3D Pose of Enzyme Could Improve Antibiotic Drug Discovery

    Sending a tiny film crew to capture the molecular actions of enzymes in motion would be an ideal way to study the mechanistic nature of these biological catalysts. However, until Asimov’s fantasy about miniaturization rays becomes reality, the researchers at McGill University will stick to their current methods, which have allowed them to take a series of 3D images from a large section of what are commonly referred to as mega-enzymes—the medicine-synthesizing proteins that play an active role in creating many common antibiotics.

    Taking clear pictures of mega-enzymes hasn’t been easy, but results from a newly published study found that McGill investigators’ persistence has paid off. These enzymes are in constant motion, with sections that flip around acrobatically to carry out necessary tasks. The researchers believe that the images they have generated will not only bring scientists closer to understanding how many antibiotics are made, but could, with further research, lead to the development of much needed next-generation antibiotics.

    “This is the most complete view we’ve ever had of these enzymes in action,” stated senior study author Martin Schmeing, Ph.D., professor in the department of biochemistry at McGill University. “Even though mega-enzymes are the second-biggest proteins known to man, they are still very small molecules, and they are very mobile, so it’s difficult to see them at work.”

    The findings from this study were published recently in Nature through an article entitled “Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase.”

    The mega-enzymes are a class of proteins that are essential to the production of antibiotics that range from penicillin to cyclosporine. These proteins, often labeled as nonribosomal peptide synthetases (NRPSs), act as catalysts inside specific bacteria, give them the ability to kill competing bacteria.

    NRPSs have been compared to miniature assembly lines, combining building blocks through repetitive chemical reactions. Similar to factory assembly lines, these enzyme assembly lines are made up of different workstations (called modules) that each add on one section of the drug and in the process create antibiotics with new chemical features.

    The McGill team was able to utilize chemical traps in order to capture the enzymes in the desired position. Subsequently, the researchers used X-ray crystallography essentially to take a series of 3D pictures of the first module of an NRPS that makes the antibiotic gramicidin (an active ingredient of the commonly used Polysporin cream).

    “These 3D pictures revealed the totally remarkable way the NRPS works to synthesize its product. Parts of other NRPSs have been pictured before, but there have never been so many snapshots of the different steps of synthesis, and never pictures of NRPSs that incorporate interesting chemical modifications into the antibiotic,” explained lead author Janice Reimer, a doctoral candidate at McGill. “These pictures reveal the exquisite way these parts repurpose and recycle their limited surfaces to interact with the rest of the enzyme. Once we understand enough, we can use modern bioengineering techniques to modify NRPSs to produce all sorts of products with designer modifications, perhaps giving a veritable treasure trove of new medicines.”