAG1/2, the diversification of antigen receptors is impossible, the maturation of the lymphocytes is disrupted, and a severe immune defect is the consequence. It is all the more remarkable that this molecule apparently originates from a jumping gene – a transposon. These are selfish DNA parasites that crept into our genome at some point and can move from one place to another as jumping genes. Because of their uncontrolled distribution, they can be involved in the development of disease. RAG1/2, however, according to David Schatz's findings, descends from a transposon that all jawed vertebrates, including us humans, tamed for their own purposes very early in evolution. To prevent it from jumping on, they had to fix it in the genome. Schatz has shown which biochemical mechanisms enable this fixation. He was also able, on the basis of structural biological studies in an ancient invertebrate RAG gene to reproduce the act of transposition over several stages. He is thus giving science a fascinating look back at a revolutionary process at the beginning of vertebrate evolution: the development of the adaptive immune system in addition to already existing innate immunity. Building on this view from basic research, translational research will be able to open up new therapeutic perspectives for diseases in which our immune system plays a crucial role.
Frederick W. Alt (Website) is the Charles A. Janeway Professor of Pediatrics and Director of the Program in Cellular and Molecular Medicine at Boston Children's Hospital, a Howard Hughes Medical Institute Investigator, and a Professor of Genetics at Harvard Medical School.
David G. Schatz (Website) is Professor of Molecular Biophysics and Biochemistry at Yale University and Chairperson of the Department of Immunobiology at Yale School of Medicine.
Photos of the award winners are available for use at www.paul-ehrlich-stiftung.de.
Background information with the title “Protected by a tamed parasite"
The prizes will be awarded by the Chairman of the Scientific Council of the Paul Ehrlich Foundation on 14 March 2023 at 5 p.m. in Frankfurt's Paulskirche. We kindly ask you to take this into consideration when planning your diary. Please do not hesitate to contact us if you have any questions.
The Paul Ehrlich and Ludwig Darmstaedter Prize is Germany's most renowned medical award, endowed with 120,000 euros. It is traditionally awarded on Paul Ehrlich's birthday, 14 March, in Frankfurt's Paulskirche. It honours scientists who have made special contributions in areas of research represented by Paul Ehrlich's achievements, namely in immunology, cancer research, haematology, microbiology and chemotherapy. The prize, which has been awarded since 1952, is funded by the Federal Ministry of Health, the German Association of Research-based Pharmaceutical Companies (Verband Forschender Arzneimittelhersteller e.V.) and by earmarked donations from the following companies, foundations and institutions: Else Kröner-Fresenius-Foundation, Sanofi-Aventis Deutschland GmbH, C.H. Boehringer Sohn AG & Co. KG, Biotest AG, Hans und Wolfgang Schleussner-Foundation, Fresenius SE & Co. KGaA, F. Hoffmann-LaRoche Ltd., Grünenthal Group, Janssen-Cilag GmbH, Merck KGaA, Bayer AG, Georg von Holtzbrinck GmbH & Co.KG, AbbVie Deutschland GmbH & Co. KG., B. Metzler seel. Sohn & Co KGaA. The award winners are selected by the Scientific Council of the Paul Ehrlich Foundation. A list of the members of the Scientific Council is available on the website of the Paul Ehrlich Foundation.
The Paul Ehrlich Foundation is a legally dependent foundation administered in trust by the Association of Friends and Benefactors of Goethe University. Honorary President of the Foundation, which was established in 1929 by Hedwig Ehrlich, is Professor Dr Katja Becker, President of the German Research Foundation, who also appoints the elected members of the Foundation Council and the Board of Trustees. The Chairman of the Scientific Council of the Paul Ehrlich Foundation is Professor Dr Thomas Boehm, Director at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, and the Chairman of the Board of Trustees is Professor Dr Jochen Maas, Managing Director Research & Development, Sanofi-Aventis Deutschland GmbH. In his function as Chairman of the Association of Friends and Benefactors of Goethe University, Prof. Dr Wilhelm Bender is also a member of the Scientific Council of the Paul Ehrlich Foundation. The President of Goethe University is in this capacity also a member of the Board of Trustees.
Heart and COVID-19 study at University Hospital Frankfurt/Goethe University Frankfurt reveals long-term effects after SARS-CoV-2 infection
The research team led by Dr Valentina Puntmann and Professor Eike Nagel from University Hospital Frankfurt and Goethe University Frankfurt followed up around 350 study participants without previously known heart problems who had recovered from a SARS-CoV-2 infection. They found that over half of them still reported heart symptoms almost a year later, such as exercise intolerance, tachycardia and chest pain. According to the study, these symptoms can be attributed to mild but persistent cardiac inflammation. Pronounced structural heart disease is not a characteristic of the syndrome. (Nature Medicine, DOI 10.1038/s41591-022-02000-0).
FRANKFURT. After recovering from a SARS-CoV-2 infection, many people complain of persistent heart complaints, such as poor exercise tolerance, palpitations or chest pain, even if the infection was mild and there were no known heart problems in the past. Earlier studies, predominantly among young, physically fit individuals, were already able to show that mild cardiac inflammation can occur after COVID-19. However, the underlying cause of persistent symptoms, and whether this changes over time, was unknown.
A team of medical scientists led by Dr Valentina Puntmann and Professor Eike Nagel from the Institute for Experimental and Translational Cardiovascular Imaging at University Hospital Frankfurt followed up 346 people – half of them women – between the age of 18 and 77 years, in each case around four and eleven months after the documented SARS-CoV-2 infection. For this purpose, the team analysed the study participants' blood, conducted heart MRIs, and recorded and graded their symptoms using standardised questionnaires.
The result: 73 percent reported heart problems at the beginning of the study and in 57 percent these symptoms persisted 11 months after the SARS-CoV-2 infection. The research team measured mild but persistent heart inflammation that was not accompanied by structural changes in the heart. Blood levels of troponin – a protein that enters the blood when the heart muscle is damaged – were also unremarkable.
Dr Puntmann, who led the Impression COVID&Heart Study, explains: “The patients' symptoms match our medical findings. It is important to note that although triggered by the SARS-CoV-2 virus, the post-COVID cardiac inflammatory involvement differs considerably from classic viral myocarditis. Extensive damage of the heart muscle leading to structural heart changes or impaired function are not characteristic at this stage of disease evolution." The clinical picture is more reminiscent, she says, of the findings in chronic diffuse inflammatory syndromes such as autoimmune conditions. “Although most likely driven by a virus-triggered autoimmune process, a lot more research is needed in order to understand the underlying pathophysiology. Similarly, the long-term effects of cardiac inflammation following a mild COVID infection need to be clarified in future studies."
Because the study is restricted to a selected group of individuals who took part because they had symptoms, the prevalence of findings cannot be extrapolated to the population as a whole. Bayer AG, the German Heart Foundation and the German Centre for Cardiovascular Research supported the study.
Publication: Valentina O. Puntmann, Simon Martin, Anastasia Shchendrygina, Jedrzej Hoffmann, Mame Madjiguène Ka, Eleni Giokoglu, Byambasuren Vanchin, Niels Holm, Argyro Karyou, Gerald S. Laux, Christophe Arendt, Philipp De Leuw, Kai Zacharowski, Yascha Khodamoradi, Maria J. G. T. Vehreschild, Gernot Rohde, Andreas M. Zeiher, Thomas J. Vogl, Carsten Schwenke, Eike Nagel Long-term cardiac pathology in individuals with mild initial COVID-19 illness. Nature Medicine (2022) https://www.nature.com/articles/s41591-022-02000-0
Background: The heart after COVID-19 – Long-term damage from COVID-19 does not always heal without treatment (Forschung Frankfurt 1.2021) https://www.forschung-frankfurt.uni-frankfurt.de/108536066.pdf
Picture download: https://www.uni-frankfurt.de/124064044
Caption: Visualisation of heart inflammation by means of MRI: cardiologist Dr Valentina Puntmann monitors a study participant at the Institute for Experimental and Translational Cardiovascular Imaging at University Hospital Frankfurt.
Dr Valentina Puntmann
University Hospital Frankfurt / Goethe University Frankfurt
Institute for Experimental and Translational Cardiovascular Imaging