Scientists find an array of protein folds unexplored in nature

A team of Japanese researchers recently set out to reveal the extent to which nature has explored the vast landscape of possible protein topologies. Their results have unveiled an astounding array of unexplored protein folds, expanding our understanding and uncovering the depth of the protein universe.

Proteins — the building blocks of life — fold into specific three-dimensional structures, enabling them to carry out their biological functions. These three-dimensional structures are dictated by the proteins’ amino acid sequences.

While experimental techniques have successfully unravelled the structures of numerous proteins over the years, the discovery of new protein folds, defined by the arrangement and connectivity of α-helices and β-strands, has become increasingly infrequent. This raised a question: how extensive is the protein fold space not explored by nature?

In attempts to answer this question, several theoretical studies have been conducted; however, experimental validation is lacking. The Japanese research team sought to address the question by embarking on a study combining theoretical prediction for novel protein folds with experimental validation of their de novo designs. Their research was published in the journal Nature Structural & Molecular Biology.

The team devised rules based on physical chemistry and protein structure data to theoretically predict possible protein folds. These rules were then employed to predict novel αβ-folds, which consist of a four- to eight-stranded β-sheet, not yet observed in the current Protein Data Bank (PDB). This led to the identification of a total of 12,356 novel folds. The team then attempted to computationally design proteins for the predicted novel folds from scratch to assess the foldability and fidelity of the novel folds.

“We attempted to computationally design proteins with all of the predicted folds that have a four-stranded β-sheet, including one forming a knot-like structure,” said Shintaro Minami, a researcher at Japan’s Exploratory Research Center on Life and Living Systems (ExCELLS). “When designing proteins, we did not expect all of them, especially knot-forming ones, to fold into the structures as anticipated.”

The results of experimental testing were surprising, according to RIKEN Senior Research Fellow Naohiro Kobayashi. “For all of the folds, the computationally designed protein structures closely matched the experimental structures,” he said.

These findings suggest the existence of at least 10,000 unexplored foldable αβ-folds, a significant revelation considering only 400 αβ-folds have been observed in nature. This suggests that many potential folds remain uncharted in the protein-folding space.

These results have given rise to several hypotheses about the structure and evolution of proteins. One hypothesis is that proteins may have not been present in biology long enough for all possible folds to have been explored. Another hypothesis is that protein folds in nature are inherently biased due to all life on Earth having descended from a common ancestor.

“Proteins may have evolved by repeatedly reusing specific folds while expressing different functions,” said George Chikenji, an assistant professor at Nagoya University. “If extraterrestrial life does exist, it might be utilising a different set of protein folds.”

Proteins are known for their diverse functions, which are generated from the diversity of protein three-dimensional structures. With the study having revealed the existence of at least 10,000 uncharted foldable αβ-folds in nature, Nobuyasu Koga, a professor at ExCELLS, said, “The design of proteins with these novel folds will lead to an even greater diversity of structures.

“This would pave the way for the de novo design of functional protein molecules, lead to breakthroughs in drug development, enzyme design and other areas.”

Image credit: iStock.com/Miyako Nakamura