Proteins get their own periodic table

An interactive periodic table of protein complexes. EMBL-EBI / SPENCER PHILLIPS

Much like Legos, proteins can come together in a number of ways to create complex structures. The various ways make it hard to organize protein complexes into categories.

But now, in a paper just out in Science, researchers describe an approach to classify protein complexes that creates a periodic table, like the periodic table that’s used in chemistry to organize elements. “We're bringing a lot of order into the messy world of protein complexes," says Sebastian Ahnert at the University of Cambridge. Ahnert is the first author on the paper.

Many proteins spend much of their time interacting with other proteins and assembling into complexes in order to carry out their functions. But the interactions and functions are specific, much like in the way different Lego bricks can latch onto each other only in certain ways. The underlying principles of protein interactions and assembly are not yet fully understood. But by organizing the different ways protein comes together into a table, Ahnert, along with Sarah Teichmann at the European Molecular Biology Laboratory–European Bioinformatics Institute, Joseph Marsh at the University of Edinburgh and others, wanted to see if some of the fundamental steps in protein complex evolution would become apparent.

They did. The investigators organized complexes based on simple rules so that they could find the most basic structures. “In the end, we discovered that three possible steps of interface evolution, combined in very specific ways, give rise to almost all known structures of protein complexes,” says Ahnert.

The investigators say that the fact that almost all known protein complexes could be arranged into a periodic table is revealing and will help understand how protein complexes come about. “Most heteromeric protein complexes—ones with more than one protein type—consist of identical repeated units of several protein types,” says Ahnert. “Because of this, heteromeric protein complexes can, in fact, be viewed as simpler, homomeric protein complexes—ones that only consist of a single type of protein—if we think of these repeated units as larger 'single proteins.’”

Rajendrani Mukhopadhyay Rajendrani Mukhopadhyay is the chief science correspondent for the American Society for Biochemistry and Molecular Biology. Follow her on Twitter.