Amodeo P, Motta A, Strazzullo G, Castiglione Morelli M A
Istituto per la Chimica di Molecole di Interesse Biologico (Istituto Nazionale di Chimica dei sistemi Biologici) del CNR, Arco Felice Napoli, Italy.
J Biomol NMR. 1999 Feb;13(2):161-74. doi: 10.1023/a:1008365322148.
We have studied the dynamic properties of human (h) and salmon (s) calcitonin (CT) in solution. For both hormones, distance geometry in torsion-angle space has been used to generate three-dimensional structures consistent with NMR data obtained in sodium dodecyl sulfate micelles. For sCT and hCT we used, respectively, 356 and 275 interproton distances together with hydrogen-bonds as restraints. To better characterize their flexibility and dynamic properties two fully unrestrained 1100-ps molecular dynamics (MD) simulations in methanol were performed on the lowest-energy structures of both hormones. Statistical analyses of average geometric parameters and of their fluctuations performed in the last 1000 ps of the MD run show typical helical values for residues 9-19 of sCT during the whole trajectory. For hCT a shorter helix was observed involving residues 13-21, with a constant helical region in the range 13-19. Angular order parameters S(phi) and S(psi) indicate that hCT exhibits a higher flexibility, distributed along the whole chain, including the helix, while the only flexible amino acid residues in sCT connect three well-defined domains. Finally, our study shows that simulated annealing in torsion-angle space can efficiently be extended to NMR-based three-dimensional structure calculations of helical polypeptides. Furthermore, provided that a sufficient number of NMR restraints describes the system, the method allows the detection of equilibria in solution. This identification occurs through the generation of 'spurious' high-energy structures, which, for right-handed alpha-helices, are likely to be represented by left-handed alpha-helices.
我们研究了溶液中人类（h）和鲑鱼（s）降钙素（CT）的动态特性。对于这两种激素，利用扭角空间中的距离几何方法生成了与在十二烷基硫酸钠胶束中获得的核磁共振（NMR）数据一致的三维结构。对于sCT和hCT，我们分别使用了356个和275个质子间距离以及氢键作为约束条件。为了更好地表征它们的柔韧性和动态特性，在甲醇中对这两种激素的最低能量结构进行了两次完全无约束的1100皮秒分子动力学（MD）模拟。在MD运行的最后1000皮秒内对平均几何参数及其波动进行的统计分析表明，在整个轨迹中，sCT的9 - 19位残基呈现出典型的螺旋值。对于hCT，观察到一个较短的螺旋，涉及13 - 21位残基，在13 - 19范围内有一个恒定的螺旋区域。角序参数S(phi)和S(psi)表明，hCT表现出更高的柔韧性，分布在整个链上，包括螺旋部分，而sCT中唯一灵活的氨基酸残基连接着三个明确的结构域。最后，我们的研究表明，扭角空间中的模拟退火可以有效地扩展到基于NMR的螺旋多肽三维结构计算。此外，只要有足够数量的NMR约束来描述系统，该方法就能检测溶液中的平衡状态。这种识别是通过生成“虚假”的高能结构来实现的，对于右手α螺旋来说，这些结构可能由左手α螺旋表示。
