March 30, 2018 — What makes pathogenic bacteria so persistent? Researchers from the Beckman Institute at the University of Illinois and the University of Munich(LMU) are using the National Center for Supercomputing Applications’ (NCSA) Blue Waters supercomputer to simulate and decipher the physical adhesion mechanism of a widespread pathogen virulence factor. This, in turn, could lead to innovation in the treatment and prevention of relatively common staph infections that can turn deadly.
Staph infections are caused by staphylococcus bacteria, types of germs commonly found on the skin of healthy individuals. Most of the time, these bacteria cause no problems or result in relatively minor skin infections. According to the Mayo Clinic, however, septicemia (also known as blood poisoning) can occur when staph bacteria enter a person’s bloodstream, giving it access to locations deep within the body, causing infections. Not surprisingly, staph infections are the leading cause of healthcare-related, nosocomial infections, frequently preying on medical devices such as artificial joints or cardiac pacemakers.
But how do these bacteria invade our bodies? Staph bacteria adhere to their hosts—us humans—with exceptional mechanical resilience. Understanding the physical mechanisms that underlie this persistent stickiness at the molecular level is instrumental to combat such invaders. Combining experimental and computational approaches, Rafael Bernardi and the late Klaus Schulten from the Beckman Institute teamed up with Lukas Milles and Hermann Gaub from the LMU Physics Department to decipher the mechanism responsible for staph adhesion. The results were published in Science Magazine.
The collaborative study, one of the last that Prof. Schulten participated in, took advantage of NCSA’s Blue Waters supercomputer to deconstruct the mechanism of the interaction between staph adhesion factors and human proteins. Using an Atomic Force Microscope (AFM) the LMU team was able to measure the forces that govern the interaction between an individual adhesin (a staph protein) and its human target molecule. Independently, the Illinois team investigated the same protein complex by performing computationally-intensive steered molecular dynamics (SMD) simulations, carried out using the Blue Waters supercomputer.
The unbinding force of a single adhesin-human protein complex measured was exceptional, reaching over two nanonewtons, a regime generally associated with the strength of covalent bonds, and nearly an order of magnitude stronger than most other protein-protein interactions known. Lukas Milles points out “the complex was so strong that, at first, we thought something had gone wrong with the experiment.”
How is this extreme binding force generated? The answer to what gives this system such exceptional mechanical strength can be found in its physical principle, which was revealed through the seamless integration of experimental and computational results.
“The large number of molecular dynamics simulations performed, over 2,400, allowed the team to compare simulations and experiments in the same framework.” said Bernardi.
“The agreement between simulation and experiments were always good in the past, yet in a qualitative way,” said Gaub. “However, the new results obtained by the Illinois team using Blue Waters allowed a direct comparison also in a quantitative manner.”
Moreover, due to the incredible agreement between simulation and experiment, the Illinois researchers felt confident to test in silico, experiments that could not be carried out in vitro. Bernardi explains that systematically “turning off” different physical variables in the simulations allowed them to understand what were the key contributors to the large mechanical strength of the complex.
The tools that allowed Dr. Bernardi to perform these simulations were developed at the Beckman Institute over the last two decades under the leadership of Prof. Schulten (1947-2016). The molecular dynamics program NAMD efficiently scales up to hundreds of thousands of computer cores, making it one of the most used software in large supercomputer centers.
Prof. Schulten was a leader in biophysics, developing the tools that his group (Dr. Bernardi included), and many others, used to solve complicated molecular puzzles like the structure of the HIV-capsid, the ribosome, the human proteasome, and the mechanism of action of many protein complexes. According to Gaub, Schulten’s contributions were “absolutely essential for the field of single-molecule biophysics. By providing the tools to understanding the molecular details of life, Klaus started the field, nourished it with excellent physics, and kept pushing the technical limits to be able to address the relevant questions in life sciences.”
With fundamental insights provided by Prof. Schulten, the team overcame the unexpected loss of their colleague by discovering that the interactions that make the staph adhesin so strong when binding human proteins were mediated mainly by hydrogen bond interactions between the protein backbones.
The supercomputer-created simulations revealed that, when exposed to mechanical stress, the hydrogen bonds lock in a cooperative shear geometry—the underlying physical principle. This specific configuration is able to reach extreme forces, as all bonds have to be broken in parallel to dissociate the target. In a simplified analogy, two strips of Velcro are difficult to separate when pulled from opposing ends, yet come apart easily when pulled orthogonally.
Through site-directed mutagenesis and studies on homologs the computational model was confirmed. This bond geometry offers a striking advantage: By confining the physics of the mechanism to the peptide backbone, which is identical for every protein, high strength can be achieved binding a large spectrum of targets. Thus, the extreme physical strength of the system is largely independent of sequence and biochemical properties, but a built-in physical property—an invasive advantage for these staphylococci.
The unexpected mechanism expands our understanding of why pathogen adhesion is so resilient and may open new ways to inhibit staphylococcalinvasion. The development of anti-adhesion therapy could promote the detachment of staph bacteria, facilitating bacterial clearance. Understanding the mechanism of staph infection at the molecular and now atomic level may open new avenues for an intelligent design of antimicrobial therapies.