RUI: Combining Experiments and Simulations to Optimize Biomolecular Ionic Liquids for Protein Stabilization

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Non-Technical AbstractIonic liquids (ILs) are liquid salts that could be used as selective protein-stabilization biomaterials if they can be designed with the right molecular properties. This project will study ILs based on biological molecules and their effects on a specific protein system. The system is the azurin-nitrite reductase complex involved in soil bacterial denitrification. Denitrification is the process of converting nitrate into atmospheric nitrogen, and usually requires a complex protein system in soil bacteria. If the azurin-nitrite reductase system can be selectively stabilized with IL-based biomaterials it can be used for removing nitrate contamination from polluted environments. The biological molecule-based ILs could be designed with the right competing molecular interactions for protein stabilization if these interactions are understood. This project will use experiments to quantify the effects of ILs on the azurin and nitrite reductase protein structures, stabilities, and functionalities. Molecular dynamics simulations will attempt to reproduce the experimental results and thereby uncover the fundamental interactions between ILs and proteins that are needed for protein stabilization. The project will use this insight to design new ILs and IL-inspired biomaterials in an iterative manner. The project will train undergraduate students on a cross-disciplinary project involving biochemistry, physical chemistry, and computational simulations. The results will be useful for designing future IL-based biomaterials.Technical AbstractIonic liquids (ILs) have potential applications in which the right cation-anion combination can selectively stabilize proteins for industrial and biotechnological applications. Novel biomolecule-based ILs could be used as versatile biocompatible materials for protein engineering. This RUI project will combine biophysical spectroscopic experiments with computer simulations to study ILs with cationic tetramethylguanidinium (TMG) and different biomolecular anions (e.g., amino acids) and their effects on protein structures, stabilities, and activities. The competing interactions in TMG-biomolecule ILs (protein-TMG, anion-protein, and TMG-biomolecule) can be tuned to destabilize some proteins and stabilize others. The target protein system is the azurin-nitrite reductase (azurin/NiR) complex involved in denitrification, which could be stabilized for engineered environmental bioremediation. The project will quantify the effects of novel TMG-biomolecule ILs interacting with target proteins to better model and design IL-based biomaterials. The project will prepare different TMG-based ILs, add ILs to the proteins (expressed and purified in the lab) in aqueous solution, quantify the effects of the ILs on protein structures and stabilities using optical spectroscopy and mass spectrometry techniques, assay enzyme activities in ILs, and use molecular dynamics (MD) simulations to interpret experimental results and develop models to predict new ILs for future study. The new ILs and new insights will potentially advance the current understanding of ILs and IL-based biomaterials for biotechnology applications, including enzyme modulation, drug delivery, antibiotic enhancement, biomass processing, and biomaterials self-assembly. The proposal contains a plan for maximizing the STEM educational impact of the research project beyond the technical results. This plan will benefit Rowan University undergraduate students as well as South Jersey high school students.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.