Proteins Get Their Own Periodic Table

This from the American Society for Biochemistry and Molecular Biology

Protein structures are apparently very complex, so it's been tough to classify them in a systematic and structured way like we see with the Table of Elements. Researchers have apparently found a way to make a Periodic Table, similar to the Table of Elements after delving deep into structures and recognized "simple rules" that dictate how the structures form.

asbmb.org...

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.

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.’”

I'm beginning to ponder on the applications this could have in pathology, pharmacology, nutrition (medicine in general), material sciences, the list goes on and on. I think this has big implications

a reply to: FamCore

Very cool! Now we just need to find that magic number on the periodic table of proteins

i read this, spent some time mulling it over, and can honestly say that this is promising.

One would expect there to be a methodology by which all groups of things can be arranged in a logical/linear manner. Understanding proteins is a key element missing from biology in general, and human medicine specifically.

I wonder what the project will mean for the discovery of prionic disease.

Wow, this could be the impetus for a big bang type event in this field.

The next few years ought to be interesting.

Was just a matter of time. Pretty interesting development.

Mapping proteins is a start, but just that. When we can interact aminos and proteins to make anything resembling life, well that will be a wow.

The corresponding Research Article provides further detail: link

Results (1)

We first examined the fundamental steps by which protein complexes can assemble, using electrospray mass spectrometry experiments, literature-curated assembly data, and a large-scale analysis of protein complex structures. We found that most assembly steps can be classified into three basic types: dimerization, cyclization, and heteromeric subunit addition. By systematically combining different assembly steps in different ways, we were able to enumerate a large set of possible quaternary structure topologies, or patterns of key interfaces between the proteins within a complex. The vast majority of real protein complex structures lie within these topologies. This enables a natural organization of protein complexes into a “periodic table,” because each heteromer can be related to a simpler symmetric homomer topology.

There are some exceptions that don't fit these 3 assembly types:

Results (2)

Exceptions are mostly the result of quaternary structure assignment errors, or cases where sequence-identical subunits can have different interactions and thus introduce asymmetry. Many of these asymmetric complexes fit the paradigm of a periodic table when their assembly role is considered. Finally, we implemented a model based on the periodic table, which predicts the expected frequencies of each quaternary structure topology, including those not yet observed. Our model correctly predicts quaternary structure topologies of recent crystal and electron microscopy structures that are not included in our original data set.

Conclusion

This work explains much of the observed distribution of known protein complexes in quaternary structure space and provides a framework for understanding their evolution. In addition, it can contribute considerably to the prediction and modeling of quaternary structures by specifying which topologies are most likely to be adopted by a complex with a given stoichiometry, potentially providing constraints for multi-subunit docking and hybrid methods. Lastly, it could help in the bioengineering of protein complexes by identifying which topologies are most likely to be stable, and thus which types of essential interfaces need to be engineered.

Truly fascinating stuff.

a reply to: FamCore

While still really cool, it's actually just breaking down and mapping one single protein, a non-organic one. A good step if we want to understand these things, but we need amino interactions with proteins and something else to create biological life. That something else is the damn mystery.

The old saying a protein is a protein was so flawed. Every protein we consume has different properties to it.

It's definitely worth paying a visit to a university bookstore. You'll see the usual mathematics and physics books that haven't changed in 20 years. Biology textbooks have changed with full-color detailed pictures. But the greatest advance has been in genetics and molecular biology, with all sorts of new branches like human genomics, transcriptomics, proteomics, going beyond virusology. And they all have detailed glossy pictures of proteins as well.