MACROMOLECULAR STRUCTURE DETERMINATION BASED ON PARAMAGNETIC NMR SHIFTS

我们已经推导出一个实验数据集，其中包含234个 通过NMR研究钴和锌可能的274个伪接触位移 d（TTGGCCAA）2与色霉素的复合物。 此外，我们还测量了 锌化合物上有812个NOE。 我们已经确定了 药物- DNA复合物使用实验位移和/或 NOE约束，并使用修改后的X-PLOR包含额外的 能量项来描述移位约束。 我们获得了一个 与观测到的非常一致的结构集合 位移，具有低能量，并形成非常紧密的结构家族。 我们目前正在研究最终结构的依赖性 在g张量参数，必须是已知的或假设的移位 计算，以及从不同的收敛方法， 出发点，以及 基于NOE和基于班次的结构。 的设施和工作人员 计算机图形实验室在这方面非常有帮助。 项目 我们已经显示并匹配了结构，计算了均方根 偏差，并产生了无数的图像，代表不同的 项目的方方面面。 其中包括对金属结合的研究 网站和MidasPlus的对接功能的使用，以确定一个 第五和第六水配体在配位领域;使用 在MidasPlus中突出显示并检查NOE的冲突 用移位为基础的结构;使用颜色按B因子来显示 在分子复合体中的位移和精度。 我们已经使用了 MidasPlus能够覆盖不同的PDB文件， 大的PDB文件，以了解我们的基于移位的 结构.

We have derived an experimental data set containing 234 out of a possible 274 pseudocontact shifts by NMR studies on cobalt and zinc complexes of d(TTGGCCAA)2 with chromomycin. In addition, we measured 812 NOE's on the zinc complex. We have determined the structure of the drug- DNA complex using either or both the experimental shift and NOE constraints, and using a modified X-PLOR containing an additional energy term to describe the shift constraints. We have obtained an ensemble of structures that conform extremely well to the observed shifts, have low energies, and form a very tight family of structures. We are currently investigating the dependence of the final structure on g-tensor parameters which must be known or assumed for the shift calculation, as well as methods for convergence from different starting points, and justifications for differences between the NOE-based and shift-based structures. The facilities and staff of the Computer Graphics Laboratory have been extremely helpful during this project. We have displayed and matched structures, calculated root mean square deviations, and generated a myriad of images representing different facets of the project. These include studies of the metal binding site and the use of the docking features of MidasPlus to identify a fifth and sixth water ligand in the coordination sphere; the use of noeshow in MidasPlus to highlight and examine NOE's which conflict with the shift-based structure; the use of color-by-Bfactor to display shift and precision across the molecular complex. We have used the ability of MidasPlus to overlay different pdb files and to handle very large pdb files to understand characteristics of our shift based structures.