When it comes to visual entertainment, three-dimensional viewing can be quite eye-opening. So, too, in science where a recent finding involving University of Iowa researchers used three-dimensional imaging to understand how a bacterial enzyme can take oxygen from air and use it to convert certain molecules into useful chemicals.
Specifically, the scientists saw that naphthalene dioxygenase, a bacterial enzyme, can bind oxygen (to iron) in a side-on fashion and add it on to naphthalene, a hydrocarbon molecule. The discovery is a result of the first three-dimensional imaging of naphthalene dioxygenase, a member of the family of enzymes called Rieske dioxygenases. The findings could help lead to the development of microorganisms that can clean up toxic and cancer-causing waste in the environment and to the development of novel drugs. The research results appear in the Feb. 14 issue of Science.
"The more we know about how enzymes catalyze reactions, the better able we are to modify them -- to improve or stop reactions, as desired" said S. Ramaswamy, Ph.D., UI professor of biochemistry and one of the study's authors.
"The question was: how does the enzyme actually work at the molecular level?" said David Gibson, Ph.D., UI professor of microbiology and one of the study's authors, whose previous research led to the discovery of the Rieske dioxygenase family of enzymes.
That seemingly straightforward question required seven years of collaborative work between the UI and the researchers in Sweden, beginning in 1996, and included assistance from the UI Center for Biocatalysis and Bioprocessing.
Ramaswamy and Gibson began research related to this investigation when Ramaswamy was a faculty member in the molecular biology department at Swedish University of Agricultural Sciences in Uppsala, Sweden. The paper's lead author is Andreas Karlsson, who was a graduate student of Ramaswamy's at the Swedish University and currently works for Aventis in Paris.
"People always thought that side-on binding of oxygen to iron existed, but no one had ever seen it in this enzyme or any other catalyst," said Ramaswamy, whose contribution to the project focused on how oxygen specifically binds to iron in the enzyme. Side-on refers to the newly visualized orientation of oxygen as it binds to iron.
The team used X-ray crystallography to determine the three-dimensional structure of the enzyme and then embarked on a series of experiments designed to take snapshots of the enzyme as it catalyzed the reaction, Gibson explained.
In all, the team had to analyze information from nearly 400 crystals in order to focus on five particular snapshots that led to the finding. The approach was revealing.
"Those five three-dimensional snapshots were the most relevant in understanding this side-on mechanism," Ramaswamy said. "Although we could not watch the reaction occur, the snapshots allowed us to see key points of the process."
Gibson likened the improved view to being able to "walk inside a molecule," just as one can walk inside a house and see the layout. By seeing how things are arranged within a molecule, scientists can better predict how to make changes to the structure and thus create desired reactions.
The researchers said the particular finding of their investigation suggests that other oxygen-using enzymes may also use a side-on binding mechanism. Thus, the study approach and results likely will impact how scientists investigate other enzymes of interest.
Scientists use a "lock and key" analogy to describe enzyme actions. In this study, naphthalene dioxygenase (enzyme) is a lock and naphthalene (substrate) is a key. For a reaction to occur between the two, the lock and key need to be complimentary.
"The thought was that there was one key and one lock, but now we are finding out that there can be many keys, or substrates, because we have the ability to go in and make a change to the lock, or enzyme," Gibson said.
"We can use this knowledge to engineer enzymes to do reactions and target other substrates in an effort to create new products or prevent other products from being created," Ramaswamy said.
For example, Gibson said, naphthalene dioxygenase is a key component in the development of the environmentally benign blue dye Indigo. In addition, a related Rieske dioxygenase synthesizes a key precursor in the production of Crixivan, an inhibitor of the AIDS virus.
The research team also included Juanito Parales, UI research assistant in microbiology; Rebecca Parales, Ph.D., UI research scientist in microbiology, and Hans Eklund, Ph.D., a faculty member at Swedish University of Agricultural Sciences.
Funding for the project included National Institutes of Health grants awarded to Ramaswamy and Gibson, a Swedish Research Council for Environment award to Ramaswamy and Eklund and a Swedish Research Council award to Eklund.
Materials provided by University Of Iowa. Note: Content may be edited for style and length.
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