Onufriev Alexey, Case David A, Bashford Donald
Department of Molecular Biology, The Scripps Research Institute, TPC15, 10550 N Torrey Pines Road, La Jolla, CA 93027, USA.
J Mol Biol. 2003 Jan 17;325(3):555-67. doi: 10.1016/s0022-2836(02)01207-x.
Protein folding is often difficult to characterize experimentally because of the transience of intermediate states, and the complexity of the protein-solvent system. Atomistic simulations, which could provide more detailed information, have had to employ highly simplified models or high temperatures, to cope with the long time scales of unfolding; direct simulation of folding is even more problematic. We report a fully atomistic simulation of the acid-induced unfolding of apomyoglobin in which the protonation of acidic side-chains to simulate low pH is sufficient to induce unfolding at room temperature with no added biasing forces or other unusual conditions; and the trajectory is validated by comparison to experimental characterization of intermediate states. Novel insights provided by their analysis include: characterization of a dry swollen globule state forming a barrier to initial unfolding or final folding; observation of cooperativity in secondary and tertiary structure formation and its explanation in terms of dielectric environments; and structural details of the intermediate and the completely unfolded states. These insights involve time scales and levels of structural detail that are presently beyond the range of experiment, but come within reach through the simulation methods described here. An implicit solvation model is used to analyze the energetics of protein folding at various pH and ionic strength values, and a reasonable estimate of folding free energy is obtained. Electrostatic interactions are found to disfavor folding.
由于中间状态的短暂性以及蛋白质 - 溶剂系统的复杂性，蛋白质折叠通常很难通过实验进行表征。原子模拟虽能提供更详细的信息，但为了应对解折叠的长时间尺度，不得不采用高度简化的模型或高温条件；直接模拟折叠则更具问题。我们报告了脱辅基肌红蛋白酸诱导解折叠的全原子模拟，其中模拟低pH值时酸性侧链的质子化足以在室温下诱导解折叠，无需添加偏置力或其他特殊条件；并且通过与中间状态的实验表征进行比较验证了轨迹。对模拟结果分析得到的新见解包括：表征了一种干燥肿胀的球状状态，它对初始解折叠或最终折叠形成障碍；观察到二级和三级结构形成中的协同性，并从介电环境角度对其进行了解释；以及中间状态和完全解折叠状态的结构细节。这些见解涉及的时间尺度和结构细节水平目前超出了实验范围，但通过这里描述的模拟方法得以实现。使用隐式溶剂化模型分析了不同pH值和离子强度下蛋白质折叠的能量学，并获得了折叠自由能的合理估计。发现静电相互作用不利于折叠。
