title: Secondary structure formations of conotoxin genes: a possible role in mediating variability.
abstract: Small venomous peptides called conotoxins produced by the predatory marine snail (genus Conus) present an interesting case for mutational studies. They have a high degree of amino acid variability among them yet they possess highly conserved structural elements that are defined by cysteine residues forming disulfide bridges along the length of the mature peptide. It has been observed that codons specifying these cysteines are also highly conserved. It is unknown how such codon conservation is maintained within the mature conotoxin gene since this entire region undergoes an accelerated rate of mutation. There is evidence suggesting that nucleic acids wield some influence in mechanisms that dictate the region and frequency where mutations occur in DNA. Nucleic acids exert this effect primarily through secondary structures that bring about local peaks and troughs in the energy relief of these transient formations. Secondary structure predictions of several conotoxin genes were analyzed to see if there was any correspondence between the highly variable regions of the conotoxin. Regions of the DNA encompassing the conserved Cys codons (and several other conserved amino acid codons) have been found to correspond to predicted secondary structures of higher stabilities. In stark contrast the regions of the conotoxin that have a higher degree of variation correlate to regions of lower stability. This striking co-relation allows for a simple model of inaccessibility of a mutator to these highly conserved regions of the conotoxin gene allowing them a relative degree of resistance towards change.
authors.affiliation: Unichem Biosciences R and D Centre, Society for Innovation and Development, Indian Institute of Science, Bangalore 560 012, Karnataka, India. kaldew@unichemindia.com
authors.forename: Kalyan Kumar
authors.initials: KK
authors.lastname: Dewan
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003062:Codon; D020916:Conotoxins / Q000737:chemistry*; D017124:Conserved Sequence; D018076:DNA, Complementary / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D012908:Snails
chemical_list: D003062:Codon; D020916:Conotoxins; D018076:DNA, Complementary