Exploring non-classical Arrhenius behavior in thermolysin: a Molecular Dynamics approach
Date
2023
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Publisher
University of Delaware
Abstract
Proteins and enzymes are dynamic molecules whose structure and function are intrinsically related to their shape and the environment in which they exist. The study of protein dynamics has led to important insights that have far reaching implications in medicine, technology, and fundamental physical processes. Many techniques to study protein dynamics were developed over the years. Each technique contributes unique insights into the structure and function of proteins. The emergence of Molecular Dynamics (MD) to probe difficult analytical problems is of ever-increasing importance, especially as computational power has increased significantly in recent years. Using MD we compare the motions of the protease thermolysin (TLS) through three simulations carried out at different temperatures (23.3 oC, 26.3 oC, and 29.4 oC), identify regions of interest, suggest additional simulations, and propose studies by Nuclear Magnetic Resonance Spectroscopy (NMR) and X-Ray Diffraction (XRD). The variations in motion are shown to be similar across the three temperatures with the highest temperatures demonstrating the most dynamic behavior. Residues 126, 197, and 199 form a hairpin loop just outside of the active site and show significant dynamic behavior in all three of the simulations. It is possible that this loop is blocking access to the active site at lower temperatures. While at higher temperatures, with greater flexibility, the site becomes more accessible to the substrate and allows for an exponential increase in the catalytic turnover. Two mutants are suggested for further simulation and analysis by XRD and NMR.
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Keywords
Arrhenius Equation, Kinetics, Molecular Dynamics, Thermolysin