June 2009
17 posts
Link to SMART →
Domain architectures
Now that we got parts pumping through the pipeline, it’s time to take a step back and reflect once again on one of our favorite themes of the summer: the modularity of protein domains. I just posted a depiction of a familiar protein, PI3K, represented not as a crystal structure or as a cartoon blob, but with respect to its DOMAIN ARCHITECTURE. By domain, I mean the smallest functional units...
Animation of Rapamycin induced dimerization →
Adaptation
Why is it that Koreans can eat kimchi 3 times a day, and if I take one bite my face turns red and my nose sweats and I start to cry?
Why do crack addicts need more and more crack as time goes by?
Why is it that I can see equally well inside and outside even though it’s more than 100x brighter outside?
The answer to all these questions is adaptation. Biological signaling systems (like the...
GTPases: Readers Writers Erasers
GEF = writer
GAP = Eraser
What is the reader?
Think globally, act locally
In order for a cell to move, it needs to choose a direction. How does the cell make the decision about which way to go? If the cell is in a gradient of attractant, it needs to become “polarized” in order to make a leading edge so it can move up the gradient toward the source.
But the problem is that there’s not much of a difference in concentration at the front and the back. The...
Big PIPin'
When it comes to movement, it’s all about phosphotidyl inositide phosphates (PIPs). At the leading edge of a moving cell, PI(3,4,5)P3 is there. Everywhere else is PI(4,5)P2. How does this happen? This means that the kinase (PI3K) must also be a the leading edge, and the phosphatase (PTEN) is everywhere else to prevent PI(3,4,5)P3 from forming in the wrong place. How does PTEN...
WatchMy first Vlog
Master of my domains
Domains are parts of proteins that perform some function, like catalysis of a certain chemical reaction, or binding to something. Domains are modules, like legos, that can be mixed and matched to create new proteins that perform all the functions that used to be in separate proteins. Props to Master C.
Right on to the real, death to the fakers. Peace out
PIPin ain't easy
I like lipids. Especially those lipids that can be modified by kinases. Of these, I think my all time favorite is PI(4,5)P2, because this one is the substrate for PI3K and it marks the plasma membrane. Phosphorylate away, and stay classy
bloggin' ain't easy
iGEM could mean lots of things. Unfortunately it only means one thing, but fortunately that one thing is cool.
