Kwasigroch JM, Wintjens R, Gilis D, Rooman M. SODa: an Mn/Fe superoxide dismutase prediction and design server.
BMC Bioinformatics 2008;
9:257. [PMID:
18518943 PMCID:
PMC2442099 DOI:
10.1186/1471-2105-9-257]
[Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 06/02/2008] [Indexed: 11/17/2022] Open
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 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.
Collapse