Abstracts

Cone snails are one of the most diverse and dominant predators in the coral reef.  These venomous snails use a complex mixture of physiologically active peptides known as conotoxins to capture prey, and also to defend themselves from predators, and to compete with other hunter species.  These conotoxins target voltage and ligand gated ion channel subtypes, and G protein-linked receptors.  These neurotoxins have a discriminatory ability to selectively target specific receptor subunits or ion channels with a very high affinity.  Many drugs used for medical purposes bind not only to their desired target, but also bind related targets, which often produce unwanted side affects.  In contrast to most drugs, conotoxins can discriminate among closely related receptors subtypes.  These conotoxins can be classified into several superfamilies namely A, M, O, P, S, T and I based on the distribution of Cys residues in the primary sequence, the nature of the disulfide pairing topology and the functional attributes of the peptides.  Each superfamily comprises one to several subfamilies, which exhibit specific pharmacological activities.

δ-conotoxins belong to O-superfamily conotoxins.  They bind to the sodium channel and inhibit its inactivation; the result is that sodium channels remain open for longer time.  These δ-conotoxins can be classified as those isolated from fish hunting cone snails and those isolated from mollusks hunting cone snails.  The sequences of many δ-conotoxins have been published to date.  But information about their structure and function are available only for very few.  For many δ-conotoxins only limited tests in very diverse physiological preparations have been performed. 

In the present study a bioinformatics analysis of δ-family conotoxins was carried out.  It was carried out in two parts.  In the first part the available protein sequence of molluscivorous and piscivorous δ-conotoxins were compared to extract a characteristic sequence pattern was done, which is likely to be useful in the functional annotation of newly determined sequences.  In the second part a comparative sequence and structure study of molluscivorous δ-conotoxins was carried out.  A member of molluscivorous δ-conotoxins, δ-GmVIA was shown to produce very similar pharmacological characteristics in mollusk and mammalian sodium channels as did another member of δ-conotoxin family, δ-TxVIA.  They were even shown to have same binding sites on sodium channel.  But when the amino acid sequences of these two conotoxins were compared they showed an alignment score of only 40 in ClustalW, even without aligning the cysteins.  Where as δ-TxVIA was showing more sequence similarity with another member of δ-conotoxin δ-Am2766.  It was showing an alignment score of 46.  Even though the sequence similarity was more, they were showing different pharmacological characteristics in vertebrate sodium channels and their binding sites on sodium channel also seems to be different.  Since the sequence study could not explain their functional similarity, a structure comparison was done.  The experimental 3D structure of δ-GmVIA was not available; so we have modeled the theoretical structure using homology modeling approach.  d-Am2766 was taken as the template for modeling and the theoretical structure was further validated using PROCHECK.  Structural comparison of d-GmVIA and d-TxVIA was done using protein structure alignment server TM-align.  The structural comparison has shown that the crucial residues of the two toxins, δ-TxVIA and δ-GmVIA which are involved in binding to the sodium channel are present in structurally equivalent position.  In all the four intercystein loops, the crucial residues are found to be in structurally equivalent position.  The positional equivalence of critical residues may be the reason for its functional similarity.  But structural comparison of δ-TxVIA and δ-Am2766 shows less conservation of the critical residues.  The crucial residues of only 2^nd and 4^th intercystein loops were found to be structurally equivalent position.  Even though they were showing more sequence similarity, their structural similarity was less, which may be the reason for its functional difference.

The study suggests that even though the sequence pattern study may be confusing in predicting the function of a protein, the three dimensional structure comparison can be quiet rewarding in predicting the function of a newly identified protein.