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In Silico Biology 7, 0018 (2007); ©2007, Bioinformation Systems e.V.  



In silico detection of binding mode of J-superfamily conotoxin pl14a with Kv1.6 channel

Sukanta Mondal1, Rajasekaran Mohan Babu2, Rajasekaran Bhavna2 and Suryanarayanarao Ramakumar1,2*

1 Department of Physics, Indian Institute of Science, Bangalore 560 012, India
2 Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India


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


Edited by E. Wingender; received January 18, 2007; revised February 20, 2007; accepted February 24, 2007; published March 26, 2007


Abstract

A novel conotoxin pl14a containing 25 amino acid residues with an amidated C-terminus from vermivorous cone snail, Conus planorbis belongs to J-conotoxin superfamily and this is the first conotoxin, which inhibits both nicotinic acetylcholine receptor subtypes and Kv1.6 channel. We have attempted through bioinformatics approaches to elucidate the extent of specificity of pl14a towards Kv1 channel subtypes (Kv1.1-Kv1.6). Our work provides rationale for the relatively high specificity and binding mode of pl14a to Kv1.6 channel.The pl14a peptide contains two types of structural elements, namely the putative dyad (Lys18 and Tyr19) and basic residue ring constituted of arginine residues. We have carried out in silico docking studies so as to assess the contribution of one or combination of both structural elements of pl14a in blocking of Kv1.6 channel. For this purpose, we have built by homology modelling, the theoretical 3D structure of Kv1.6 channel based on the available crystal structure of mammalian shaker Kv1.2 channel. Docking studies suggest that positively charged residues ring may be involved in the blocking mechanism of Kv1.6 channel. The models suggest that the peptide interacts with negatively charged extracellular loops and pore-mouth of the potassium channel and blocks the channel by covering the pore as a lid, akin to previously proposed blocking mechanism of κM-conotoxin RIIIK from Conus radiatus to Tsha1 potassium channel. The newly detected pharmacophore for pl14a interacting with Kv1.6 channel provides a pointer to experimental work to validate the observations made here. Based on differences in the number and distribution of the positively-charged residues in other conopeptides from the J-superfamily, we hypothesize different selectivity profiles against subtypes of the potassium channels for these conopeptides.


Keywords: conotoxin superfamily, Kv1 channel inhibitor, functional dyad, basic residues ring, pore-loop region, homology modelling, docking