Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA.
J Chem Phys. 2011 Aug 14;135(6):065101. doi: 10.1063/1.3617250.
The growth of amyloid fibrils is studied by replica exchange molecular dynamics in an implicit solvent. Our data indicate that extremely long simulation times (at least a few hundred ns) are necessary to study the thermodynamics of fibril elongation in detail. However some aspects of the aggregation process are already accessible on the time scales available in the present study. A peak in the specific heat indicates a docking temperature of T(dock) ≈ 320 K. Irreversible locking requires lower temperatures with the locking temperature estimated as T(lock) ≈ 280 K. In our simulation the fibril grows from both sides with the C-terminal of the incoming monomer attaching to the C-terminal of the peptides in the fibril forming a β-sheet on the fibril edge. Our simulation indicates that the C-terminal is crucial for aggregation.
在隐溶剂中通过复制交换分子动力学研究淀粉样纤维的生长。我们的数据表明，要详细研究纤维延伸的热力学，需要进行极长的模拟时间（至少几百纳秒）。然而，在本研究中可用的时间尺度上，已经可以研究聚合过程的某些方面。比热中的峰值表明对接温度 T(dock) ≈ 320 K。不可逆锁定需要较低的温度，锁定温度估计为 T(lock) ≈ 280 K。在我们的模拟中，纤维从两侧生长，进入的单体的 C 末端附着在纤维中的肽的 C 末端上，在纤维边缘形成 β-片层。我们的模拟表明，C 末端对于聚集至关重要。
