Numbat: an interactive software tool for fitting Deltachi-tensors to molecular coordinates using pseudocontact shifts.
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 Deltachi-tensor, which in turn can be determined from the PCS. Once the Deltachi-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 Deltachi-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 Deltachi-tensor parameters (including 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 epsilon186 and theta using PCS.
Schmitz
Christophe
C
School of Molecular and Microbial Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
Stanton-Cook
Mitchell J
MJ
Su
Xun-Cheng
XC
Otting
Gottfried
G
Huber
Thomas
T
D000465:Algorithms; D000818:Animals; D016880:Anisotropy; D004258:DNA Polymerase III / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D012984:Software; D014584:User-Computer Interface
D029968:Escherichia coli Proteins; D004258:DNA Polymerase III