Orton Henry William, Huber Thomas, Otting Gottfried
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
Magn Reson (Gott). 2020 Feb 14;1(1):1-12. doi: 10.5194/mr-1-1-2020. eCollection 2020.
Paramagnetic metal ions with fast-relaxing electrons generate pseudocontact shifts (PCSs), residual dipolar couplings (RDCs), paramagnetic relaxation enhancements (PREs) and cross-correlated relaxation (CCR) in the nuclear magnetic resonance (NMR) spectra of the molecules they bind to. These effects offer long-range structural information in molecules equipped with binding sites for such metal ions. Here we present the new open-source software Paramagpy, which has been written in Python 3 with a graphic user interface. Paramagpy combines the functionalities of different currently available programs to support the fitting of magnetic susceptibility tensors using PCS, RDC, PRE and CCR data and molecular coordinates in Protein Data Bank (PDB) format, including a convenient graphical user interface. Paramagpy uses efficient fitting algorithms to avoid local minima and supports corrections to back-calculated PCS and PRE data arising from cross-correlation effects with chemical shift tensors. The source code is available from 10.5281/zenodo.3594568 .
具有快速弛豫电子的顺磁性金属离子会在它们所结合分子的核磁共振(NMR)谱中产生赝接触位移(PCSs)、剩余偶极耦合(RDCs)、顺磁弛豫增强(PREs)和交叉相关弛豫(CCR)。这些效应为配备此类金属离子结合位点的分子提供远程结构信息。在此,我们展示了新的开源软件Paramagpy,它是用Python 3编写的,带有图形用户界面。Paramagpy结合了当前不同可用程序的功能,以支持使用PCS、RDC、PRE和CCR数据以及蛋白质数据库(PDB)格式的分子坐标来拟合磁化率张量,包括一个方便的图形用户界面。Paramagpy使用高效的拟合算法来避免局部最小值,并支持对因与化学位移张量的交叉相关效应而反算得到的PCs和PRE数据进行校正。源代码可从10.5281/zenodo.3594568获取。