Protein folding is a popular topic in the life science. However, due to the limited sampling ability of experiments and simulations, the general folding mechanism is not yet clear to us. In this work, we study the folding of the N-terminal domain of ribosomal protein L9 (NTL9) in detail by a mixing replica exchange molecular dynamics method. The simulation results are close to previous experimental observations. According to the Markov state model, the folding of the protein follows a nucleation-condensation path. Moreover, after the comparison to its 39-residue β-α-β motif, we find that the helix at the C-terminal has a great influence on the folding process of the intact protein, including the nucleation of the key residues in the transition state ensemble and the packing of the hydrophobic residues in the native state.

中文翻译：

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研究核糖体蛋白 L9 N 端结构域的折叠机制

蛋白质折叠是生命科学中的热门话题。然而，由于实验和模拟的采样能力有限，我们尚不清楚一般的折叠机制。在这项工作中，我们通过混合复制交换分子动力学方法详细研究了核糖体蛋白 L9 (NTL9) N 末端结构域的折叠。模拟结果接近于先前的实验观察。根据马尔可夫状态模型，蛋白质的折叠遵循成核-缩合路径。而且，与它的 39 个残基β - α - β 比较后 基序，我们发现 C 端的螺旋对完整蛋白质的折叠过程有很大影响，包括过渡态集合中关键残基的成核和天然状态下疏水残基的堆积。