bkoep Staff Lv 1
Scientists at UC Berkeley are studying the bacterial microcompartment protein PduN, and we think Foldit players can help answer some questions about how PduN folds into symmetric assemblies:
"Bacterial microcompartments are protein-based organelles. Despite some glycosylation, they are almost entirely made of protein, even the outer shell. They are large complexes, shaped like icosahedrons, containing thousands of protein subunits. They have an outer layer with pores that tightly control what molecules enter and leave. Inside each microcompartment is a series of related enzymes from a particular metabolic pathway. The microcompartments act like little factories, organizing the enclosed enzymes so that intermediates pass efficiently from one enzyme to the next and unwanted side reactions are carefully controlled. There are microcompartments specialized for CO2 fixation, propanediol metabolism, ethanol utilization, ethanolamine metabolism, fucose metabolism, and rhamnose metabolism. All of these functions are very important to life on earth: CO2 fixation is important to synthesize carbon sources for almost all life on earth, especially humans; propanediol and ethanolamine utilization have been shown to give an advantage to some pathogens; and fucose and rhamnose metabolism are important in the conversion of plant biomass into biofuels. For those interested in further reading, here is a great review on microcompartments:
http://dx.doi.org/10.1146/annurev.micro.112408.134211
There are many unresolved questions regarding these bacterial microcompartments; for example, what are the structures of the various subunits, and how do these subunits fit together? There are also many opportunities for protein engineering; for example, can these bacterial microcompartments be made more efficient or adapted to perform other chemical reactions?
As a start, we would like to use Foldit player models to determine the oligomeric structure of PduN, a protein with homology to other proteins known to form pentamers shaped like pentagons. These petamers become the 12 vertices of the icosahedral outer shell of each one's respective microcompartment. Although almost all known structures of these homologs are pentamers, one has been shown to be a hexamer. We are wondering if PduN is a hexamer or pentamer and if that structure could form the vertex of an icosahedral shell."
The first PduN puzzle will be a prediction puzzle for the monomeric protein, and can be found here.
