New development makes tiny structural changes in biomolecules visible
FRANKFURT. Even more detailed insights into the cell will be possible in future with the help of a new development in which Goethe University was involved: Together with scientists from Israel, the research group led by Professor Harald Schwalbe has succeeded in accelerating a hundred thousand-fold the nuclear magnetic resonance (NMR) method for investigating RNA.
In the same way that a single piece of a puzzle fits into the whole, the molecule hypoxanthine binds to a ribonucleic acid (RNA) chain, which then changes its three-dimensional shape within a second and in so doing triggers new processes in the cell. Thanks to an improved method, researchers are now able to follow almost inconceivably tiny structural changes in cells as they progress – both in terms of time as well as space. The research group led by Professor Harald Schwalbe from the Center for Biomolecular Magnetic Resonance (BMRZ) at Goethe University has succeeded, together with researchers from Israel, in accelerating a hundred thousand-fold the nuclear magnetic resonance (NMR) method for investigating RNA.
“This allows us for the first time to follow the dynamics of structural changes in RNA at the same speed as they occur in the cell,” says Schwalbe, describing this scientific breakthrough, and stresses: “The team headed by Lucio Frydman from the Weizmann Institute in Israel made an important contribution here.”
The new types of NMR experiments use water molecules whose atoms can be followed in a magnetic field. Schwalbe and his team produce hyperpolarized water. To do so, they add a compound to the water which has permanently unpaired electron radicals. The electrons can be aligned in the magnetic field through excitation with a microwave at -271°C. This unnatural alignment produces a polarization which is transferred at +36°C to the polarization of the hydrogen atoms used in the NMR. Water molecules polarized in this way are heated in a few milliseconds and transfered, together with hypoxanthine, to the RNA chain. The new approach can in general be applied to observe fast chemical reactions and refolding changes in biomolecules at atomic level.
In particular the imino groups in RNA can be closely analyzed using this method. In this way, the researchers were able to measure structural changes in RNA very accurately. They followed a small piece of RNA from Bacillus subtilis, which changes its structure during hypoxanthine binding. This structural change is part of the regulation of the transcription process, in which RNA is being made from DNA. Such small changes at molecular level steer a large number of processes not only in bacteria but also in multicellular organisms and even humans.
This improved method will in future make it possible to follow RNA refolding in real time – even if it needs less than a second. This is possible under physiological conditions, that is, in a liquid environment and with a natural molecule concentration at temperatures around 36 °C. “The next step will now be not only to study single RNAs but hundreds of them, in order to identify the biologically important differences in their refolding rates,” says Boris Fürtig from Schwalbe’s research group.
Publication: Mihajlo Novakovic, Gregory L. Olsen, György Pintér, Daniel Hymon, Boris Fürtig, Harald Schwalbe, Lucio Frydman: A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR, PNAS, 16 January 2020 https://doi.org/10.1073/pnas.1916956117
A picture can be downloaded from: http://www.uni-frankfurt.de/84996281
Caption: Frankfurt researchers followed the movements of this tiny molecule – just two-thousandths of the thickness of a piece of paper. The RNA aptamer changes its structure when it binds hypoxanthine. The green nucleobases change shape particularly quickly, the ones coloured blue more slowly. The grey regions do not change.
Further information: Professor Harald Schwalbe, Center for Biomolecular Magnetic Resonance (BMRZ), http://www.bmrz.de/, Institute of Organic Chemistry and Chemical Biology, Riedberg Campus, Tel.: +49(0)69-798-29737 or -40258, e-mail: firstname.lastname@example.org.
Reported reduction of HFC-23 did not happen
FRANKFURT. According to the two main producers – China and India – the release of the potent greenhouse gas HFC-23 into the atmosphere should have almost completely stopped by 2017. However, the reality is that a team of atmospheric researchers led by the University of Bristol has measured record levels. Dr Kieran Stanley, lead author of the study published in the current issue of “Nature Communications", has been working at Goethe University for six months.
Over the past two decades, researchers have monitored the concentration of the hydrofluorocarbon HFC-23 very closely. “It is a very potent greenhouse gas: The emission of one tonne of this substance does just as much damage as the emission of 12,000 tonnes of carbon dioxide," says atmospheric researcher Professor Andreas Engel from Goethe University. HFC-23 primarily occurs as an unwanted by-product in the manufacture of the refrigerant HCFC-22.
In 2015 India and China, which are considered the main emitters, announced ambitious plans to abate their factory emissions and in 2017 they reported that almost no more HFC-23 was being vented to the atmosphere. This would mean that emissions of this greenhouse gas into the atmosphere between 2015 and 2017 ought to have shown a 90 percent reduction. However, as the international team now reports, emissions have risen further and in 2018 reached an all-time high.
The reduction of HFCs is part of the Kigali Amendment to the Montreal Protocol agreed in 2016. It entered into force in January 2020. Although China and India have not ratified the Amendment, by their own account they had achieved a massive reduction in emissions. “Our study indicates that China has not managed to reduce HFC-23 as reported," concludes Dr Kieran Stanley, who conducted the measurements at the University of Bristol in the framework of the international AGAGE measurement network. Additional measurements will show whether India has successfully implemented its abatement programme.
“This is not the first time there's been controversy about HFC-23 emissions," says Kieran Stanley ruefully. With the United Nations Framework Convention on Climate Change, between 2005 and 2010 the industrial nations created incentives for emerging countries to reduce their emissions. Although emissions of this hazardous greenhouse gas did indeed decrease during that period, the system backfired: Manufacturers did not optimize their processes but instead produced more harmful by-products in order to pocket more funds for destroying them.
The Institute for Atmospheric and Environmental Sciences at Goethe University, where Kieran Stanley is now working as a postdoctoral researcher, has measured a large number of halogenated trace gases at its Kleiner Feldberg measuring station at regular intervals since 2013. Since recently, these measurements are part of the AGAGE network.
Publication: K. Stanley, D. Say, J. Mühle, C. Harth, P. Krummel, D. Young, S. O'Doherty, P. Salameh, P. Simmonds, R. Weiss, R. Prinn, P. Fraser and M. Rigby: Increase in global emissions of HFC-23 despite near-total expected reductions, in Nature Communications, https://doi.org/10.1038/s41467-019-13899-4
Further information: Dr Kieran Stanley, Institute for Atmospheric and Environmental Sciences, Riedberg Campus, Tel.: +49(0)69-798-40249; email@example.com
Single-molecule microscopy visualises the dance of receptors
FRANKFURT. Whether a sick cell dies, divides, or travels through the body is regulated by a sophisticated interplay of signal molecules and receptors on the cell membrane. One of the most important molecular cues in the immune system is Tumour Necrosis Factor α (TNFα). Now, for the first time, researchers from Goethe University have visualised the molecular organisation of individual TNFα receptor molecules and the binding of TNFα to the cell membrane in cells using optical microscopy.
Before TNFα can bind to a membrane receptor, the TNFR receptor must first be activated. By doing so, the key will only fit the lock under certain circumstances and prevents, among other things, that a healthy cell dies from programmed cell death. “For TNFR1 in the membrane, the binding of TNFα is mediated through several cysteine-rich domains, or CRDs," explains Sjoerd van Wijk form the Institute for Experimental Cancer Research in Paediatrics and the Frankfurt Stiftung für Krebskranke Kinder at Goethe University.
In particular, CRD1 of the TNFR1 makes it possible for TNFα to “attach". Researchers already knew that TNFR1 molecules cluster in a fashion similar to a dance, in which two, three or more partners grasp hands – with the dimers, trimers or oligomers consisting of single TNFR1 molecules – in the case of TNFR1. This kind of “structural reorganization" also takes place when there is no TNFα present. “Despite the significance of TNFα for many diseases, including inflammation and cancer, the physiology and patterns of TNFR1 in the cell membrane still remain largely unknown up to now," says Sjoerd Van Wijk, explaining the starting point for his research.
In order to understand the processes in the cell membrane in detail, van Wijk approached Mike Heilemann from the Institute for Physical and Theoretical Chemistry at Goethe University. Using a combination of quantitative microscopy and single-molecule super-resolution microscopy that he developed, Heilemann can visualise individual protein complexes as well as their molecular organisation in cells. Together with Ivan Dikic (Institute for Biochemistry II) and Simone Fulda (Institute for Experimental Cancer Research in Paediatrics) from Goethe University, Harald Wajant from the University Hospital Würzburg and Darius Widera from University Reading/UK, they were able to observe the dance of the TNFα receptors. Financial support was provided by the Deutsche Forschungsgemeinschaft (DFG) through the Collaborative Research Centre 807 “Transport and Communication across Biological Membranes".
As the researchers report in the current issue of “Science Signalling", membrane TNFR1 receptors exist as monomers and dimers in the absence of TNFα. However, as soon as TNFα binds TNFR1, receptor trimers and oligomers are formed in the membrane. The researchers also found indications for mechanisms that determine cell fate independently of TNFα. These findings could be relevant for cancer or and inflammatory diseases such as rheumatoid arthritis. “It clearly opens new paths for developing novel therapeutic approaches," states van Wijk.
Publication: C. Karathanasis, J. Medler, F. Fricke, S. Smith, S. Malkusch, D. Widera, S. Fulda, H. Wajant, S. J. L. van Wijk, I. Dikic, M. Heilemann, Single-molecule imaging reveals the oligomeric state of functional TNFα-induced plasma membrane TNFR1 clusters in cells. Sci. Signal. 13, eaax5647 (2020). DOI: 10.1126/scisignal.aax5647
Further information: Dr Sjoerd van Wijk, Institute for Experimental Cancer Research in Paediatrics, Niederrad Campus, Tel.: +49 69 67866574, Email: firstname.lastname@example.org
Prof Mike Heilemann, Institute for Physical and Theoretical Chemistry, Riedberg Campus, Tel.: +49 69 798 29424, Email: email@example.com