Nilges M, Habazettl J, Brünger A T, Holak T A
Howard Hughes Medical Institute, Yale University, New Haven, CT 06511.
J Mol Biol. 1991 Jun 5;219(3):499-510. doi: 10.1016/0022-2836(91)90189-d.
The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A.
通过直接最小化观察到的二维核Overhauser增强（NOE）强度与通过完全弛豫矩阵方法计算的强度之间的差异，对小型南瓜胰蛋白酶抑制剂CMTI-I的结构进行了优化。为实现这一点，将与该差异成比例的一项添加到分子动力学程序X-PLOR的势能函数中。通过解析计算相对于原子坐标的导数。因此，在优化过程中充分考虑了自旋扩散效应。用于优化的初始结构是最近通过溶液核磁共振使用孤立双自旋近似来推导距离范围估计所确定的结构。在共轭梯度最小化的几个循环中，仅在优化结构中有小的位移时，对核磁共振数据的拟合就有显著改善。然而，在模拟退火期间构象发生了较大变化（约1 Å），同时实验和计算的二维NOE强度之间的差异进一步减小。优化后的结构比初始结构更接近与胰蛋白酶复合的抑制剂的X射线结构。初始结构与X射线结构之间主链原子的均方根差异为0.96 Å，优化结构与X射线结构之间为0.61 Å。
