Dr. Jocelyne Vreede,
Van 't Hoff Institute for Molecular Sciences,
University of Amsterdam
Proteins are very versatile: they can cause muscles to contract, or enable us to perceive light. But proteins are not only indispensable to people and animals – to bacteria they can even be life-saving. Jocelyne Vreede conducts research into light receptors in bacteria, and uses the supercomputer Huygens and the national compute cluster Lisa to perform her calculations.
Blue light is damaging to bacteria. To protect themselves, they have developed a defense mechanism: a special protein that registers blue light. Once the light has been perceived, the protein changes shape, sending a signal to the tail of the bacterium. This in turn causes the bacterium to swim away from the damaging light. Vreede conducts research into how light makes these proteins change their shape.
Vreede has characterized the transformation of the specific protein that responds to blue light [see image]: “Proteins are constructed from amino acids, which in turn are made up of atoms. I put all the atoms into a supercomputer, and then I make them move. I try to track how the atoms take on a series of different positions, and how long it lasts. Once we know that, we can start proposing experiments. If the method proves to work well, we can then apply it to other proteins.”
Performing calculations on proteins with huge quantities of atoms requires computers with multiple processors. Vreede therefore performs her calculations using the Huygens supercomputer and the Lisa compute cluster at SURFsara: “With parallel computing, you divide the data among several processors, which then all start calculating for you.”
Vreede has been using computers at SURFsara for six years now. The collaboration recently became even closer: “Last year we submitted a proposal as part of the DEISA Extreme Computing Initiative (DECI), also on the topic of light-sensitive proteins. The proposal was approved, and the consultant from SURFsara has helped us to develop a program that makes optimum use of what Huygens has to offer. This means that we can simulate transformations and calculate how many transformations are successful or not.”
Vreede could not do much without the computing power and support. But there’s more, says Vreede: “The DEISA project was also the first time I had worked with a consultant from SURFsara. It was very nice, because he knew much more than me about software optimization, so I didn’t need to figure it all out myself. Ultimately it was much more efficient.”
The light-sensitive protein (yellow and black) changes shape once it registers blue light, with the black sections moving from the inside to the outside. The transformation occurs along specific pathways (indicated in red) across an energy landscape. These pathways are calculated using advanced computer simulations.