PDF(Pubmed)
Abstract：
The effect of β-sheet ratio and chain length on all-β proteins was investigated by MD simulations. Protein samples composed of different repeating units with various β-sheet ratios or a different number of repeating units were simulated under a broad temperature range. The simulation results show that the smaller radius of gyration was achieved by the protein with the higher proportion of β-sheet secondary structure, which had the lower nonbonded energy with more HBs within the protein. The root mean square deviation (RMSD) and the root mean square fluctuation (RMSF) both increased with temperature, especially in the case of a longer chain. The visible period was also shown according to the repeated secondary structure. Several minimum values of RMSF were located on the skeleton of Cα atoms participating in the β-sheet, indicating that it is a kind of stable secondary structure. We also concluded that proteins with a short chain or a lower ratio of β-sheet could easily transform their oriented and compact structures to other ones, such as random coils, turns, and even α-helices. These results clarified the relationship from the primary level to the 3D structure of proteins and potentially predicted protein folding.
摘要：
通过MD模拟研究β-折叠比率和链长度对全β蛋白的影响。在宽温度范围内模拟由具有各种β-折叠比率或不同数量的重复单元的不同重复单元组成的蛋白质样品。模拟结果表明,β-折叠二级结构比例较高的蛋白质获得了较小的回转半径,其具有较低的非结合能量，蛋白质内具有更多的HBs。均方根偏差(RMSD)和均方根波动(RMSF)均随温度的升高而增大,尤其是在链条较长的情况下。根据重复的二级结构也显示了可见周期。RMSF的几个最小值位于参与β-折叠的Cα原子的骨架上，表明它是一种稳定的二级结构。我们还得出结论，具有短链或较低比例β-折叠的蛋白质可以很容易地将其定向和紧凑的结构转化为其他结构，如随机线圈，turns,甚至是α-螺旋。这些结果阐明了从蛋白质的初级水平到3D结构以及潜在预测的蛋白质折叠的关系。
