Force Fields

These days I’m working quite a lot on Force fields. The first thing that comes to mind is of course Star Wars…but I’m not working on that… at least not yet!

So what then are force fields? Well, they are the way we introduce the laws of physics to model the behavior of objects or particles. For example, in the movie of the lord of the rings, when they had those huge fighting scenes, they didn’t have to tell each orc where to move… they applied some physical rules and let the battle begin! They are also behind most of the realistic feel in computer games (hair or cape moving with wind, …)

In my case I’m working on protein and DNA force fields. That is, improving the physics that describe how proteins and nucleic acids interact. By improving the physics we can effectively make better computer simulations of proteins that gives us more insight to design and understand how proteins work.

Proteins? Yes, please!! (…but folded)

More than half our body weight is water…and yet we don’t fall apart or behave like water at all! Why? Taking away the water, half of our body mass is protein. They are responsible to give structure and consistency to the cells that make up our bodies, but also of carrying out much of the functionality we need by helping in metabolism, immune defense, cell division,…

What do proteins look like? This is not a matter of just curiosity: most medicines interact with proteins and alter their behavior by either promoting or avoiding them to do their work. So, if we want to design better medicines, we need to know how proteins look like to improve medicine-protein interactions. This can make medicines more specific (less secondary effects), reduce dose, …

Unfortunately, the cost in time and money to “see” how proteins look like is huge. Luckily, new technologies give rise to alternative methods. Currently I’m working on cheaper computational tools that mimic the behavior of proteins.  Instead of using expensive techniques to “take a picture” of how the protein looks like, we simulate the process from the moment the protein is made until it adopts the shape that allows it to work (this end point is the cheaper equivalent of ‘taking a picture’). This process is called protein folding and it is crucial to us since only proteins that fold correctly can do their work. Proteins that fold incorrectly are not only useless to carry out their work, but they might even lead to disease like Alzheimer or Parkinson’s. In order to be successful we use big super computers like the BNL’s Bluegene machine, similar to the one that defeated world champion Garry Kasparov at chess.

You can help out solving these life puzzles in different ways:

-David Baker’s group at Washington university developed foldit, a game in which you can fold proteins yourself.
– Vijay Pande’s group at Stanford University has a different approach, in which you can contribute spare computer time for scientist to fold proteins.