Abstract
In addition to large domains, many short motifs mediate functional post-translational modification of proteins as well as protein-protein interactions and protein trafficking functions. We have constructed a motif database comprising 312 unique motifs and a web-based tool for identifying motifs in proteins. Functional motifs predicted by MnM can be ranked by several approaches, and we validated these scores by analyzing thousands of confirmed examples and by confirming prediction of previously unidentified 14-3-3 motifs in EFF-1.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Blom, N., Gammeltoft, S. & Brunak, S. J. Mol. Biol. 294, 1351–1362 (1999).
Kreegipuu, A., Blom, N. & Brunak, S. Nucleic Acids Res. 27, 237–239 (1999).
Blom, N., Sicheritz-Ponten, T., Gupta, R., Gammeltoft, S. & Brunak, S. Proteomics 4, 1633–1649 (2004).
Puntervoll, P. et al. Nucleic Acids Res. 31, 3625–3630 (2003).
Obenauer, J.C., Cantley, L.C. & Yaffe, M.B. Nucleic Acids Res. 31, 3635–3641 (2003).
Wheeler, D.L. et al. Nucleic Acids Res. 28, 10–14 (2000).
Naderi-Manesh, H., Sadeghi, M., Arab, S. & Moosavi Movahedi, A.A. Proteins 42, 452–459 (2001).
Kloczkowski, A., Ting, K.L., Jernigan, R.L. & Garnier, J. Proteins 49, 154–166 (2002).
Thiruv, B., Quon, G., Saldanha, S.A. & Steipe, B. BMC Struct. Biol. 5, 12 (2005).
Mohler, W.A. et al. Dev. Cell 2, 355–362 (2002).
delCampo, J.J. et al. Curr. Biol. 15, 413–423 (2005).
Tzivion, G. & Avruch, J. J. Biol. Chem. 277, 3061–3064 (2002).
Pruitt, K.D. & Maglott, D.R. Nucleic Acids Res. 29, 137–140 (2001).
Bateman, A. et al. Nucleic Acids Res. 32, D138–D141 (2004).
Bairoch, A. & Boeckmann, B. Nucleic Acids Res. 19 (Suppl.), 2247–2249 (1991).
Acknowledgements
This research was funded in part by US National Institutes of Health grants MH65567 to M.R.S., CCR-9912395 and ITR-0326155 to S.R., EB001496 to M.R.G. and HD43156 to W.A.M., and a Muscular Dystrophy Association grant to W.A.M. We thank R. Holz for providing the GST–14-3-3η construct.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Fig. 1
Output windows of a MnM Analysis. (PDF 423 kb)
Supplementary Fig. 2
14-3-3 motifs are required for EFF-1 function. (PDF 408 kb)
Supplementary Table 1
Enrichment of selected motifs in the human proteome. (PDF 17 kb)
Supplementary Video 1
Time-lapse video microscopy of normal embryonic cell fusions rescued with wild-type EFF-1. (MOV 703 kb)
Supplementary Video 2
Time-lapse video microscopy of normal embryonic cell fusions rescued with S632/634T mutant EFF-1. (MOV 976 kb)
Supplementary Video 3
Time-lapse video microscopy of abnormal embryonic cell fusions not rescued with S632/634A mutant EFF-1. (MOV 1051 kb)
Rights and permissions
About this article
Cite this article
Balla, S., Thapar, V., Verma, S. et al. Minimotif Miner: a tool for investigating protein function. Nat Methods 3, 175–177 (2006). https://doi.org/10.1038/nmeth856
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nmeth856
This article is cited by
-
Impact of the Synthetic Scaffold Strategy on the Metabolic Pathway Engineering
Biotechnology and Bioprocess Engineering (2023)
-
Splicing-accessible coding 3′UTRs control protein stability and interaction networks
Genome Biology (2020)
-
Expression of ZAT12 transcripts in transgenic tomato under various abiotic stresses and modeling of ZAT12 protein in silico
BioMetals (2014)
-
Searching for transcription factor binding sites in vector spaces
BMC Bioinformatics (2012)
-
RITA, a novel modulator of Notch signalling, acts via nuclear export of RBP-J
The EMBO Journal (2011)