Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610, United States.
J Phys Chem B. 2012 Jan 12;116(1):646-52. doi: 10.1021/jp209791a. Epub 2011 Dec 13.
BBL is a small independently folding domain with two main parallel helices. The experiment of C(α) secondary shifts has shown that changing the pH from ~7 to ~5 results in the reduced helicity at the C-terminus of helix 2. Combining constant pH molecular dynamics with replica exchange, we sampled the protein conformation space and protonation states extensively under a neutral pH condition and an acidic condition. Our results reveal that the solvent conditions influence the free energy landscape. Under the neutral pH condition, the denatured state and the native state are well separated. The condition of the acidic pH reshapes the free energy surface, leading to a broadly populated denatured-state basin and a low free energy barrier between the denatured state and the native state. The acidic pH shifts the equilibrium between the denatured state and the native state in favor of the denatured state. Caution must be used to interpret experimental data under the acidic condition because the contribution of the denatured state is significant. Our simulation results are supported by the fact that the calculated chemical shifts are in good agreement with the experiment data.
BBL 是一个具有两个主要平行螺旋的小型独立折叠结构域。C(α)二级位移实验表明，将 pH 值从7 改变到5 会导致螺旋 2 的 C 末端螺旋减少。我们通过恒定 pH 值分子动力学和复制交换相结合，在中性 pH 值和酸性条件下广泛采样了蛋白质构象空间和质子化状态。我们的结果表明，溶剂条件会影响自由能景观。在中性 pH 值条件下，变性状态和天然状态很好地分离。酸性 pH 值重塑了自由能表面，导致变性状态的盆地广泛分布，以及变性状态和天然状态之间的自由能障碍降低。酸性 pH 值使变性状态和天然状态之间的平衡向变性状态倾斜。在酸性条件下解释实验数据时必须小心，因为变性状态的贡献是显著的。我们的模拟结果得到了计算化学位移与实验数据吻合良好的事实的支持。
