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.
School of Molecular and Microbial Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
Christophe
C
Schmitz
Mitchell J
MJ
Stanton-Cook
Xun-Cheng
XC
Su
Gottfried
G
Otting
Thomas
T
Huber
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