Book Notes: Signaling Part 1

• allosteric enzymes have multiple sites
• active: binds substrate and performs reaction
• regulatory: binds regulatory molecule (activator or inhibitor) and alters active site to modify function
• active sites and regulatory sites are often very far away, how can one affect the other?
• binding of regulatory molecule causes conformational change of entire protein, which may "open" or "close" the active site
• coupled binding: essentially binding of substrate at one site affects binding at another site
• affinity coupling: binding at one site increases binding affinity at the other site (I bind, you bind, we all bind!)
• reciprocal coupling: binding at one site decreases affinity at the other site (I bind, you don't bind, *insert evil laughter*)
• cooperative allosteric transition: swapping a collection of proteins from active to inactive (or vice versa) is made faster and more efficient when you group the proteins into SYMMETRIC gangs
• binding of a few inhibitor upsets the symmetry, and the whole system wants to go back to symmetry (a symmetrical arrangement is energetically favorable), so all the other proteins in the group quickly grab inhibitors
• they go back to being symmetric, but are now all turned off
• proteins are also regulated by phosphorylation
• attaching a phosphate gives the protein 2 more negative charges, which can change the protein shape by attracting a positive cluster somewhere along the polypeptide
• the extra phosphate can also be (1) blocking an active site (2) serving as part of the active site to bind the substrate or (3) serving as the complement of another protein's binding site--i.e. the substrate protein is phosphorylated, enabling the enzyme to bind to the phosphorylated substrate
• the reversibility of phosphorylation makes it a very versatile form of protein control
• kinases: attach phosphate
• phosphatases: remove an attached phosphate
• GTPases are regulated by their own activity
• its own hydrolytic degradation of GTP to GDP turns off the GTPase, but the exchange of a used GDP for a new GTP turns on the GTPase
• GAPs help the hydrolytic process, while GEF helps the GDP release process so the GTPase can grab a new GTP
• a small chemical change can generate large protein movements (to create the new conformation)
• e.g. EF-TU protein shifts about a tenth of a nm at the GTP binding site when dephosphorylated
• a switch helix nearby can no longer bind and swings loose
• the domains of the protein are connected on a hinge, and the switch helix is like the deadbolt: when the lock is released, the "door" swings open, so the two domains open up about 4 nm, releasing the substrate (in EF-TU's case, it's the tRNA with an A.A. bound)

pg. 171 - 181 (from Chapter 3)