A new study, published this week in the Proceedings of the National Academy of Sciences, reveals a previously overlooked feature of protein molecules that could be key to their interactions with other proteins.
Researchers from The Ohio State University and the University of Regensburg discovered tiny bits of molecular material on the outer edges of the protein interface that customize what a protein can do. These bits of molecular material may explain how a protein is able to find other key proteins within the crowded cellular environment. The researchers named these pieces of molecule “add-ons” because they customize interface between proteins in much the same way that software add-ons customize a user’s web interface.
To make their discovery the team analyzed protein sequences derived from more than 15,000 bacterial and archaeal genomes. Proteins that shared common evolutionary ancestors were sorted into a tree and compared to proteins in their “relatives”. It was here that the researchers spotted interface structures present in some proteins but missing in others.
The team then used native mass spectrometry to detect how presence or absence of add-ons influenced the ability of proteins to interact with one another. This revealed that add-ons allow bacteria to find each other in a crowded environment.
Using live bacteria as a model, the researchers demonstrated the importance of add-ons to cellular functions. For example, in the organism Bacillus subtilis, in which a unique interface add-on was missing, bacteria colony growth was reduced by 80 percent under certain conditions.
"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 chemistry and biochemistry at Ohio State and co-author of the study.
Big data has seen increasing use in scientific discovery, such as in finding a new role for flagella or tracking modern human evolution.