Innovative technique pinpoints protein locations, helping scientists figure out their functions

Scientist from MIT have now developed a technique that can tag all of the proteins in a particular region of a cell, allowing them to more accurately map those proteins.

"There was no previous high-quality map of the matrix subdomain of mitochondria, and now we have one" said Alice Ting, the Ellen Swallow Richards Associate Professor of Chemistry at MIT. "We're still really far from that goal, but the overarching motivation is to get closer to that goal."

This innovative technique combines the strengths of two existing techniques -- microscopic imaging and mass spectrometry -- to map proteins in a specific cell location and generate a comprehensive list of all the proteins in that area.

In a paper appearing in the Jan. 31 online edition of Science, Rhee and colleagues used the new technique to identify nearly 500 proteins located in the mitochondrial matrix -- the innermost compartment found in mitochondria, which can be thought of as the power houses of the cell where energy is generated. Previous attempts to map the entire set of proteins in the matrix (proteome) yielded a list of only 37 proteins.

Protein labeling

To demonstrate the technique's power, the researchers created a comprehensive list of the proteins found in the mitochondrial matrix. Most of a cell's energy generation takes place in mitochondria, as well as many biosynthetic processes.

Using the new method, the team increased the number of proteins known to be located in the mitochondrial matrix. "There was no previous high-quality map of the matrix subdomain of mitochondria, and now we have one," says Ting, adding that this new wealth of information should help biologists to learn more about the functions of many of those proteins.

Already, the team has found that an enzyme called ppox -- involved in synthesizing heme, the iron-porphyrin complex found in hemoglobin -- is not located where biologists had thought it was. As heme precursors move through the biosynthetic pathway, they are shuttled to different parts of the cell. Finding that ppox is in the matrix means that there must be unknown transporter proteins bringing heme precursors into the matrix, Ting says.

The researchers are now investigating proteins found in another compartment of the mitochondria, the intermembrane space. They are also modifying the chemistry of the labeling system so they can use it for other tasks such as mapping the topology of membrane proteins and detecting specific protein-protein interactions.

The lead scientists of this research are Hyun-Woo Rhee (former MIT postdoc, currently Assistant Professor, School of Nano-Bioscience and Chemical Engineering, UNIST) and Peng Zou, who received a PhD from MIT in 2012.