DHAP to GAP isomerization by TIM Flashcards
Why is DHAP to GAP an efficiency step?
DHAP and GAP are two diff structures.
So they bind differently to an enzyme, which means one must be converted to the other to be used.
Isomerized by TIM
TIM
homodimeric, catalytic perfect which means it works at diffusion control limit
Also operate at equil.
Favors DHAP, which means more favorable in GNG direction.
Coupled le chateliers: one enzyme produces a product that is then used up in the next enzyme step
TIM structure
a/b barrel system
- 8 loops between a-helices and b-sheets.
- loops are involved in the active site of TIM
What catalysis model of TIM use
GABC
Must be isolated from solvent in order to do this.
The functional groups are strange.
Glutamic acid as glutamate removes an a-H from the substrate. This pKa difference is massive
(Glu = 4, a-H = 17), which should never happen, but it does anyways.
This can happen due to being isolate in the active site, so the differences are much smaller and makes the removal possible.
Step 1 of DHAP to GAP
DHAP pro-R Hydrogen at C1 is removed by glutamate
a proton transfer also occurs here (proton hopping)
pKa Glu and His
Glu = 4.07
His = 6.04
How does Glu deprotonate alpha H of DHAP?
Removing Pro-R H
Must be a very large pKa change.
What role does the lys in TIM active site play in DHAP to GAP isomerization?
the lys in the TIM active site works through electrostatic catalysis to stabilize the developing negative charge in the TS. The positive charge on the N interacts with the TS negative charge.
What are low barrier H bonds ?
Low barrier H bonds: provide a rationale for substantial change in pKa. There is always a carbon involved.
First condition: DO NOT occur in bulk water.
pKa of donor atom and pKa of acceptor become approximately equal, because they are sharing a proton.
Barrier between swapping places between the two possible acceptor and donor atoms shrinks to nothing, due to sharing proton in the middle.
(LBHB occurs when two atoms with similar pka values are both H-bonding with a proton. This means that the energy required to transfer the proton between these two atoms is pretty low (that’s why it’s a low barrier H bond lol).
LBHB have free E of association, which means free energy is released when association between two atoms are formed.
When LBHB are formed, free energy of association is much more, which means releasing more energy, which goes to lowering transition state. LBHB are MORE STABLE
Where are low barrier H bonds occuring in DHAP to GAP isomerization?
between a-H of a-Carbon of DHAP and Oxygen of glu side chain.
reason: loop 6 closes of active site which excludes bulk water, which means glu properly positioned with substrate, isolated from bulk water active site, pka changes, forms LBHB, which helps you to form enediol
