Oct 13, 2008 - Claremont, Calif. - Communication between active domains on protein chains in bacteria play a vital role in antibiotic production, according to a recent paper in the journal Nature co-authored by David Vosburg, Harvey Mudd College assistant professor of chemistry.

Knowledge about such protein dynamics could one day open avenues for the design of new therapeutic compounds.

“Protein interactions are so important,” said Vosburg, who began this research in 2002, as a postdoctoral student, with colleagues at Harvard Medical School. “If we know how they work, we can better engineer proteins to make novel drugs and improve existing antibiotics.”

Using a technique known as nuclear magnetic resonance (NMR), the research team focused on a large, multifunctional family of bacterial enzymes to learn more about non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS)—enzymes that both produce potent antibiotics, including penicillin and vancomycin, which microbes use against each other.

NRPS and PKS enzymes generally consist of multiple active site domains grouped in clusters known as modules.

Starting with simple organic molecules, these modules each orchestrate a series of reactions in which new molecular building blocks are added to a growing chain of antibiotic.

During this process, chemical components needed for the antibiotic are secured to carrier proteins, which shuttle them in sequence to the active sites in the module—the molecular equivalent of a moving assembly line.

“Communication at the end of this molecular assembly line is of particular importance,” explained Vosburg. “This is when the domain known as a thioesterase catalyzes the final release of antibiotic molecules from the NRPS and PKS proteins.”

Vosburg and his colleagues discovered the importance of the dynamics between the active modules by closely monitoring the interactions of components in the assembly line.

“We could see how the last two domains in the final module of a synthetase work in concert with each other and also with other components of the assembly line,” said Vosburg. “This gives us a better understanding of how certain pieces of large proteins work with other pieces.”

Furthermore, the NMR technique that the team utilized for the study provided a more intricate picture of protein dynamics than the more commonly used technique of X-ray crystallography.

X-ray crystallography reveals detailed, three-dimensional structure of molecules based on the scattering of X-rays through a crystal of the molecule, but the images are static.

In contrast, NMR—a powerful spectroscopic technique that provides information about the structural and chemical properties of molecules in solution—offers a more dynamic view of proteins and other flexible molecules.

“If crystallography gives you a snapshot of a molecule, NMR can give you a movie,” Vosburg explained. “This is invaluable because many enzymes undergo conformational changes as they catalyze reactions and interact with other proteins.”

As with all research, the team’s findings are just one piece of a puzzle.

Other studies have shown that modules from different proteins can sometimes be mixed and matched to create new assembly lines for new antibiotics or other medicinal molecules. But these engineered systems—even in cases where they do work—are typically much less efficient than the wild-type enzymes.

“The reason is that protein-protein interactions present an exceedingly complex problem,” noted Vosburg. “But there is real joy and hope in each new discovery of nature’s molecular logic, and we may yet attain that ‘holy grail’ of coaxing a whole new generation of medicines out of bacterial hosts.”