University of Wollongong (UOW) researchers created a piece of molecular “velcro” to stick a light probe to a protein with the help of a 3D printed visual aid. Certain proteins signal the repair of damaged DNA, and if researchers can better understand that process, they may be able to reduce or prevent antibiotic resistance.
RecA is one of those proteins in bacteria. When it detects damage to the DNA, it assesses what repairs are needed and calls on over 40 genes to respond. But some of those genes are overly aggressive in their repairs, causing errors that are not recognized as such. Molecular Horizons Research Fellow and study lead author Dr. Harshad Ghodke elaborates, "These changes or mutations are no longer recognised as errors, and the new sequence is replicated in new generations of cells. It doesn't revert back to its original form."
This is especially problematic when treating bacterial infections. When antibiotics try to kill the bacteria cells, ReaC tries to save them, and the cells that do survive may include mutations that counteract the effects of the antibiotic drug. Affecting the behavior of ReaC could greatly reduce the chances of those mutations and thus antibiotic resistance.
But to affect its behavior, researchers need to better understand its behavior, and that has proven difficult. "RecA surrounds a single strand of DNA to form a filament that then signals the SOS response," Ghodke said. "Typically, researchers would attach a bright fluorescent tag to RecA so they can take images of it as it goes to work. But with the attached tag, the RecA doesn't do its job very well, and stops functioning as it would in the cellular environment."
As a workaround, the team illuminated a protein that naturally bonds with the ReaC filament as Ghodke explains, "We used a viral protein that naturally interacts with the RecA filament so it wouldn't interfere with how it works, while lighting up the RecA filament as it takes part in the damage response."
Using a Stratasys Mojo, the researchers 3D printed models of ReaC to help them visualize how other proteins might interact with it. "We know from the imaging we do that proteins are dynamic objects. If we think of them as 3-D structures we can start to visualise how they change and what causes those changes, leading to a clearer understanding of how these proteins work,” relates Molecular Horizons Director, professor Antoine van Oijen. "With a physical structure, you can see the interfaces and design methods to attach other proteins. Then using sophisticated imaging tools we can take short films that for the first time, really show us how they work."
The discovery could lead the way to advanced drugs that don’t cause antibiotic resistance. "Antibiotic resistance is a hugely important global challenge. We don't want to get rid of antibiotics altogether because when they work they're incredibly effective. If we can visualise these processes we can then understand the physical connections between molecules and the structure of proteins and potentially design new drugs that will prevent bacterial cells from becoming resistant." 3D printing is great for prototyping and creating functional parts, but sometimes you just need a visual aid, and it can help with that too.