Department of Applied Physics, China Jiliang University, Hangzhou 310018, China.
Molecules. 2024 Jun 21;29(13):2967. doi: 10.3390/molecules29132967.
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.
通过 MD 模拟研究了β-折叠比例和链长对全β 蛋白的影响。在较宽的温度范围内模拟了由不同重复单元组成的具有不同β-折叠比例或不同重复单元数的蛋白质样品。模拟结果表明，具有较高β-折叠二级结构比例的蛋白质具有更小的回转半径，其非键能更低，蛋白质内的氢键更多。均方根偏差（RMSD）和均方根波动（RMSF）都随温度升高而增加，特别是在链较长的情况下。根据重复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 原子骨架上，表明它是一种稳定的二级结构。我们还得出结论，短链或β-折叠比例较低的蛋白质很容易将其定向和紧凑的结构转化为其他结构，如无规卷曲、转角，甚至α-螺旋。这些结果从一级水平阐明了蛋白质与 3D 结构的关系，并可能预测了蛋白质折叠。
