Numbat:: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts
Numbat:: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts
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DOI：
10.1007/s10858-008-9249-z
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发表时间：
2008-07-01
影响因子：
2.7
通讯作者：
Huber, Thomas
中科院分区：
文献类型：
--
作者：
Schmitz, Christophe;Stanton-Cook, Mitchell J.;Huber, Thomas
伪接触位移（PCS）的影响引起的顺磁性镧系元素结合到蛋白质已成为越来越受欢迎的NMR光谱，因为它们产生一组互补的取向和远程结构的限制。PCS是卡张量各向异性的表现，即Delta卡张量，它又可以从PCS中确定。一旦确定了Delta chi张量，PCS就成为研究蛋白质结构和蛋白质-配体复合物的强有力的长程约束。在这里，我们提出了新开发的软件包Numbat（新的用户友好的方法建立自动三角洲卡张量测定）。通过允许高度交互的图形用户界面（GUI），Numbat专门设计用于从一组实验测量的PCS和蛋白质结构坐标计算完整的Delta chi张量参数（包括相对于蛋白质的形状，位置和方向）。通过构建E. coli DNA聚合酶III亚基p186和theta。
Pseudocontact shift (PCS) effects induced by a paramagnetic lanthanide bound to a protein have become increasingly popular in NMR spectroscopy as they yield a complementary set of orientational and long-range structural restraints. PCS are a manifestation of the chi-tensor anisotropy, the Delta chi-tensor, which in turn can be determined from the PCS. Once the Delta chi-tensor has been determined, PCS become powerful long-range restraints for the study of protein structure and protein-ligand complexes. Here we present the newly developed package Numbat (New User-friendly Method Built for Automatic Delta chi-Tensor determination). With a Graphical User Interface (GUI) that allows a high degree of interactivity, Numbat is specifically designed for the computation of the complete set of Delta chi-tensor parameters (inclu(d)ing shape, location and orientation with respect to the protein) from a set of experimentally measured PCS and the protein structure coordinates. Use of the program for Linux and Windows operating systems is illustrated by building a model of the complex between the E. coli DNA polymerase III subunits epsilon 186 and theta using PCS.