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Giving enzymes floppy surfaces can enhance their activity

Added surface glycine residues cause partial unfolding that adapts enyzyme to low temperatures

by Stu Borman
June 7, 2018 | A version of this story appeared in Volume 96, Issue 24

Protein ribbon structures show how glycine substitutions partially unfold two protein domains.
Credit: Nature
Glycine substitutions in adenylate kinase’s LID (red) and AMPbd (blue) domains enhanced domain unfolding. Most of the active site is located in the CORE domain (gray).

The speed at which an enzyme catalyzes a reaction typically doubles with every 10 °C increase in temperature. But analogous enzymes found in tropical fish and Arctic fish tend to work at the same rate despite the organisms’ living at widely different temperatures. A new study suggests that partial unfolding caused by differences in the structures of the proteins’ surfaces may explain how enzymes maintain their activity at low temperatures.

The findings suggest an approach to engineering enzymes to work more effectively in the cold. And the work uncovers a new underlying mechanism for allostery, the phenomenon in which interactions in one part of a protein affect functions elsewhere in the structure.

Enzymes in cold-environment organisms often have the amino acid glycine in positions that contain more complex amino acids in corresponding enzymes from warm-weather organisms. Glycine is the smallest amino acid, so it tends to destabilize nearby parts of a protein by promoting temporarily unfolded conformations. To see if such fluctuations enhance adaptation to low temperatures, Vincent J. Hilser and coworkers at Johns Hopkins University introduced glycines into surface sites on two of the three structural domains in the enzyme adenylate kinase.

Glycine substitutions in the AMPbd domain encouraged local unfolding and increased catalytic activity at the active site, parts of which are in each of the three domains. Substitutions in the LID domain also promoted unfolding and affected a completely different enzyme function: They reduced binding affinity for the enzyme’s substrate at the active site. The activity and binding affinity changes both improve the enzyme’s ability to work efficiently at low temperatures, demonstrating a molecular mechanism for cold adaptation (Nature 2018, DOI: 10.1038/s41586-018-0183-2).

Scientists generally believed that allostery works by inducing minor structural variations that propagate through a protein, not by domain unfolding. Also, protein researchers typically thought that unfolding fluctuations affect global enzyme properties but not individual functions one at a time.

Controlling local protein structure as a way to regulate enzyme function allosterically is a new concept, and its discovery is “a significant breakthrough,” comments Magnus Wolf-Watz, a protein scientist at Umeå University.

Enzymologist Mikael Elias at the University of Minnesota, St. Paul, says it remains to be seen if glycine substitutions have the same unfolding effects on other enzymes as they do on adenylate kinase, but the study’s findings on enzyme adaptation and allostery are nevertheless “a tour de force—absolutely unique and exceptional.”

“The work offers pathways to bioengineers who wish to tinker with the properties of enzymes at the laboratory bench,” adds molecular evolution expert George N. Somero of Stanford University.


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