Department of Crop and Soil Science, Oregon State University , Corvallis, Oregon 97331, United States.
Institut für Bodenlandschaftsforschung, Leibniz Zentrum für Agrarlandschaftsforschung (ZALF) , Eberswalder Straβe 84, 15374 Müncheberg, Germany.
Langmuir. 2016 Jun 21;32(24):6194-209. doi: 10.1021/acs.langmuir.6b01198. Epub 2016 Jun 10.
Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na(+)-montmorillonite (001), Ca(2+)-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.
采用分子动力学模拟（常规模拟和元动力学模拟），研究了模型蛋白 Gb1 与高岭石（001）、钠蒙脱石（001）、钙蒙脱石（001）、针铁矿（100）和钠水辉石（001）矿物表面的相互作用。Gb1 是一种小（56 个残基）蛋白，其溶液状态的核磁共振（NMR）结构具有很好的特征，具有α-螺旋、4 倍β-折叠和疏水核心特征，被用作模型蛋白，用于研究蛋白-土壤矿物相互作用，并深入了解蛋白结构变化和潜在降解。从我们的模拟中可以看出，与没有这些矿物表面存在的情况下的其溶剂化结构相比，水合 Gb1 结构在高岭石、蒙脱石和针铁矿表面几乎没有变化。然而，在钠水辉石基底表面，Gb1 结构由于与该水辉石表面的相互作用而受到高度干扰。在水辉石上观察到 Gb1 β-折叠在特定转角处的解开和α-螺旋的部分解开，这表明可能导致碎片化的特定易氧化或水解的残基位点。
