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Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

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  • Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na⁺-montmorillonite (001), Ca²⁺-montmorillonite (001), goethite (100), and Na⁺-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na⁺ -birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.
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  • Andersen, A., Reardon, P. N., Chacon, S. S., Qafoku, N. P., Washton, N. M., & Kleber, M. (2016). Protein-mineral interactions: molecular dynamics simulations capture importance of variations in mineral surface composition and structure. Langmuir, 32(24), 6194-6209. doi:10.1021/acs.langmuir.6b01198
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  • 32
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  • 24
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  • The research is part of the "Understanding Molecular-Scale Complexity and Interactions of Soil Organic Matter" Intramural Project at EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. PNNL is operated by Battelle for the U.S. DOE under Contract DE-AC05-76RL01830.
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