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

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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 χ-tensor anisotropy, the Δχ-tensor, which in turn can be determined from the PCS. Once the Δχ-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 Δχ-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 Δχ-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 ε186 and θ using PCS.

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Abbreviations

α:

Subunit α of the E. coli polymerase III

ε186:

N-terminal 185 residues of the E. coli polymerase III subunit ε

θ:

Subunit θ of the E. coli polymerase III

CSA:

Chemical shielding anisotropy

GUI:

Graphical user interface

HOT:

The bacteriophage P1-encoded homolog of θ

PCS:

Pseudocontact shift

RACS:

Residual anisotropic chemical shift

RDC:

Residual dipolar coupling

UTR:

Unique Δχ-tensor representation

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Acknowledgment

Financial support from the Australian Research Council for project grants to G.O and T.H. is gratefully acknowledged.

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Authors and Affiliations

  1. School of Molecular and Microbial Sciences, University of Queensland, Brisbane, QLD, 4072, Australia

    Christophe Schmitz, Mitchell J. Stanton-Cook & Thomas Huber

  2. Research School of Chemistry, Australian National University, Canberra, ACT, 0200, Australia

    Xun-Cheng Su & Gottfried Otting

  3. Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, 4072, Australia

    Thomas Huber

Authors
  1. Christophe Schmitz
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  2. Mitchell J. Stanton-Cook
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  3. Xun-Cheng Su
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  4. Gottfried Otting
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  5. Thomas Huber
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Correspondence to Thomas Huber.

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Schmitz, C., Stanton-Cook, M.J., Su, XC. et al. Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts. J Biomol NMR 41, 179–189 (2008). https://doi.org/10.1007/s10858-008-9249-z

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  • DOI: https://doi.org/10.1007/s10858-008-9249-z

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