Methyl groups set proteins in motion at very low temperature
CEA
Proteins are made of one or more chains of amino acids. These chains fold to give proteins complex forms called 3-dimensional structures within which their amino acids make specific movements, and these movements are critical to normal protein functioning. The protein undergoes a flurry of movements at its ideal, or “physiological” temperature, which is generally above the 0°C mark. In order to dissect and understand these movements, it is first necessary to cut down the number of movements going on, which is done by dropping the temperature of the protein-of-interest.
Even at low temperature, there are still a few movements completing inside the protein. But which ones? A team of scientists from the CEA’s institute of structural biology (IBS) studied the movements inside a membrane protein called bacteriorhodopsin, which they forced down to temperatures around the -150°C mark. Methyl groups were suspected to play a role in the few movements that occurred. To confirm this hypothesis, researchers from the IBS-run Molecular Biophysics Laboratory collaborated with a number of institutes and universities abroad* to pool skilled knowledge and competencies in several scientific approaches ranging from neutron scattering to molecular dynamics and back to NMR.
Neutron scattering consists in bombarding this protein with a beam of neutrons that will interact violently with the hydrogen atoms inside the protein. This technique makes it possible to measure energy exchanges (between the protein and the neutron beam) and thus, by extension, to quantify the movements in the protein-of-interest. To confirm whether methyl groups were involved, the team targeted bacteriorhodopsin to track the movements of lysine, a methyl-less amino acid. They achieved this by replacing the hydrogen atoms in the other amino acids with deuterium. These deuterium atoms no longer interact as violently with the neutrons, leaving only unlabelled amino acids (the lysine) visible on measurements. The experiment revealed a clear drop in movements in the specifically-labelled sample compared to non-labelled sample (figure). In other words, movements continued in the rest of the protein but not in the lysine.
These findings, together with results from NMR studies and molecular dynamics simulations, confirmed that the drop in dynamic signals was indeed due to the absence of methyl groups in the lysines. The team was therefore able to conclude that at very low temperatures, the movements still occurring in proteins were rotations of methyl groups.
These methyl group movements must doubtless be hugely important to protein function, given that they are already visible at extremely low temperatures and get stronger and stronger as the protein approaches its physiological temperature!
Figure (a): Structure of bacteriorhodopsin in the cell membrane
Figure (b): Lysines within bacteriorhodopsin (in blue)
Figure (c): Movements continue to occur in bacteriorhodopsin, even at temperatures as low as -150°C (120 K). The red diamond shapes show the mean square displacements measured by neutron scattering experiments. There is an inflection in these movements when specifically observing only lysines (blue diamonds).
-------
Note
*This study is the fruit of a collaboration between the Institut Laue Langevin in Grenoble, the Bragg Institute in Australia, the University of Groningen in The Netherlands, Max-Planck Institute of Biochemistry in Germany, and the University of California, Irvine, USA.