Transporter Mechanism

Rocking bundle mechanism?

This is when the core domains rotates as one unit about an axis that incorporates the substrate binding site and is parallel to the membrane. So when the conformation of the transporter changes from being opened on the outside to opened on the inside, the core domains rotate together in a coordinated manner to allow the substrate binding site to be exposed to the inside, so substrates can be deposited.

The fact that TMs 1-5 and TMs 6-10 are almost symmetrical and how TMs 1, 2, 6 and 7 forms a helix bundle lead to a postulation that LeuT follows this mechanism. 

But we have seen that some of the core domains don't rotate as a rigid structure and the different domains rotate by different degrees, which suggest that the movements are not coupled. Therefore, LeuT does not strictly follow the rocking bundle mechanism.

Here are some evidences:

• TM2 and TM7 bends at conserved Gly residues.
• TM1a and TM6b moves independently.
• The r.m.s.d.* of the core domains in outward-occluded and inward-open conformations come up as 3.5Å, while the r.m.s.d. for the scaffold domains is 0.7Å. But when TM1a is excluded, the r.m.s.d. for the core domains is only 0.83Å. This indicates that some of core rotate together as one, but not all, where TM1a is a main contributor to the big change in conformation.

Figure 2- The bending of TM2 and TM7 at Gly residues

*r.m.s.d.= Root mean square deviation, which is the average distance between the backbone atoms on superimposed protein structures. In this case, the superimposed structures are the outward-occluded structure and the inward-open structure of LeuT.

Basically, how it all happens....

The opening and closing of the transporter occur by the bending of transmembrane helices at hinges that are in  non-helical regions, the formations and disruption of sodium and substrate binding sites, and the opening and closing of intra/extracellular gates caused by bundles of helices and loops. The locations of the hinges relative to the positions of the binding sites determine the level of disruption caused to the binding sites.

In other terms, a whole series of movements of different domains within the transporter changes the shape of the transporter. The changes in shape is what cause the opening and closing.