Gu Wei, Wang Tingting, Zhu Jiang, Shi Yunyu, Liu Haiyan
Key Laboratory of Structural Biology, University of Science and Technology of China, Chinese Academy of Sciences, School of Life Sciences, Hefei, Anhui 230026, PR China.
Biophys Chem. 2003 May 1;104(1):79-94. doi: 10.1016/s0301-4622(02)00340-x.
Four 10-ns molecular dynamics (MD) simulations of the human prion protein domain (HuPrP 125-228) in explicit water solution have been performed. Each of the simulations mimicked a different environment of the protein: the neutral pH environment was simulated with all histidine residues neutral and bearing a ND proton and with other titratable side chains charged, the weakly acidic environment was simulated with all titratable side chains charged, the strongly acidic environment was simulated with all titratable side chains protonated. The protein in neutral pH environment was simulated at both ambient (298 K) and higher (350 K) temperatures. The native fold is stable in the neutral pH/ambient temperature simulation. Through out all other simulations, a quite stable core consisted of 10-20 residues around the disulfide bond retain their initial conformations. However, the secondary structures of the protein show changes of various degrees compared to the native fold, parts of the helices unfolded and the beta-sheets extended. Our simulations indicated that the heat-induced unfolding and acid-induced unfolding of HuPrP might follow different pathways: the initial stage of the acid-induced unfolding may include not only changes in secondary structures, but also changes in the tertiary structures. Under the strongly acidic condition, obvious tertiary structure changes take place after 10-ns simulation, the secondary structure elements and the loops becoming more parallel to each other, resulting in a compact state, which was stabilized by a large number of new, non-native side chain-side chain contacts. Such tertiary structure changes were not observed in the higher temperature simulation, and intuitively, they may favor the further extension of the beta-sheets and eventually the agglomeration of multiple protein molecules. The driving forces for this tertiary structure changes are discussed. Two additional 10-ns MD simulations, one with Asp202 protonated and the other with Glu196 protonated compared to the neutral pH simulation, were carried out. The results showed that the stability of the native fold is very subtle and can be strongly disturbed by eliminating a single negative charge at one of such key sites. Correlations of our results with previous experimental and theoretical studies are discussed.
已对人朊病毒蛋白结构域（HuPrP 125 - 228）在明确的水溶液中进行了四次10纳秒的分子动力学（MD）模拟。每次模拟都模拟了蛋白质的不同环境：中性pH环境通过使所有组氨酸残基呈中性并带有一个ND质子且其他可滴定侧链带电来模拟，弱酸性环境通过使所有可滴定侧链带电来模拟，强酸性环境通过使所有可滴定侧链质子化来模拟。中性pH环境中的蛋白质在环境温度（298 K）和较高温度（350 K）下均进行了模拟。在中性pH/环境温度模拟中，天然折叠是稳定的。在所有其他模拟中，围绕二硫键由10 - 20个残基组成的相当稳定的核心保持其初始构象。然而，与天然折叠相比，蛋白质的二级结构显示出不同程度的变化，部分螺旋展开且β - 折叠延伸。我们的模拟表明，HuPrP的热诱导展开和酸诱导展开可能遵循不同的途径：酸诱导展开的初始阶段可能不仅包括二级结构的变化，还包括三级结构的变化。在强酸性条件下，10纳秒模拟后发生明显的三级结构变化，二级结构元件和环变得彼此更平行，导致一种紧凑状态，这种状态通过大量新的、非天然的侧链 - 侧链接触得以稳定。在较高温度模拟中未观察到这种三级结构变化，直观地说，它们可能有利于β - 折叠的进一步延伸并最终导致多个蛋白质分子的聚集。讨论了这种三级结构变化的驱动力。与中性pH模拟相比，还进行了另外两次10纳秒的MD模拟，一次使Asp202质子化，另一次使Glu196质子化。结果表明，天然折叠的稳定性非常微妙，并且通过消除此类关键位点之一的单个负电荷可能会受到强烈干扰。讨论了我们的结果与先前实验和理论研究的相关性。
