Unraveling Molecular Mechanisms of Extreme Mechanostability in Proteins with Molecular Dynamics Simulations
Dr. Rafael Bernardi, University of Illinois at Urbana-Champaign
Mechanical forces play a fundamental role in biological systems. Cells can sense and respond to mechanical cues in their environment by, for example, exhibiting differential biochemical activities. At the molecular level, these behaviors are governed by mechanically active proteins. Such proteins can sense and respond to force by undergoing conformational changes or modulating their function in a variety of ways. Many of these proteins, particularly those living outside of bacterial cell walls, are exposed to a turbulent environment, where they face shear force gradients much larger than inside cells. These proteins, e.g., cellulosome complexes from cellulolytic bacteria, or adhesion proteins from pathogenic bacteria, were found to be the most mechanically stable proteins we know to date. What are the mechanics that make pathogenic bacteria adhere to their human hosts so viciously, and how do cellulosomal complexes become ultrastable when exposed to force. We investigated these questions by a combination of experimental and theoretical techniques. We resolve the mechanism of these mechanical stabilities through AFM-based single molecule force spectroscopy in vitro and steered molecular dynamics in silico. Through our enhanced sampling approaches, experimental data and simulation results be compared on the same raw dataset size and the same analzsis techniques. Thousands of individual simulations were performed using GPU nodes of the NCSA/Blue Waters supercomputer. In silico and in vitro force spectroscopy agree exceptionally well. We could predict that for a key cellulosomal protein a single point mutation was sufficient to increase its force resilience by a factor of two. For a staphylococcal adhesion protein, which binds to a human peptide in a key step for pathogenic invasion, we revealed a novel mechanism of force resilience that allows for extremely high force stabilities. In summary, our in silico/in vitro strategy provides an efficient way to investigate and adjust the mechanical resilience of protein domains and protein complexes.