Bacterial Leucine Transporter, LeuT

May 2009

Many antidepressant drugs, as well as drugs of abuse such as cocaine, block the traffic of neurotransmitters across the cell membrane of nerve axons and glial cells. They bind to a specific transport protein that clears the synapse after a nerve signal, transporting neurotransmitters back into the axon and making it ready for another signal. Researchers at NYCOMPS have made the first steps towards understanding this transporter at the atomic level, by looking to bacteria for help.

Bacterial Homologue

The transporter in our nerve cells has proven difficult to purify and crystallize, but a homologous bacterial transporter, LeuT, has been more cooperative. Like the transporter in our nerves, it has a bundle of twelve alpha helices that form a transport channel through the membrane. LeuT is more compact than our transporter, however, and is missing several extensions at the ends of the chain that interact with proteins in the nerve cell. The transport function is similar, though, and is even inhibited by compounds like antidepressants that block transport of neurotransmitters. So, the bacterial protein is providing a powerful model for studying the atomic details of the nerve protein.

Sodium Symport

LeuT is one of dozens of transporters that shuttle amino acids in and out of bacterial cells. LeuT specializes in small hydrophobic amino acids like leucine and alanine. The transport is powered by the gradient of sodium ions that is normally maintained by healthy cells across their membranes. LeuT acts as a symporter, which links the passage of a sodium ion across the membrane with the transport of the amino acid in the same direction.

Looking at LeuT

The crystal structures solved by NYCOMPS researchers, included in PDB entries 2q6h, 2q72, 2qb4, 2qei, and 2qju, capture LeuT frozen by the antidepressant in the middle of performing its job. An amino acid (shown in yellow) is bound deep inside the protein, held by two sodium ions (shown in green). The protein recognizes all aspects of the amino acid, forming specific interactions with both the amino group and the acid group, and forming a hydrophobic pocket perfectly fitted to the small hydrophobic sidechain.

Rocker Blocker

The protein is thought to act like a rocker switch. It starts with an opening towards the outside of the cell. Leucine and sodium enter and bind, then the protein shifts to open inside the cell, releasing the amino acid and sodium. The Jmol image below highlights two sets of alpha helices that are thought to perform the rocking action. The antidepressant molecule binds in the large cavity at the outer entrance to the protein, not directly blocking the binding site for amino acids, but presumably blocking the motion of the protein that is necessary for transport. There is some evidence, however, that antidepressants may bind a bit deeper in the opening of neurotransmitter transporters, so the LeuT structures are only the first installment in this fascinating story.

LeuT with clomipramine (PDB entry 2q6h)

LeuT is composed of twelve alpha helices that cross back and forth across the cell membrane. Four helices that surround the binding site for leucine (yellow) and sodium (green) are highlighted here. Notice that two of them are kinked, wrapping around the sodium ions and forming a specific binding site for them. Imagine rocking these two helices back and forth to open alternately a path upwards and downwards. The antidepressant molecule (magenta) is bound on the side facing outside the cell.
You can also use the buttons below to view a spacefilling representation. It is colored to highlight the hydrophobic characteristics of the molecule. Nitrogen and oxygen atoms that carry strong electric charges are colored bright blue and red, and all other atoms are colored in pastel shades. Notice that there is a band of white around protein--this is the portion that is buried in the cell membrane. You can also look down from the outside to see the drug bound in the deep opening, and see that the presumed exit on the other side is tightly shut.

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  1. Z. Zhou, J. Zhen, N. K. Karpowich, R. M. Goetz, C. J. Law, M. E. A. Reith and D.-N. Wang (2007) LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake. Science 317, 1390-1393.
  2. S. K. Singh, A. Yamashita and E. Gouaux (2007) Antidepressant binding site in a bacterial homologue of neurotransmitter transporters.
  3. S. K. Singh (2008) LeuT. Channels 2, 380-389.