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In Silico Biology 5, 0050 (2005); ©2005, Bioinformation Systems e.V.  



I-superfamily conotoxins: sequence and structure analysis

Sukanta Mondal1, Ramachandran Vijayan2, Kannambath Shichina2, Rajasekaran Mohan Babu3 and Suryanarayanarao Ramakumar1,3*

1 Department of Physics, Indian Institute of Science, Bangalore 560 012, India
2 Department of Botany, Bharathiar University, Coimbatore, India
3 Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India

* Corresponding authors
   Email: ramak@physics.iisc.ernet.in


Edited by E. Wingender; received June 30, 2005; revised and accepted October 15, 2005; published October 30, 2005


Abstract

I-superfamily conotoxins have four-disulfide bonds with cysteine arrangement C-C-CC-CC-C-C, and they inhibit or modify ion channels of nerve cells. They have been characterized only recently and are relatively less well studied compared to other superfamily conotoxins. We have detected selective and sensitive sequence pattern for I-superfamily conotoxins. The availability of sequence pattern should be useful in protein family classification and functional annotation. We have built by homology modeling, a theoretical structural 3D model of ViTx from Conus virgo, a typical member of I-superfamily conotoxins. The modeling was based on the available 3D structure of Janus-atracotoxin-Hv1c of Janus-atracotoxin family whose members have been suggested as possible biopesticides. A study comparing the theoretically modeled structure of ViTx, with experimentally determined structures of other toxins, which share functional similarity with ViTx, reveals the crucial role of C-terminal region of ViTx in blocking therapeutically important voltage-gated potassium channels.


Keywords: I-superfamily conotoxins, protein sequence pattern, homology modeling, shaker K+ channel, inhibitor cystine knot