Sticht H, Willbold D, Rösch P
Lehrstuhl für Struktur und Chemie der Biopolymere, Universität Bayreuth, FRG.
J Biomol Struct Dyn. 1994 Aug;12(1):019-36.
Two molecular dynamics (MD) simulations were performed in order to increase the understanding of the dependence of protein conformation on solvent environment. The protein used for these simulations is the transcriptional activator of the equine infectious anemia virus (EIAV-Tat). The structure of this protein has been determined by nuclear magnetic resonance (NMR) in aqueous solution (Willbold et al., Science 264, 1584 (1994)) and in 40% (v/v) trifluoroethanol (TFE) (Sticht et al., Eur. J. Biochem., submitted) showing considerable differences in the stability of the secondary structure elements. In order to investigate the influence of the solvent MD simulations (300 K: 200 ps) were carried out in water and in a solvent containing 40% (v/v) TFE. In both simulations the structure as determined in 40% TFE by NMR showing three-helices and a tight type II turn, was used as the initial structure. The MD simulations clearly indicate a decreased stability of the secondary structure elements in aqueous environment as made obvious by larger atomic motions and stronger fluctuations in the length of the hydrogen bonds. Complete unfolding of the helices was not observed on a 200 ps timescale. The root mean square deviation (RMSD) values of the backbone atoms after 200 ps simulation compared to the starting structure underline the strong influence of the solvent on the protein stability. This RMSD value is 1.95 A for the simulation in water and 1.29 A for the simulation in TFE/water. This result supports the notion that TFE acts as a secondary structure inducing and stabilizing solvent. The differences apparent from the MD simulations are in good agreement with the data derived from NMR measurements, showing the relevance of MD as a method for estimating conformational and dynamical properties of proteins.
为了增进对蛋白质构象与溶剂环境依赖性的理解，进行了两次分子动力学（MD）模拟。用于这些模拟的蛋白质是马传染性贫血病毒转录激活因子（EIAV-Tat）。该蛋白质的结构已通过核磁共振（NMR）在水溶液中（威尔博尔德等人，《科学》264, 1584 (1994)）以及在40%（v/v）三氟乙醇（TFE）中（施蒂希特等人，《欧洲生物化学杂志》，已投稿）测定，结果显示二级结构元件的稳定性存在显著差异。为了研究溶剂的影响，在水和含40%（v/v）TFE的溶剂中进行了MD模拟（300 K，200 ps）。在这两种模拟中，均采用通过NMR在40% TFE中测定的显示三个螺旋和一个紧密II型转角的结构作为初始结构。MD模拟清楚地表明，在水性环境中二级结构元件的稳定性降低，这从较大的原子运动以及氢键长度更强的波动中明显体现出来。在200 ps的时间尺度上未观察到螺旋完全展开。与起始结构相比，200 ps模拟后主链原子的均方根偏差（RMSD）值突显了溶剂对蛋白质稳定性的强烈影响。水中模拟的该RMSD值为1.95 Å，TFE/水混合溶剂中模拟的RMSD值为1.29 Å。这一结果支持了TFE作为一种诱导和稳定二级结构的溶剂的观点。MD模拟中明显的差异与NMR测量得到的数据高度吻合，表明MD作为一种估算蛋白质构象和动力学性质的方法具有相关性。
