Numbat: an interactive software tool for fitting Deltachi-tensors to molecular coordinates using pseudocontact shifts

J Biomol NMR. 2008 Jul;41(3):179-89. doi: 10.1007/s10858-008-9249-z. Epub 2008 Jun 24.

Abstract

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.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Anisotropy
  • DNA Polymerase III / chemistry
  • Escherichia coli Proteins / chemistry
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Conformation*
  • Software*
  • User-Computer Interface

Substances

  • Escherichia coli Proteins
  • DNA Polymerase III