Week 6 Bollough Lecture 16

Question 1

Describe the structure of the proton pore of bR in the resting state

Answer 1

he cavity containing the retinal is
quite rigid
a) the protonated Schiff base (pKa ~13.5) is stabilised by Asp85, which is charged
b) there is a clear proton path from Asp85 via polar side chains and waters to the outside of the cell
c) there is no clear path on the intracellular side and Asp96 has a very high pKa because of the non- polar environment
d) This is effectively a hydrophobic gate

Question 2

How does the bR photocycle work?

Answer 2

So

a) Retina is protonated
b) Proton is released between L and M, which changes the colour from red to yellow
c) Another proton is taken up between M and N, which changes the colour from yellow to red
d) Key residues are; D96 and D85

Question 3

Explain the proton movements during the photocycle?

Answer 3

Retinal is isomerised from the light and the Schiff base isomerises

a) Proton goes to Asp 85
b) Reprotonation of Schiff base from Asp 96
c) Proton from Asp 85 leaves the protein
d) Asp 96 donates the proton to the Schiff base
e) Asp 96 gets another proton
f) Another cycle is ready

Question 4

How is directionality and gating achieved in bR?

Answer 4

By changing the curvature of the protein

a) Helix F swings out to open up the cytoplasmic half channel. This allows water to enter that part of the channel, making the channel lining more hydrophilic.
b) Gating; by switching accessibility and the hydrophobic gate is also opened up to allow reprotonation

Question 5

How are protons conducted?

Answer 5

From the formation of a proton wire