Grape-like clusters of the bacterium Staphylococcus aureus might look harmless under a microscope. But they’re capable of causing great mayhem.
Think food poisoning, a result of S. aureus’ most common toxin, Staphylococcal enterotoxin A, SEA for short. In fact, the bacterium produces more than 20 toxins known as superantigens, which trick the body’s immune system into going haywire. Precisely why S. aureus harbors these toxins and how some help the bacterium spread has remained largely unknown.
Now, researchers at Lund University in Sweden and the Institute for Protein Innovation (IPI) have shown that SEA could be capable of binding to a receptor that is expressed on every type of cell in the body, adding a new piece to the puzzle of how superantigens hijack our immune system. The findings indicate that the toxins may play a role in more illnesses than previously thought and could help explain how superantigens’ molecular interactions cause illness.
“It’s a matter of saying that we don’t know everything about these toxins,” said Karin Lindkvist, senior author of the study and professor of medical structural biology at Lund University, “and we shouldn’t forget about them.”
Superantigens are named for their remarkable ability to seize and take over human immune systems. An invader like SARS-CoV-2 might activate about .001% of a person’s T cells, primarily responsible for controlling antigens that invade the body. A superantigen might activate about 20%.
“It’s like toxic shock, basically. Really, your immune system goes crazy,” Lindkvist said.
SEA usually makes its way into the body via S. aureus in contaminated food. Once there, the toxin binds to other gut-anchored proteins, prodding pores to open and flooding the intestines with water. The result is the symptoms of food poisoning: vomiting, diarrhea and the like. They actually help S. aureus spread.
In the new study, researchers showed that SEA binds to a cell receptor called glycoprotein 130 (gp130) on immune cells, possibly by mimicking proteins the immune system relies on to communicate among its cells.
While previous studies suggest that SEA’s toxicity comes from its ability to activate large proportions of immune cells, the new findings indicate its virulence might also stem from its ability to interact with gp130, a ubiquitous receptor in the human body.
“Superantigens could be involved in more things than we believed from the start,” Lindkvist said. “The fact that it binds to gp130 opens up the window, really, for possibilities to study where else it can have a role.”
To find out, Arturo Vera Rodriguez, a former postdoctoral fellow at IPI, and Christopher Bahl, former head of the Protein Design Laboratory, created a computational model to visualize possible interactions between SEA, gp130 and two of gp130’s common binding partners, LIF and IL-6, which help immune cells mount responses.
To determine the most viable interaction between SEA and gp130 out of millions of possibilities, Vera Rodriguez virtually modeled all of them. A technique called molecular docking, which predicts how proteins bind to one another, enabled him to hone in on the one that was the most stable.
Because Lindkvist and her team knew the binding capability of SEA hinged on the presence of zinc, the researchers crosslinked the two proteins in the mineral’s presence to capture the configuration of the entire complex. That structural data enabled Vera Rodriguez to narrow the possible interactions between SEA and gp130 from millions to 57.
“Knowing all those clues, the zinc, the crosslink, the proteins; there are only very few possibilities that can satisfy all of them at the same time,” he said.
In a process of modeling elimination — based on finding the lowest binding energy of a LIF-gp130-SEA complex — Vera Rodriguez identified two likely configurations. But, due to space constraints, the three-protein complex could only exist in one.
Combined with experimental data from Lindkvist’s team, Vera Rodriguez showed for the first time that SEA and LIF could simultaneously bind to gp130. This mechanism hints at how SEA stymies immune cells and, Lindkvist said, paves the way for future drug design.
Back in the lab, the findings also help solve a conundrum in infectious disease studies. Researchers have long puzzled over why mice exposed to the same toxin don’t get food poisoning. It turns out SEA cannot bind gp130 in mice.
The work also demonstrates the importance of protein modeling. Structural biology is founded on techniques such as X-ray crystallography, which involves coaxing proteins into crystal structures and blasting them with high-powered X-rays, or averaging together pictures taken under an electron microscope.
But, in this case, the difficulty of cultivating gp130 in a lab has made generating a crystal structure of the interaction impossible so far. Modeling using IPI’s supercomputer accelerated discovery and allowed the Lund researchers to more quickly confirm their experimental data.
“Right now, it’s all about speed,” Vera Rodriguez said.
The team published its results in Febs Letters.
Sibel Uzunçayır, Paulina Regenthal, Hannah Åbacka and Cecilia Emanuelsson also contributed to this study.
Funding for this research came from the Diabetes Fund, the Novo Nordisk Foundation, the Craaford Foundation and the Swedish Research Council.
Writer: Halle Marchese, halle.marchese@proteininnovation.org
Sources: Karin Lindkvist, karin.lindkvist@med.lu.se;
Arturo Vera Rodriguez; arturo@aiproteins.bio
Christopher Bahl, chris@aiproteins.bio