Mehler E L, Pascual-Ahuir J L, Weinstein H
Department of Physiology and Biophysics, Mount Sinai School, New York, NY 10029.
Protein Eng. 1991 Aug;4(6):625-37. doi: 10.1093/protein/4.6.625.
We present the results of computational simulation studies of the structures of calmodulin (CAM) and troponin C (TNC). Possible differences between the structures of these molecules in the crystal and in solution were suggested by results from some recent experimental studies, which implied that their conformations in solution may be more compacted than the characteristic dumbbell shape observed in the crystal. The molecular dynamics simulations were carried out with the CHARMM system of programs, and the environment was modeled with a distance-dependent dielectric permittivity and discrete water molecules surrounding the proteins at starting positions identified in the crystals of CAM and TNC. Methods of macromolecular structure analysis, including linear distance plots, distance matrices and a matrix representation of hydrogen bonding, were used to analyze the nature, the extent and the source of structural differences between the computed structures of the molecules and their conformations in the crystal. Following the longest simulation, in which intradomain structure was conserved, the crystallographically observed dumbbell structure of the molecule changed due to a kinking or bending in the region of the central tether helix connecting the two Ca(2+)-binding domains which moved into close proximity. The resulting structure correlates with experimental observations of complexes between CAM and peptides such as melittin and mastoparan. Analysis of the corresponding pair distance distribution functions in comparison to experimental results suggests the dynamic existence of a non-negligible fraction of the compacted structure in aqueous solutions of CAM. In this more nearly globular shape, CAM reveals to the environment two interior pockets that contain a number of hydrophobic residues, in agreement with NMR data suggesting involvement of such residues in the binding of inhibitors and proteins to CAM.
我们展示了钙调蛋白（CAM）和肌钙蛋白C（TNC）结构的计算模拟研究结果。最近一些实验研究的结果表明了这些分子在晶体和溶液中的结构可能存在差异，这意味着它们在溶液中的构象可能比在晶体中观察到的典型哑铃形状更为紧凑。使用CHARMM程序系统进行分子动力学模拟，并在CAM和TNC晶体中确定的起始位置，用距离依赖的介电常数和围绕蛋白质的离散水分子对环境进行建模。采用大分子结构分析方法，包括线性距离图、距离矩阵和氢键的矩阵表示，来分析分子计算结构与其在晶体中构象之间结构差异的性质、程度和来源。在最长的模拟中，结构域内结构得以保留，由于连接两个Ca(2+)结合结构域的中央系链螺旋区域发生扭结或弯曲，分子晶体学观察到的哑铃结构发生了变化，两个结构域彼此靠近。所得结构与CAM和蜂毒肽、mastoparan等肽形成的复合物的实验观察结果相关。与实验结果相比，对相应的成对距离分布函数的分析表明，在CAM水溶液中，不可忽略比例的紧凑结构动态存在。在这种更接近球状的形状中，CAM向周围环境暴露了两个内部口袋，其中包含一些疏水残基，这与NMR数据一致，表明这些残基参与了抑制剂和蛋白质与CAM的结合。
