Trapped protein tells biology’s secrets

U. CHICAGO (US) — For the first time, researchers have observed a key step in the chemical process that repairs DNA and plays a role in biological functions that affect obesity, cancer, and diabetes.

The observations focused on the bacterial DNA repair protein AlkB, but the results also apply to several proteins in the same family that play key regulatory roles in humans. Findings are reported this week in the journal Nature.

Researchers may one day develop methods for blocking the protein’s efforts to perform the biologically important demethylation function in human cells, says Chuan He, a chemistry professor at the University of Chicago.

“This family of proteins is the most exciting protein family now in biology,” says He, who led the study. “These proteins directly impact obesity, cancer and diabetes, and they do not go through the traditional pathways of DNA or protein modification. Most likely they go through RNA modification and demodification. It’s a new area of biological research.”

The Nature article presents new details about how proteins chemically alter biological molecules and their functioning via a process called oxidative demethylation. Methylation is a chemical process that helps control how DNA and proteins carry out their functions in the body.

Chuan He by Lloyd DeGrane_1

Chemist Chuan He grows cancer cell lines in his laboratory to study DNA/RNA repair and modification and other important biological processes. (Credit: Lloyd DeGrane)

Tethered and trapped
In the case of DNA, methylation and demethylation affect how the genetic code gets made into proteins. In recent years scientists had assumed that AlkB and related proteins initiate an oxidizing reaction to remove a hydrocarbon group (the methyls) from the group’s host molecule.

“Biological methylation is one of the most important processes in nature to regulate all kinds of things,” He says, including how cells differentiate into their final state and how genetic information is transmitted to proteins.

The Chicago team recently invented a chemical technique to trap the AlkB protein when it reacts with its host molecule—a previously unobserved, ephemeral process. The technique tethers the protein to the host molecule. “It’s stuck there. It can react and stop at the intermediate stage,” He explains.

Bizarre biochemistry
Two of the enzymatic intermediates that He’s team trapped and observed were predicted and expected based on the chemical principles involved, but these fleeting species were directly observed for the first time.

For a third intermediate, however, “we observed something bizarre,” He says.

Researchers at University of Wisconsin-Madison then carried out computational calculations on the electronic and structural properties of the intermediates that He observed in his experiments. The calculations showed that the bizarrely behaving intermediate was “zwitterionic,” meaning that it carried an overall neutral charge, but displayed positive or negative charges when interacting with different atoms.

“We were able to show that the intermediate captured by Chuan’s beautiful experiment is zwitterionic in nature, which offers new clues regarding the chemical steps of the biological demethylation process,” says Qiang Cui, professor of chemistry at UW-Madison.

The National Institutes of Health supported this study.

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