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Scientists identify crucial guiding protein in neurogenesis.

In the developing brain, special proteins that act like molecular tugboats push or pull on growing nerve cells, or neurons, helping them navigate to their assigned places amidst the brain’s wiring.  How a single protein can exert both a push and a pull force to nudge a neuron in the desired direction is a longstanding mystery that has now been solved by scientists from Dana-Farber Cancer Institute, Peking University and the European Molecular Biology Laboratory (EMBL).  The report published in the journal Neuron explains how one guidance protein, netrin-1, can either attract or repel a brain cell to steer it along its course.

The team used X-ray crystallography to reveal the three-dimensional atomic structure of netrin-1 as it bound to a docking molecule, called DCC, on the axon of a neuron. The axon is the long, thin extension of a neuron that connects to other neurons or to muscle cells.

As connections between neurons are established, in the developing brain and throughout life, axons grow out from a neuron and extend through the brain until they reach the neuron they are connecting to. To choose its path, a growing axon senses and reacts to different molecules it encounters along the way. One of these molecules, netrin-1, posed an interesting puzzle: an axon can be both attracted to and repelled from this cue. The axon’s behavior is determined by two types of receptors on its tip; DCC drives attraction, while UNC5 in combination with DCC drives repulsion.

How netrin works at the molecular level has long been a puzzle in neuroscience field.  The team have provided structural evidence that reveal a novel mechanism of this important guidance cue molecule.  The structure showed that netrin-1 binds not to one, but to two DCC molecules. And most surprisingly, it binds those two molecules in different ways.

Normally a receptor and a signal are like lock-and-key, they have evolved to bind each other and are highly specific and that’s what was seen in one netrin site.  But the second binding site is a very unusual one, which is not specific for DCC.

Not all of the second binding site connects directly to a receptor. Instead, in a large portion of the binding interface, it requires small molecules that act as middle-men. These intermediary molecules seem to have a preference for UNC5, so if the axon has both UNC5 and DCC receptors, netrin-1 will bind to one copy of UNC5 via those molecules and the other copy of DCC at the DCC-specific site. This triggers a cascade of events inside the cell that ultimately drives the axon away from the source of netrin-1. The researchers surmised that, if an axon has only DCC receptors, each netrin-1 molecule binds two DCC molecules, which results in the axon being attracted to netrin-1.  By controlling whether or not UNC5 is present on its tip, an axon can switch from moving toward netrin to moving away from it, weaving through the brain to establish the right connection.

Knowing how neurons switch from being attracted to netrin to being repelled opens the door to devise ways of activating that switch in other cells that respond to netrin cues, too. For instance, many cancer cells produce netrin to attract growing blood vessels that bring them nourishment and allow the tumour to grow, so switching off that attraction could starve the tumour, or at least prevent it from growing.

On the other hand, when cancers metastasize they often stop being responsive to netrin. In fact, the DCC receptor was first identified as a marker for an aggressive form of colon cancer, and DCC stands for deleted in colorectal cancer.  Since colorectal cancer cells have no DCC, they are ‘immune’ to the programmed cell death that would normally follow once they move away from the lining of the gut and no longer have access to netrin. As a result, these tumour cells continue to move into the bloodstream, and metastasize to other tissues.  Therefore, to understand the molecular mechanism of how netrin works should also have a good impact in cancer biology.

The guidance issue is a very complicated cell biology problem. The researchers are now investigating how other receptors bind to netrin-1, exactly how the intermediary molecules ‘choose’ their preferred receptor, how other guidance molecule binds to DCC, and how the system is regulated. The answers could one day enable researchers to steer a cell’s response to netrin and other guidance cues, ultimately changing its fate.

Source:  Dana-Farber Cancer Institute

 

Detailed Molecular View of Generic Receptor Binding Site 2 on Netrin-1.  (A) An open book view of the regions on netrin-1 and DCC involved in binding site 2 showing the electrostatic surface potential to emphasize the positively charged regions within the binding site interface.  (B) View of the sulfate cluster at binding site2,withsulfate ions shown as sticks and the surface of the netrin-1 molecule shown with its electrostatic surface potential. The FN5 and FN6 domains of DCC are shown as a ribbon diagram in green.  (C) Identification of a chloride ion (green ball) at the interface of binding site 2, between the EGF-1 domain of netrin-1 colored salmon and the FN5 domain of DCC colored light green. An Fo-Fc omit map was calculated using the CCP4 suite (Winn et al., 2011) for a model lacking the chloride ion, and the electron density is displayed at a contour level of 5s.  Wang et al 2014.
Detailed Molecular View of Generic Receptor Binding Site 2 on Netrin-1. (A) An open book view of the regions on netrin-1 and DCC involved in binding
site 2 showing the electrostatic surface potential to emphasize the positively charged regions within the binding site interface. (B) View of the sulfate cluster at binding site2,withsulfate ions shown as sticks and the surface of the netrin-1 molecule shown with its electrostatic surface potential. The FN5 and FN6 domains of DCC are shown as a ribbon diagram in green. (C) Identification of a chloride ion (green ball) at the interface of binding site 2, between the EGF-1 domain of netrin-1 colored salmon and the FN5 domain of DCC colored light green. An Fo-Fc omit map was calculated using the CCP4 suite (Winn et al., 2011) for a model lacking the chloride ion, and the electron density is displayed at a contour level of 5s. Wang et al 2014.

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