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Create Guidelines for Characterization of Venom Peptides

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In the course of my duties as a curator for the ArachnoServer database, I recently came across the article published by Binda et al. in Toxins... Despite these obvious differences in the toxin sequences (Figure 1) and masses (Table 1), the authors of the Binda et al. article mix up these toxins when referring to the activity and sequence of PhTx3-4, which was actually the only toxin used in their experiments... However, just because a toxin was isolated from venom of the same species and has similar activity as an already-characterized toxin from that venom, it does not imply that both toxins are identical (i.e., have the same mature toxin sequence)... It is well known that spiders often produce many homologs of a single toxin to increase their chemical diversity of venom peptides... Vice versa, if two homologous toxins have slight differences in their toxin sequence, one cannot simply conclude that these toxins will have a similar activity at a certain target, especially if the cysteine framework is not identical... The first 40 residues of the sequence of PhTx3-4 presented by Binda et al. actually match the N-terminal sequence reported for... Given than the native molecular masses of these toxins also match, I would assume that at least one of the residues in position 41–77 in the complete sequence provided for PhTx3-4 was not correctly assigned (as indicated in Figure 1), which would explain the 10 Da difference in molecular mass between the native toxin and the proposed sequence (the respective toxin card in ArachnoServer now also reflects this discrepancy)... Hence, a digestion of the toxin followed by N-terminal Edman sequencing of the unclear C-terminal residues is required to clarify this issue and to once and for all provide the correct and complete sequence of PhTx3-4... The fact that the correct sequence of PhTx3-4 (matching the native molecular mass of 8449 Da) still remains unknown makes it impossible for other researchers (which do not have access to the crude venom of P. nigriventer) to verify the results presented by Binda et al. (e.g., by using chemically synthesized or recombinantly produced toxin)... However, it is an essential part of science to be able to reproduce results from other researchers in order to verify their results... These points listed here might not be complete, but should provide a basis for discussion on the minimum standards that an article has to meet to be considered for publication... Using these guidelines will ensure a high standard for scientific publications and help all scientists to obtain all the information from published literature that is essential for their research.

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Sequence alignment of toxins from the ω-ctenitoxin-Pn3 family with close sequence homology to PhTx3-4 (extracted from ArachnoServer database on 17.3.2016). All residues that are different to the sequence proposed for PhTx3-4 [3] are in red colour.
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toxins-08-00252-f001: Sequence alignment of toxins from the ω-ctenitoxin-Pn3 family with close sequence homology to PhTx3-4 (extracted from ArachnoServer database on 17.3.2016). All residues that are different to the sequence proposed for PhTx3-4 [3] are in red colour.

Mentions: In the course of my duties as a curator for the ArachnoServer database [1,2], I recently came across the article published by Binda et al. in Toxins [3]. In this article, the effects of a toxin termed PhTx3-4 (isolated from the venom of the Brazilian wandering spider Phoneutria nigriventer) are studied in an animal model of retinal injury, in which the toxin showed neuroprotective effects from NMDA-induced retinal injury. According to this article, PhTx3-4 has a native molecular mass of 8449 Da. However, the sequence that is provided has a predicted (average oxidised) mass of 8459 Da, which is a difference of 10 Da. Given the accuracy of mass spectrometry, this difference cannot simply be explained by an imprecise measurement. For the suggested activity of PhTx3-4 on voltage-gated calcium channels, the authors then referred to the sequence of ω-Phonetoxin IIA (ω-PtxIIA) as published by dos Santos et al. [4]. However, the sequence of ω-PtxIIA has six residues difference to PhTx3-4 and the molecular mass of ω-PtxIIA is 8363 Da, which is 86 Da less than the native mass of PhTx3-4. Furthermore, there is also a difference in the cysteine-framework in position 15 and 19 of these toxins, which could have a significant impact on the toxin folding and activity (Figure 1).


Create Guidelines for Characterization of Venom Peptides
Sequence alignment of toxins from the ω-ctenitoxin-Pn3 family with close sequence homology to PhTx3-4 (extracted from ArachnoServer database on 17.3.2016). All residues that are different to the sequence proposed for PhTx3-4 [3] are in red colour.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037478&req=5

toxins-08-00252-f001: Sequence alignment of toxins from the ω-ctenitoxin-Pn3 family with close sequence homology to PhTx3-4 (extracted from ArachnoServer database on 17.3.2016). All residues that are different to the sequence proposed for PhTx3-4 [3] are in red colour.
Mentions: In the course of my duties as a curator for the ArachnoServer database [1,2], I recently came across the article published by Binda et al. in Toxins [3]. In this article, the effects of a toxin termed PhTx3-4 (isolated from the venom of the Brazilian wandering spider Phoneutria nigriventer) are studied in an animal model of retinal injury, in which the toxin showed neuroprotective effects from NMDA-induced retinal injury. According to this article, PhTx3-4 has a native molecular mass of 8449 Da. However, the sequence that is provided has a predicted (average oxidised) mass of 8459 Da, which is a difference of 10 Da. Given the accuracy of mass spectrometry, this difference cannot simply be explained by an imprecise measurement. For the suggested activity of PhTx3-4 on voltage-gated calcium channels, the authors then referred to the sequence of ω-Phonetoxin IIA (ω-PtxIIA) as published by dos Santos et al. [4]. However, the sequence of ω-PtxIIA has six residues difference to PhTx3-4 and the molecular mass of ω-PtxIIA is 8363 Da, which is 86 Da less than the native mass of PhTx3-4. Furthermore, there is also a difference in the cysteine-framework in position 15 and 19 of these toxins, which could have a significant impact on the toxin folding and activity (Figure 1).

View Article: PubMed Central - PubMed

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

In the course of my duties as a curator for the ArachnoServer database, I recently came across the article published by Binda et al. in Toxins... Despite these obvious differences in the toxin sequences (Figure 1) and masses (Table 1), the authors of the Binda et al. article mix up these toxins when referring to the activity and sequence of PhTx3-4, which was actually the only toxin used in their experiments... However, just because a toxin was isolated from venom of the same species and has similar activity as an already-characterized toxin from that venom, it does not imply that both toxins are identical (i.e., have the same mature toxin sequence)... It is well known that spiders often produce many homologs of a single toxin to increase their chemical diversity of venom peptides... Vice versa, if two homologous toxins have slight differences in their toxin sequence, one cannot simply conclude that these toxins will have a similar activity at a certain target, especially if the cysteine framework is not identical... The first 40 residues of the sequence of PhTx3-4 presented by Binda et al. actually match the N-terminal sequence reported for... Given than the native molecular masses of these toxins also match, I would assume that at least one of the residues in position 41–77 in the complete sequence provided for PhTx3-4 was not correctly assigned (as indicated in Figure 1), which would explain the 10 Da difference in molecular mass between the native toxin and the proposed sequence (the respective toxin card in ArachnoServer now also reflects this discrepancy)... Hence, a digestion of the toxin followed by N-terminal Edman sequencing of the unclear C-terminal residues is required to clarify this issue and to once and for all provide the correct and complete sequence of PhTx3-4... The fact that the correct sequence of PhTx3-4 (matching the native molecular mass of 8449 Da) still remains unknown makes it impossible for other researchers (which do not have access to the crude venom of P. nigriventer) to verify the results presented by Binda et al. (e.g., by using chemically synthesized or recombinantly produced toxin)... However, it is an essential part of science to be able to reproduce results from other researchers in order to verify their results... These points listed here might not be complete, but should provide a basis for discussion on the minimum standards that an article has to meet to be considered for publication... Using these guidelines will ensure a high standard for scientific publications and help all scientists to obtain all the information from published literature that is essential for their research.

No MeSH data available.