Scientists use “molecular GPS” to study enzymes

Chuck Bednar for – Your Universe Online

The same device that helps keep you from getting lost on long trips has inspired scientists to track the metal ions in enzymes essential for metabolism and the synthesis of biological products, according to research published in the latest edition of the journal Angewandte Chemie.

Professor Dr. Olav Schiemann of the Institute for Physical and Theoretical Chemistry at the University of Bonn and his colleagues are developing novel methods for exploring the structure of enzymes that were inspired by the global positioning system (GPS), which is used to detect where people are and to reliably guide them from one place to another.

Enzymes are essential to life on Earth, as they enable and control a variety of biochemical reactions, including digestion and the duplication of genetic information. While complex in structure, enzymes contain a “protein knot” or “active center” that is usually comprised of at least one metal ion to which substances undergoing change in chemical reactions attach.

The metal ion facilitates the breaking or reforming of one of more bonds in the attached substance, causing it to be converted into a new substance through the enzyme. One example of these processes takes place in our stomachs, where food is regularly broken down into substances that can be easily absorbed by the human body.

Scientists are studying how these essential enzymes work, but to do so, they have to know exactly how individual atoms are arranged within the biomolecules. When they the location of the metal ion, they can better understand precisely how the reactions proceed, Schiemann explained. To make that happened, they developed a method similar to a car’s navigation system.

“The structure of enzymes is frequently, at first glance, just as confusing as the maze of traffic during rush hour,” he explained. Similar to how a single vehicle is difficult to point out on a busy highway, the metal ion is initially hard to spot in the folds and coils of the enzyme. Even so, just as GPS makes it easy to know a car’s location, the new technique helps them spot the metal ion.

Whereas GPS systems use orbiting satellites, the novel method of hunting metal ions uses “spin labels,” or tiny organic molecules which have an unpaired electron and are stable, explained University of Bonn doctoral student Dinar Abdullin. They distributed six of these “molecular satellites” in their enzyme model “azurine” (a blue protein that contains a copper ion).

Next, they used computer programs to first track the “orbits” of these “satellites,” then determined the distance between them and a metal ion using a spectroscopic method. They were able to successfully determine metal ion’s exact position of the enzyme’s active center using this technique.

While the method was developed for basic research purposes, Professor Schiemann said that it can also be used “to clarify the structure of other enzymes.” As a result, the tool could lead to improved industrial drug manufacturing or other fields that could benefit from a better understanding of substance conversions at active centers, the study authors added.


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