Study Sheds Light on Young Miniproteins

In a new paper published in Molecular Cell, a research team describes how they were able to systematically study miniproteins, a diverse subclass of protein scaffolds characterized by small size, stability, and versatility. “We were able to show which genome sequences the proteins are encoded in, and when DNA mutations occurred in their evolution,” explains lead author Dr. Jorge Ruiz-Orera, an evolutionary biologist at the Max Delbrück Center. Ruiz-Orera’s bioinformatic gene analyses revealed that most human microproteins developed millions of years later in the evolutionary process than the larger proteins currently known to scientists.

Unlike the older, “traditional” proteins encoded in our genome, most microproteins emerged more or less “out of nowhere—in other words, out of DNA regions that weren’t previously tasked with producing proteins,” says Ruiz-Orera. Microproteins, therefore, didn’t take the “conventional” route of being copied and derived from existing versions. 

Since these small proteins only emerged during human evolution, they’re absent from the cells of most other animals, such as mice, fish and birds. These animals, however, have been found to possess their own collection of young, small proteins.

The researchers were surprised to find that the vastly younger microproteins could interact with the much older generation. This observation came from experiments performed using a biotechnical screening method developed at the Max Delbrück Center in 2017.

In collaboration with Dr. Philipp Mertins and the Proteomics Platform, the miniproteins were synthesized on a membrane and then incubated with a solution containing most of the proteins known to exist in a human cell. Sophisticated experimental and computer-aided analyses then allowed the researchers to identify individual binding pairs.

During their work, the researchers also discovered the smallest human proteins identified to date. “We found over 200 super-small proteins, all of which are smaller than 16 amino acids,” says Dr. Clara Sandmann, the study’s third lead author. Sandmann says this raises the question of how small a protein can be—or rather, how big it must be to be able to function. Usually, proteins consist of several hundred amino acids.

Peptides, a small protein already well known to scientists, function as hormones or signaling molecules and are formed once they split from large precursor proteins. “Our work now shows that peptides of a similar size can develop in a different way,” says Sandmann. These smallest-of-the-small proteins can also bind very specifically to larger proteins—but it remains unclear whether they can become hormones or similar.

This study reveals how these small molecules can impact medical research communities, especially scientists studying cardiovascular disease and cancer. “These initial findings open up numerous new research opportunities,” says senior author Sebastian van Heesch.