My wife calls me “ulterior motive man” because I have this firm belief that a single reason is rarely if ever justification for any action. Thus taking out the garbage should be done when you can button hole that neighbor kid about mowing your lawn for you.
Today the L.A. Times has a story that gives ma a reason to play an on-line game, Foldit. This game allows users to work on determining the shape of molecules and more importantly viruses. In a mere three weeks this game has done something that more than a decade of traditional bio-molecular science has failed to do, it has map a protein that the HIV virus uses to replicate itself and become AIDS.
The protein is called M-MPV. It is the part of the replication mechanism of a simian AIDS variant. It has been remarkably resistant to the normal mapping technique of Molecular Replacement (MR). MR is in the field of X-ray crystallography and it can get a little deep, but bear with me and I’ll try to break it down to understandable bites.
X-ray crystallography allows us to map the position of electrons in the material embedded in the crystal. When we know where the electrons are we know where the atoms are and can determine the bonds between them. This technique has been in use since the 1920’s and moved into the field of bio-chemistry in the 1950’s.
MR is the process of taking a known structure map and then comparing it to a new sample and looking for the differences then trying to determine what the differing molecules are. It has been very useful but it uses a ton of computing power and has some notable failures, like M-MPV.