Wednesday, March 21, 2012

Actin part two: Formin

Like everything in the cell, the nucleation and elongation of actin filaments is highly regulated. Here to perform part of this regulation is the Formin family of proteins. Formins are cool because they stay associated with the growing end of an actin filament, stepping along the elongating filament as each monomer is added. In this way they protect the growing filament from being capped (and its growth terminated) by the abundant capping protein. Formins are usually big long proteins with many different domains, so the domain I've chosen to represent is the Formin Homology 2 (FH2) domain, because it's the one responsible for keeping the Formin protein stepping along at the growing end of the actin filament.
Here's a single FH2 domain from the formin bni1p (pdb code 1y64). The N-terminus is on the top right and the C terminus at the bottom. Check out the lasso domain! That is how the FH2 domain dimerizes; that lasso loops around the post (knob at bottom left) of another monomer. Actin binds in the middle of the resulting doughnut shape. The thin linker part was printed along with the main portion of the protein, and the lasso was made separately. Then I glued the lasso on, but the linker part broke so that's why I'm holding it like that.

This is how the two FH2 monomers would be oriented in the dimer. These are printed with the lasso wrapped around the post, but I didn't print the linkers because I wanted to glue the monomers together with something flexible to emulate how they would move in real life. I tried gluing a nylon rope but the glue I used didn't seem to take.. I'll update when I come up with something better. For now, imagine the linkers there.
And here's a dimer bound to two actin monomers (almost like in the pdb structure!) Imagine this sitting at the top of a filament, the FH2 domains walking up along the filament when new actin monomers get added.

So that's it for now; I'm building a new extruder with a smaller nozzle, so hopefully soon I'll get that working and I will be getting even better print resolution. Or it will explode/melt. Time will tell.

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