Single-molecule force spectroscopy has become a powerful tool to investigate molecular mechanisms in biophysics and materials science. In particular, the new field of polymer mechanochemistry has emerged to study how tension may induce chemical reactions in a macromolecule. A rich example is the mechanical unfolding of the metalloprotein rubredoxin coupled to dissociation of iron–sulfur bonds that has recently been studied in detail by atomic force microscopy. Here, we present a simple molecular model composed of a classical all-atom force field description, implicit solvation, and steered molecular dynamics simulation to describe the mechanical properties and mechanism of forced unfolding coupled to covalent bond dissociation of macromolecules. We apply this model and test it extensively to simulate forced rubredoxin unfolding, and we dissect the sensitivity of the calculated mechanical properties with model parameters. The model provides a detailed molecular explanation of experimental observables such as force–extension profiles and contour length increments. Changing the points of force application along the macromolecule results in different unfolding mechanisms, characterized by disruption of hydrogen bonds and secondary protein structure, and determines the degree of solvent access to the reactive center. We expect that this molecular model will be broadly applicable to simulate (bio)polymer mechanochemistry.

中文翻译：

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结合键解离的高分子的机械展开。

单分子力谱已成为研究生物物理学和材料科学中分子机理的强大工具。尤其是，出现了高分子机械化学的新领域，以研究张力如何诱导大分子中的化学反应。一个很好的例子是金属蛋白氧化还原酶的机械展开与铁硫键的解离偶联，最近已通过原子力显微镜进行了详细研究。在这里，我们提出了一个简单的分子模型，该模型由经典的全原子力场描述，隐式溶剂化和受控分子动力学模拟组成，以描述与大分子共价键解离偶联的力学性质和机理。我们应用了该模型并对其进行了广泛的测试，以模拟强迫的氧化还原酶展开过程，并使用模型参数剖析了计算出的机械性能的敏感性。该模型提供了实验可观察物的详细分子解释，例如力-延伸曲线和轮廓长度增量。改变沿大分子施加力的点会导致不同的展开机制，其特征在于氢键和二级蛋白质结构的破坏，并确定溶剂接近反应中心的程度。我们希望该分子模型将广泛应用于模拟（生物）聚合物机械化学。改变沿大分子施加力的点会导致不同的展开机制，其特征在于氢键和二级蛋白质结构的破坏，并确定溶剂接近反应中心的程度。我们希望该分子模型将广泛应用于模拟（生物）聚合物机械化学。改变沿大分子施加力的点会导致不同的展开机制，其特征在于氢键和二级蛋白质结构的破坏，并确定溶剂接近反应中心的程度。我们希望该分子模型将广泛应用于模拟（生物）聚合物机械化学。