Coral Gables, FL, USA. A multidisciplinary team is developing the first map of protein interactions within neurons, in a live organism.

The map will be based on a systematic survey of protein interactions within brain cells, designed to reconstruct genome-wide in situ protein-protein interaction networks (isPIN) within the neurons of a multicellular organism.


University of Miami biology professor Akira Chiba is leading the team that presented preliminary data at the 2011 Annual Meeting of the American Society for Cell Biology (ASCB) in (December 2011; Denver, Colorado). "This work brings us closer to understanding the mechanics of molecules that keep us functioning," says Chiba, principal investigator of this project. "Knowing how our cells work will improve medicine. Most importantly, we will gain a better understanding of what life is at the molecular level."


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Förster Resonance Energy Transfer (FRET)

At the core of the new imaging technology is the phenomenon known as FRET that occurs only when two fluorescently tagged molecules come within the distance of eight nanometer or less.

Detecting the FRET serves as a proxy for the two proteins X and Y associating with each other within a living cell.

Image courtesy of Akira Chiba, University of Miami.Neurons are the cells that are mainly responsible for signaling in the brain. Like all other cells, each neuron produces millions of individual proteins that associate with one another and form a complex communication network. Until recently, observing these protein-protein interactions had not been possible due to technical difficulties. Individual proteins are small and typically less than 10 nm (nanometer) in diameter. Yet, this nanoscale distance was considered to be off-limits even with super-resolution microscopy.

Human Interactome Network

The lead image to this article is a network visualization of the human interactome. Each point represents a protein and each blue line between them is an interaction.

Keiono created the image with Cytoscape, a bioinformatics software platform for vizualizing molecular interaction networks and biological pathways, then integrating these networks with annotations, gene expression profiles and other state data.

The original dataset was created by Andrew Garrow at Unilever UK.Chiba and his collaborators have developed a novel methodology to examine interaction of individual proteins in the fruit fly model organism. The researchers are creating genetically engineered specimens that are capable of expressing over 500 fluorescently-tagged assorted proteins, two at a time.

The fluorescent tags make it possible to visualize the exact spot where a given pair of proteins associates with each other.

The team utilizes a custom-built 3D FLIM (fluorescent lifetime imaging microscopy) system to quantify this association event within the cells of a live animal. FLIM shows the location and time of such protein interaction, providing the data that allow creation of a point-by-point map of protein-protein interactions.

The pilot phase of this project employs advanced genetics, molecular imaging technology and high-performance computation, among other fields. Collaborating fluorescent chemistry, laser optics and artificial intelligence, the team works in the jungle of the molecules of life within the living cells.

Chiba says "This is a new kind of ecology played out at the scale of nanometers — creating a sense of deja vu 80 years after the birth of modern ecology."

At present, the researchers still need to extrapolate from data obtained in test tubes. In the future, they will begin to visualize directly how the individual proteins interact with one another in their native environment, which are the cells in our body.

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