New research proves cellular proteins identify and communicate with one another using molecular "add-ons." Scientists liken the protein add-ons to web browser plug-ins.

Slowly, researchers are beginning to understand how proteins develop to perform specific functions. Many proteins work only in tandem with another specific proteins, or must communicate with another protein to carry out their task. But until now, scientists weren't sure how different proteins find each other inside a cell.

The latest discovery -- detailed this week in the journal PNAS -- suggests proteins use their add-ons to identify one another.

Researchers discovered the add-ons, bits of molecular materials on the outside of protein molecules, using computer models designed to analyze the evolutionary development of related proteins.

Scientists analyzed proteins among 15,000 bacterial genomes, sorting different proteins into family tree-like groupings based on their genetic sequences. The analysis revealed interface structures present on some proteins but not on others. Researchers realized the so-called add-ons could explain the diversity of protein functionality.

While only about 1,000 basic protein structures have been identified by scientists. Research shows cellular proteins have evolved the ability to perform thousands of specialized tasks.

"Much work has been put into analyzing how proteins interact with each other and what the interfaces look like, how they are constructed, and how they evolved," Maximilian Plach, a biochemist at the University of Regensburg, said in a news release. "But the peripheral regions of interfaces have not received as much attention. I think the novelty in our approach was to look at regions that have been, as yet, regarded as less important."

Researchers manipulated molecular add-ons to see how their absence might affect bacterial colonies. They found the deletion of one particular add-on hampered the growth of Bacillus subtilis.

"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," said Vicki Wysocki, a molecular biologist at Ohio State University.

The new findings were made possible by large databases of protein and bacterial genomic data.

"I consider our work to be one important example of how to make use of publicly available data in order to understand fundamental principles in nature, and I think that data mining will become increasingly important in the biomedical field in the future," said Florian Busch, a postdoctoral researcher in biochemistry at Ohio State.

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