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News : Researchers uncover secrets of a shape-shifting protein


The two possible folds of human signaling protein XCL1. It directs the migration of white blood cells when in the red fold and directly kills invading pathogens in the gold fold. (Acacia Dishman)

 

A search through evolutionary time led scientists to learn how and why a particular human protein can fold into a second structure to fulfill a different role, a phenomenon rarely found in proteins.

Their findings, shared in a paper published in Science, contradict common knowledge in biology by suggesting that there is an evolutionary benefit for a protein to perform different tasks in two forms. The researchers also present guidelines for how to create these metamorphic proteins for therapeutic use.

The study investigated XCL1, a metamorphic signaling protein belonging to the chemokine family of immune-response proteins. In 2008, the same lab confirmed that XCL1 folded its amino acids into two distinct shapes: a typical “chemokine” fold that aids the movement of white blood cells, and a unique second fold in which it binds with a copy to kill invading viruses, bacteria and fungi. 

“This protein (can) interconvert between two totally different three-dimensional structures in seeming violation of pretty basic principles of protein folding,” which say each amino-acid sequence folds into a single structure, said Brian Volkman, the senior author of the study and a professor of biochemistry at the Medical College of Wisconsin. He has researched XCL1 for the last 20 years and co-authored the 2008 study confirming its shape-shifting nature.

Using the genetic codes of XCL1 and other chemokines — which all have only one known folding shape — Volkman and his co-authors traced the protein’s evolutionary family tree back hundreds of millions of years and “resurrected” several of its ancestors in the lab to test their structures and metamorphic abilities.

XCL1 and at least one other chemokine were found to share a single-shape ancestor from 350 million years ago, and the first metamorphic ancestor emerged about 150 million years later. The team found that a few structural deviations from other chemokines were necessary to allow XCL1 to change shape, which happens when it emerged in different temperature and salt levels. 

The initial shapeshifter used the chemokine fold about 92% of the time, while a subsequent ancestor took it about 9.3% of the time, the researchers found. Currently, XCL1 uses either fold about 50% the time; the chemokine fold’s rebound implies that being metamorphic was evolutionarily preferred.

“This is interesting because some scientists have hypothesized that metamorphic proteins are proteins that are caught in the act of evolving from one fold to another,” said Acacia Dishman, the paper’s lead author and a Ph.D. and M.D. student at the Medical College of Wisconsin. “But our data suggests that that’s not actually true.”

Dishman speculated that changing folds in certain conditions allows XCL1 to fulfill its roles more efficiently than if it performed both functions in a single form or if the body needed to create two different proteins. 

Only about six metamorphic proteins have been identified and well-understood, according to her team. One estimate, however, predicted that as many as 4% of Protein Data Bank’s 150,000 entries could be metamorphic.

“Maybe there are other proteins in the world that are also evolving to be metamorphic on purpose, and there might be a lot more metamorphic proteins than we expected before,” Dishman said. “Maybe we just haven’t found them because … they can be really difficult to work with.”

Despite years of findings by his lab and other researchers, Volkman said metamorphic proteins remain a relatively new and unheard-of concept among structural biologists. They were not included in biology textbooks until 2009, and Volkman said he has heard stories from younger scientists who have been discouraged from investigating them.

Yet the new study not only discovered new mechanisms behind metamorphic proteins but also described how they might be created to be used in treatments or other applications. Features deemed essential to create two-fold protein include structural flexibility strain that can trigger a shape-change and residue contact networks that prevent them from getting stuck in one of the two folds.

In addition to better understanding XCL1’s ancestors and learning how to identify metamorphic proteins more easily, Dishman said she is interested in doing more work to learn how to create them from scratch.

“Nature designed this one, and we sort of figured out the instruction manual that it used to do so,” Dishman said. “So we’d like to know, can we make our own metamorphic proteins using the principles that we uncovered in this study?”

The article, “Evolution of fold switching in a metamorphic protein,” was published Jan. 1 inScience. The authors of the study were Acacia Dishman, Robert Tyler, Jamie Fox, Andrew Kleist, Francis Peterson and Brian Volkman, Medical College of Wisconsin; Kenneth Prehoda, University of Oregon; and M. Madan Babu, St. Jude Children’s Research Hospital. The lead author was Acacia Dishman.

Correction: A previously published version of this article misidentified the institution with which Brian Volkman and Acacia Dishman are affiliated. The error has been corrected.

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