SODa: an Mn/Fe superoxide dismutase prediction and design server

BMC Bioinformatics. 2008 Jun 2;9:257. doi: 10.1186/1471-2105-9-257.

Abstract

Background: Superoxide dismutases (SODs) are ubiquitous metalloenzymes that play an important role in the defense of aerobic organisms against oxidative stress, by converting reactive oxygen species into nontoxic molecules. We focus here on the SOD family that uses Fe or Mn as cofactor.

Results: The SODa webtool http://babylone.ulb.ac.be/soda predicts if a target sequence corresponds to an Fe/Mn SOD. If so, it predicts the metal ion specificity (Fe, Mn or cambialistic) and the oligomerization mode (dimer or tetramer) of the target. In addition, SODa proposes a list of residue substitutions likely to improve the predicted preferences for the metal cofactor and oligomerization mode. The method is based on residue fingerprints, consisting of residues conserved in SOD sequences or typical of SOD subgroups, and of interaction fingerprints, containing residue pairs that are in contact in SOD structures.

Conclusion: SODa is shown to outperform and to be more discriminative than traditional techniques based on pairwise sequence alignments. Moreover, the fact that it proposes selected mutations makes it a valuable tool for rational protein design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Binding Sites
  • Drug Design*
  • Enzyme Activation
  • Iron / chemistry*
  • Manganese / chemistry*
  • Molecular Sequence Data
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Sequence Analysis, Protein / methods*
  • Software*
  • Superoxide Dismutase / chemistry*

Substances

  • Manganese
  • Iron
  • Superoxide Dismutase