Evolutionary trace analysis of scorpion toxins specific for K‐channels

Abstract

Scorpion alpha-K(+) channel toxins are a large family of polypeptides with a similar structure but diverse pharmacological activities. Despite many structural and functional data available at present, little progress has been made in understanding the toxin's molecular basis responsible for the functional diversification. In this paper, we report the first complete cDNA sequences of toxins belonging to subfamily 6 and identify five new members, called alpha-KTx 6.6-6.10. By analyzing the rates of mutations that occurred in the corresponding cDNAs, we suggest that accelerated evolution in toxin-coding regions may be associated with the functional diversification of this subfamily. To pinpoint sites probably involved in the functional diversity of alpha-KTx family, we analyzed this family of sequences using the evolutionary trace method. This analysis highlighted one channel-binding surface common for all the members. This surface is composed of one conserved lysine residue at position 29 assisted by other residues at positions 10, 26, 27, 32, 34, and 36. Of them, the positions 29, 32, and 34 have been reported to be the most major determinants of channel specificity. Interestingly, another contrary surface was also observed at a higher evolutionary time cut-off value, which may be involved in the binding of ERG (ether-a-go-go-related gene) channel-specific toxins. The good match between the trace residues and the functional epitopes of the toxins suggested that the evolutionary trace results reported here can be applied to predict channel-binding sites of the toxins. Because, the side-chain variation in the trace positions is strongly linked with the functional alteration and channel-binding surface transfer of alpha-KTx family, we conclude that our findings should also be important for the rational design of new toxins targeting a given potassium channel with high selectivity.

Evolutionary and functional epitopes of the Spätzle protein: New insights into activation of the Toll receptor

“…ET analysis is a method developed to utilize this phylogenetic information to predict functional sites in proteins [15,16] and has been successfully used in different biological systems [17, 26 -35]. For example, Zhu et al successfully highlighted one channel-binding surface common for the scorpion a-KTx family of neurotoxins [34]. Supported by these facts, we believe that it is also possible to use evolution-guided information to identify key residues of Spätzle and then to direct further mutational analyses.…”

Four Novel Tarantula Toxins as Selective Modulators of Voltage-Gated Sodium Channel Subtypes

“…The ET analysis was carried out based on a phylogenetic tree created with the unweighted pair group method with arithmetic mean. To summarize briefly, the ET method divides all residues of aligned sequences into three classes: neutral, conserved, and class-specific, based on the comparison of consensus sequences for groups of proteins that originate from a common node defined by the evolutionary time cut-off in a phylogenetic tree (for details, see Zhu et al, 2004). Class-specific trace residues identified were mapped onto the structure of HnTX-IV (PDB code 1NIY) in the PyMOL molecular modeling program (http://pymol.sourceforge.net).…”

A two‐entropies analysis to identify functional positions in the transmembrane region of class A G protein‐coupled receptors

“…[53][54][55][56][57][58][59] Recently, this method was used to analyze class A GPCR sequences to identify globally conserved residues and opsin subfamily-specific residues. 17 In that study, only four subfamilies of class A GPCRs-visual opsin, bioamine, olfactory, and chemokine-were included to trace 39 "globally" conserved residues.…”