Problem -
They say that you don't really understand something until you can build it de novo ("from scratch"). Last year for the very first time, scientists created an active rocker-switch transporter, able to antiport H+ against the H+ gradient using the energy in the gradient of a divalent cation (call it X2+). The structure of the transporter is shown here. The key amino acids are glutamic acids at positions 4 and 18 in the protein's primary structure (pink circles labeled E4 and E18), and histidine at position 7 (red square labeled H7). You'll want to look at the table in Lecture 3 to see how these amino acids' R-groups are characterized. (Histidine is very weakly positive, even though it doesn't have a full positive charge anywhere.)
A. Briefly explain how a rocker-switch transporter functions. What structural considerations would be involved in building one?
B. In this particular transporter, what is the function of the glutamic acid at position 18 and the histidine at position 7 at each end of the bundle of alpha helices?
C. The space between the helices was measured to be 0.5 nm when X2+ was bound, and 1.2 nm when it was not. Explain how the transporter can use the energy in the X2+ gradient to transport H+ in the opposite direction. (I don't expect you to understand all the details; just the basics. Start by sketching the membrane gradients of X2+ and H+, and then figure out toward which side of the membrane the transporter will be open more frequently.)