SAN FRANCISCO, Sept. 23 (Xinhua) -- Researchers in the United States and Germany have discovered a part of protein molecules that could be key to find how proteins interact with each other inside living cells to carry out specialized functions.
Named by the researchers as "add-ons," because they work the way that computer software add-ons customize a web interface with a user, the tiny bits of molecular material on the outer edges of the protein interface are found to be able to customize what a protein can do.
Proteins are known to have an interface region where they connect with other proteins. However, before the new findings published in the Proceedings of the National Academy of Sciences, or PNAS, it was not clear how key proteins are able to find each other within a cellular environment that may contain tens of thousands of other proteins.
The researchers at the Ohio State University in the United States and the University of Regensburg in Germany experimented with live bacteria, determined that in the organism Bacillus subtilis, or B. subtilis, in which a unique interface add-on is missing, bacteria colonies grew 80 percent less under certain conditions. The reason for this was that the missing interface add-on led to un-healthy cross-interactions of proteins in the B. subtilis cells.
The University of Regensburg team, led by computational biologist Rainer Merkl and protein biochemist Reinhard Sterner, analyzed the protein sequences derived from more than 15,000 bacterial and archaeal genomes on a large computer cluster, sorted proteins that shared common evolutionary ancestors into a kind of family tree, and compared individual proteins to their protein "relatives," thus leading them to spot interface structures that were present in some proteins but missing in others.
The Ohio State team then used native mass spectrometry to detect how the presence and absence of add-ons influenced the ability of proteins to interact with each other.
"We're really pleased that our native mass spectrometry technology could help identify the role of these interface 'add-ons' - a way for a protein to find its critical partner protein even in a crowded cellular environment with similar structures present," Vicki Wysocki, director of the Campus Chemical Instrument Center at Ohio State, was quoted as saying in a news release.
It is difficult to overstate the importance of proteins to life as we know it, according to the researchers. Enzymes are proteins that enable chemical reactions in cells; antibodies are proteins that bind to foreign invaders in the body. The list goes on to include thousands of critical functions. In most cases, proteins have to connect to each other and form groups called protein complexes to perform diverse tasks.
