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Designed Protein Shelters Radical

Biochemistry: Metalloprotein protects and stabilizes an organic radical anion, a first step toward mimicking the function of natural redox enzymes

by Stu Borman
February 18, 2016 | A version of this story appeared in Volume 94, Issue 8

Reaction scheme shows how the designed protein DFsc-Zn(II)2 hosts the radical anion species SQ·- in a binding pocket (right), stabilizing it in aqueous solution.
Designed protein DFsc-Zn(II)2 hosts the radical anion species SQ•- (red) in a binding pocket (right), stabilizing it in aqueous solution. SOURCE: Nat. Chem.

A new paper reports a truly radical development: Researchers designed a metalloprotein that can stabilize a reactive organic radical that is not normally stable in water. The work is a first step toward designed proteins that harness radical species to initiate reactions, a trick some natural redox proteins and enzymes employ.

William F. DeGrado of the University of California, San Francisco, and coworkers designed and synthesized their protein, called DFsc-Zn(II)2, to bind and subdue the semiquinone anion radical form of 3,5-di-tert-butylcatechol (QH2). The team picked this radical because previous studies by other groups had shown that Zn(II) ions can change the redox properties of the semiquinone radical, referred to as SQ•–, in organic solution.

DeGrado and coworkers had earlier designed a four-helix-bundle protein with two Fe(III) ions, and they speculated that replacing the protein’s Fe(III) ions with Zn(II) ions might enable it to stabilize the radical species in water. In the new paper, they report that this worked (Nat. Chem. 2016, DOI: 10.1038/nchem.2453). The researchers also used optical spectroscopy, electron paramagnetic resonance spectroscopy, nuclear magnetic resonance spectroscopy, redox titrations, and computational modeling to figure out exactly why it worked.

The radical is actually the monkey in the middle of a so-called redox triad, in that it can be formed by QH2 losing an electron or 3,5-di-tert-butyl-o-benzoquinone (Q) gaining one. The protein shepherds the radical into a binding pocket as soon as the species is generated by either reduction or oxidation, respectively, of Q and QH2. The radical-protein interaction is so stabilizing that the radical doesn’t react with water molecules when it is generated.

The researchers found that the organic radical remains stable by binding to the two Zn(II) ions, as predicted, and because the radical’s hydrophobic tert-butyl groups get buried in the protein structure, protecting them from exposure to water.

Inorganic chemist Akif Tezcan and his postdoc Jon Rittle at the University of California, San Diego, both say that the new study “sets an important precedent in the field of protein design.” However, “its true impact will be determined by what the authors or others can do based on this starting point.” For example, they would like to see whther the radical could be harnessed for chemical reactivity.

Also, natural redox proteins can stably host all three states of such redox triads and cycle among them. “And this is achieved without requiring stabilization by a metal center,” Tezcan and Rittle say. “An exciting future direction will be to achieve the same feat” by design.

Protein designer Ronald L. Koder of City College of New York says, “the DeGrado group achieved something noteworthy here—moving beyond designing proteins that merely bind small molecules to creating the kind of high-energy bound states needed to fashion effective catalysts. Learning how to create and control reactive intermediates is a critical step on the pathway to the rational design of enzymes superior to their natural counterparts.”

This article has been translated into Spanish by and can be found here.


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