By "smashing" proteins and looking at the broken bits, scientists at Rutgers University say they've discovered four basic building blocks that can be stacked like Legos to build all kinds of different proteins.
The results described in Proceedings of the National Academy of Sciences could help researchers better understand the origins of life and design new biomolecules with special industrial and medical uses.
"We've developed methods for really looking at the deep-time evolution of proteins," said senior author Vikas Nanda, a biochemist at Rutgers University.
Many scientists think that some of the earliest forms of life would have hung out where natural electric currents exist -- at the bottom of the sea floor, for example, where hydrothermal vents spew material into the ocean.
Ancient microbes would have needed special proteins to take advantage of those energy sources. These metal-bearing "metalloproteins" would have been able to carry and move electrons around in specific ways. But what exactly did such proteins look like, some 4 billion years ago?
It's hard to judge by what's in modern-day microbes because their proteins are pretty complex, Nanda said. He pointed to proteins such as nitrogenase, an essential enzyme that takes nitrogen and makes ammonia, which is then used to make DNA and amino acids.
"You couldn't imagine that complex nanomachine just emerging out of the primordial soup and just coming into existence," Nanda said. "There had to have been simpler intermediates. But the challenge is we don't have any fossil record of what proteins look like. All we have is the modern proteins, and we have to somehow infer what the simpler proteins may have looked like."
The average protein today is made up of around 200 to 250 amino acids, and still larger proteins can be made out of those amino acid chains. Nanda and his colleagues wanted to figure out which pieces within those chains truly did the work, and thus might resemble more ancient proteins from early life.
To get at this question, the researchers dug through the university's RCSB Protein Data Bank to analyze the atomic 3-D structure of 9,500 proteins. Using computers, they picked through the amino acid chains, looking for common subunits shared across different proteins that seemed to have similar functions.
It was basically like trying to understand a radio's most essential parts by taking a bunch of radios, smashing them with a hammer and then comparing the fragments, Nanda said.