Florida Center for Advanced Aero Propulsion (FCAAP), Department of Mechanical Engineering, Florida A&M/Florida State University, Tallahassee, Florida 32310, USA.
J Chem Phys. 2011 Aug 7;135(5):055102. doi: 10.1063/1.3622489.
We quantify the formation and evolution of protein nanofibers using a new phase field modeling framework and compare the results to transmission electron microscopy measurements (TEM) and time-dependent growth measurements given in the literature. The modeling framework employs a set of effective continuum equations combined with underlying nanoscale forces and chemical potential relations governing protein nanofiber formation in solution. Calculations based on the theoretical framework are implemented numerically using a nonlinear finite element phase field modeling approach that couples homogenized protein molecular structure via a vector order parameter with chemical potential relations that describe interactions between the nanofibers and the surrounding solution. Homogenized, anisotropic molecular and chemical flux relations are found to be critical in obtaining nanofiber growth from seed particles or a random monomer bath. In addition, the model predicts both sigmoidal and first-order growth kinetics for protein nanofibers for unseeded and seeded models, respectively. These simulations include quantitative predictions on time scales of typical protein self-assembly behavior which qualitatively match TEM measurements of the RADA16-I protein and growth rate measurements for amyloid nanofibers from the literature. For comparisons with experiments, the numerical model performs multiple nanofiber protein evolution simulations with a characteristic length scale of ∼2.4 nm and characteristic time scale of ∼9.1 h. These results provide a new modeling tool that couples underlying monomer structure with self-assembling nanofiber behavior that is compatible with various external loadings and chemical environments.
我们使用新的相场建模框架来量化蛋白质纳米纤维的形成和演变，并将结果与透射电子显微镜（TEM）测量和文献中给出的时间依赖性生长测量进行比较。该建模框架采用了一组有效的连续方程，结合控制蛋白质纳米纤维在溶液中形成的潜在纳米尺度力和化学势关系。基于理论框架的计算通过非线性有限元相场建模方法进行数值实现，该方法通过向量序参量将均匀化的蛋白质分子结构与描述纳米纤维与周围溶液之间相互作用的化学势关系相耦合。发现均匀化、各向异性的分子和化学通量关系对于从种子颗粒或随机单体浴中获得纳米纤维的生长至关重要。此外，该模型分别预测了无种子和有种子模型中蛋白质纳米纤维的阶跃和一级生长动力学。这些模拟包括对典型蛋白质自组装行为时间尺度的定量预测，这些预测与 RADA16-I 蛋白质的 TEM 测量和文献中淀粉样纳米纤维的生长速率测量定性匹配。为了与实验进行比较，数值模型进行了多次具有特征长度尺度约为 2.4nm 和特征时间尺度约为 9.1h 的纳米纤维蛋白演化模拟。这些结果提供了一种新的建模工具，将潜在的单体结构与自组装纳米纤维行为相结合，与各种外部载荷和化学环境兼容。
