Protein reactions identified with subatomic resolution
Combination of infrared spectroscopy and computer simulations is the key
Why some switch proteins are slower than others
Switch proteins Ran and Ras control important processes in the cell
The switch proteins Ran and Ras control important processes such as the import of substances into the nucleus and cell growth. An impairment of their function may trigger severe diseases. A slowed down Ras protein, for example, causes intestinal cancer. Ran and Ras belong to the so-called GTPases. When the GTP molecule has bound to them, the proteins are switched on. If a phosphate group dissociates from the GTP molecule, the proteins are switched off. The team of Prof Dr Klaus Gerwert and PD Dr Carsten Kötting have been tracking that switch-off process in detail, together with colleagues from the Max Planck Institute of Molecular Physiology in Dortmund and the Partner Institute for Computational Biology in Shanghai
Amino acids impair switch-off process
The Ran protein is switched off more slowly than the Ras protein. To date, researchers had assumed that this was linked to the position of a magnesium ion in the binding pocket for the GTP molecule. However, the current study has proved that the magnesium ion is located in exactly the same spot in Ran and Ras. Instead, the side chain of an amino acid in Ran prevents an attacking water molecule from assuming the optimal position for dissociating the phosphate group from GTP.
Resolution of one-hundredth of the atomic diameter achieved
For such detailed observations, a subatomic resolution is required. That is enabled through the combination of X-ray structure analysis, infrared spectroscopy and computer simulations. The X-ray structure analysis supplies graphic atomic models, which, however, are rigid. The infrared spectroscopy grants insights into dynamic processes with high temporal and spatial resolution; but it does not provide any graphic models. Using computer simulations, the data gathered via both these methods can be combined to generate high-resolution videos. The team from the Ruhr-Universität Bochum have been promoting the combination of computer simulations and IR spectroscopy. That was, for example, addressed at the "European Conference on the Spectroscopy of Biological Molecules", which Klaus Gerwert organised at the Ruhr-Universität in September 2015.
Two cover stories in three months
Twice within three months, the RUB biophysicists have been featured on the cover of the Journal of Biological Chemistry. In the previous publication, they identified the molecular mechanisms of the protein Gαi1. Here, too, the combination of infrared spectroscopy and computer simulation played the decisive role.
The funds for the project have been supplied by the Collaborative Research Centre 642, the spokesman of which is Professor Gerwert.
T. Rudack, S. Jenrich, S. Brucker, I. R. Vetter, K. Gerwert, C. Kötting (2015): Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental and theoretical IR spectroscopy, Journal of Biological Chemistry, DOI: 10.1074/jbc.M115.648071 G. Schröter, D. Mann, C. Kötting, K. Gerwert (2015): Integration of Fourier Transform Infrared Spectroscopy, Fluorescence Spectroscopy, Steady-state Kinetics and Molecular Dynamics Simulations of Gαi1 distinguishes between the GTP hydrolysis and GDP release mechanism, Journal of Biological Chemistry, DOI: 10.1074/jbc.M115.651190