Researchers at the Department of Chemistry at the Technical University of Munich (TUM) have developed a process that enables them to monitor local movements of proteins in time frames of nanoseconds to microseconds. When they were examining agitations of the Villin-protein, they found two otherwise hardly differentiable structures: in one, fast changes in structure could occur that are essential for the protein's function and last only nanoseconds. The other one is stiff. These results are published in the recent online issue of the "Proceedings of the Natural Academy of Sciences, USA" (PNAS) journal.
One of the five most important proteins within a cell is Actin. Its filaments keep the cell in shape and the most important elements in place. The Villin interlinks the long Actin filaments and thereby contributes significantly to the stabilization of the cell's structures. The part of the protein responsible for the connection to Actin filaments, HP35, has been subject to a large number of computer simulations for understanding protein dynamics better due to its small size. However, there have not been experimental studies because those protein movements occur in time frames of microseconds or even nanoseconds, time spans that were hardly accessible experimentally.
With the process developed by the team around Thomas Kiefhaber, based on a quick electron transfer between different parts of a protein, those quick structural changes could now be examined directly. For the modelling system they chose the Actin binding part of the Villin protein, HP35. The new experimental studies by the team around Thomas Kiefhaber now show that the folded protein exists in two conformations that differ structurally only slightly, but have quite different qualities. Large changes in structure cannot occur in a stiff conformation, whereas in the flexible conformation certain parts of the protein responsible for binding onto the Actin fold and unfold within 100 nanoseconds.
Both conformations are in balance and are transformed into each other within a microsecond. The structural similarity of both conformation accounts for why they have not been discovered either in computer simulations or structural examinations so far. By deploying electron transfer measuring, the different states can be differentiated and characterized according to their diverse flexibility.
This study's findings are of fundamental significance in order to understand the functions of proteins and contribute to elucidating the mechanisms of folding and mis-folding of proteins. The researchers are now hoping they can develop this method further so it can be applied to larger proteins that are of importance for the regulation of cellular functions.