Solving the structure of fundamental bacterial protein

Bacteria seen under a scanning microscope

Bacteria seen under a scanning microscope. Credit: Dreamstime
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Scientists have discovered the much debated structure of a fundamental bacterial protein, through a combination of neutron and x-ray studies, and computational modelling The protein, known as a single-stranded DNA binding protein (SSB),is involved in a variety of essential DNA mechanisms such as replication and repair. Now the structure of this ‘messy’ protein has been found, it could present a new bullseye for future antibiotics to hit bacteria right at its heart.

In 2014, 700,000 deaths were attributable to antimicrobial resistance, and this number is estimated to rise to 10 million fatalities by 2050 according to a review that the UK government commissioned on antimicrobial resistance in collaboration with the Wellcome Trust.

As we approach an era of antibiotic resistance, the ability to target a key protein behind bacterial growth may offer a solution for delivering new and effective antibiotics.

Single-stranded DNA binding proteins, or SSBs are fundamental proteins in molecular biology. Every time there is a transaction in the genome there is single strand of DNA that needs to be protected by these proteins. Seeing as these proteins are essential to bacteria, targeting them could make it difficult for bacteria to develop resistance.

Most proteins are usually neatly folded, however the jelly-like nature of SSB made it difficult to study in the past. It was previously thought that during replication and repair, the protein folded around DNA after binding.  But in a turn of events, scientists now understand that the protein remains unfolded whilst working and collapses further upon binding to single-stranded DNA.

The results have been published in the Journal of Molecular Biology

In the study, a team from the University of Nottingham used the unique contrast matching technique at ISIS to look at the structure of the protein whilst bound to DNA. When studying the protein-DNA complex on LOQ, they discovered that not only does this protein compact when it was thought to expand, it is also functional whilst unfolded.

Before the study it was known that the tail of the protein was unfolded but beyond that it was thought that the carboxyl- or C-terminus of the protein would stick out into solution and capture an array of proteins. However through work at ISIS the researchers could see that the protein didn’t work in this way and actually moved things closer together by nanometres.

The protein binds to DNA and then recruits other proteins for functions such as DNA repair and replication, much like a ‘molecular tool belt’.

 “Single-stranded DNA binding proteins are everywhere. Every time you do a transaction in the genome you have single-stranded DNA which needs to be protected,” said Dr Dave Scott, project leader from the University of Nottingham.

The more that is understood about the fundamental mechanisms of bacterial life, the more they can be potentially targeted for antimicrobial treatments. The SSBs studied are specifically bacterial proteins and crucial to survival, meaning that targeting them could kill bacteria without damaging the host’s cells.

“As we move through an era where our antibiotics are failing we’re looking for new target areas. This sort of structural information is invaluable for helping us understand not only the fundamentals of how this works but how we can apply this research,” Dr Scott added.

The unfolded nature of the protein will prove interesting for further research as the protein offers an alternative to the usual folded proteins  often used as drug targets in antimicrobial treatments.

“This is our first step to understanding how this protein works on DNA. It’s an obvious antimicrobial target but as it’s unfolded, it makes studying it difficult because you usually look for proteins with a folded structure to act as drug targets. So it’s provided us with a mystery of how we’re going to interfere with this process,” said Dr Scott.

Next, the scientists plan next to look at some of the proteins that are involved with these genetic transactions by building bigger complexes and mimics of those complexes to see how they work, and importantly how they can be interrupted.

Ellie Welch

Research date: May 2016

Further Information

The work was a collaboration between ISIS, European Synchrotron Radiation Facility (ESRF), Research Complex at Harwell, University of Nottingham and University of Texas.

The structure of the protein was studied at ESRF and the DNA-protein complex was studied on LOQ at ISIS after the complex was prepared at Research Complex at Harwell.  

The paper has been published online in the Journal of Molecular Biology and belongs to their special issue on the Study of biomolecules and biological systems: Proteins.

http://www.sciencedirect.com/science/article/pii/S0022283615006981

The research was funded by the Wellcome Trust and BBSRC.

Computational modelling, to calculate 100,000 possible structures of the protein that were compared to the experimental data, was funded by EPSRC and NSF (USA).

Dr Dave Scott is a Senior Molecular Biology and Neutron Fellow supported by STFC.

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