Which structures do complex proteins adopt in solution? Biophysicists answer this question using the example of ubiquitin dimers as well as a new combination of high-resolution NMR spectroscopy and sophisticated computer simulations.
Proteins consist of amino acids, which are linked to form long amino acid chains as specified by our genetic material. In our cells, these chains are not simply rolled up like strings of pearls, but fold into complex, three-dimensional structures. How a protein is folded decisively influences its function: It determines, for example, which other molecules a protein can interact with in the cell.
"Unfortunately, elucidating the structure of a protein is anything but trivial, and focusing on a single state does not always provide meaningful information, especially if the protein is highly flexible in terms of its structure," says Tobias Schneider, a member of Michael Kovermann's lab team in the Department of Chemistry at the University of Konstanz.
"Through NMR spectroscopy, for example, we get information about the dynamic properties of such proteins. Complex computer simulations, on the other hand, provide a good overview of the range of possible folds," explains Kovermann."So far, no general approach that comprehensively maps the dynamic and structural properties of multi-domain proteins had existed.
The researchers were able to show that the ubiquitin dimers they studied exhibit a high structural variability and that this can be described in detail using the developed combination of methods. The results also explain the different structural models that currently exist of ubiquitin dimers."We are convinced that our approach -- combining complementary methods -- will work not only for ubiquitin dimers but also for other multi-domain proteins," Schneider says.
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