Proteomic Analysis and Functional Characterization of Venom

A special issue of Toxins (ISSN 2072-6651). This special issue belongs to the section "Animal Venoms".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 8419

Special Issue Editors


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Guest Editor
Biotechnology Institute (IBTEC), São Paulo State University (UNESP), Botucatu, SP, Brazil
Interests: venom proteomic analysis; analytical techniques; mass spectrometry; diagnostic/prognostic biomarkers; clinical proteomics

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Guest Editor
Fundação Oswaldo Cruz (FIOCRUZ), Rondônia, RO, Brazil
Interests: functional characterization of venoms and toxins

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Guest Editor
Fundação Oswaldo Cruz (FIOCRUZ), Rondônia, RO, Brazil
Interests: purification; biochemical; structural; and biotechnological characterization of proteins and peptides

Special Issue Information

Dear Colleagues,

Studies conducted over the past 50 years have revealed the diversity of animal venoms’ chemical composition, and further research is increasingly exploring the synergic and/or individual effects of toxins. Improvements in modern instrumentation have supported large-scale measurement of animal venom proteomes, such as:

  • Purification of proteins and peptides by liquid chromatography (LC);
  • Analysis of selective proteins by enzyme-linked immunosorbent assay (ELISA) and Western blotting;
  • Separation of complex protein samples by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis (2-DE) and two-dimensional differential gel electrophoresis (2D-DIGE) techniques;
  • Mass spectrometry (MS) for analyzing the complex protein mixtures with higher sensitivity;
  • Free and stable isotopes labeling (ICAT, SILAC and iTRAQ) techniques for quantitative proteomic;
  • X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy providing three-dimensional (3D) structure of protein, furthering the understanding of its biological function;
  • Bioinformatics tools for 3D structure prediction, protein domain and motif analysis, rapid analysis of protein–protein interaction, evolutionary relationship and data analysis of MS.

This Special Issue will cover recent progress in proteomics techniques for the proteome and functional characterization of animal venoms and/or individual toxins to promote an improved understanding of the mechanisms of envenomation and/or to reveal bioactive molecules for the development of novel drugs.

Dr. Lucilene Delazari dos Santos
Dr. Juliana Pavan Zuliani
Prof. Dr. Andreimar M. Soares
Guest Editors

Manuscript Submission Information

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Keywords

  • venom proteomic analysis
  • venomous animals
  • bioactive molecules
  • functional protein characterization, protein quantification
  • protein isolation
  • peptide sequencing
  • mass spectrometry
  • bioinformatic proteomic
  • proteome database

Published Papers (5 papers)

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Research

17 pages, 6414 KiB  
Article
Immunochemical Recognition of Bothrops rhombeatus Venom by Two Polyvalent Antivenoms
by Karen Sarmiento, Jorge Zambrano, Carlos Galvis, Álvaro Molina-Olivares, Marisol Margarita Villadiego-Molinares, Johanna Alejandra Ramírez-Martínez, Ana Lucía Castiblanco and Fabio A. Aristizabal
Toxins 2024, 16(3), 152; https://doi.org/10.3390/toxins16030152 - 15 Mar 2024
Viewed by 871
Abstract
The protein profile of Bothrops rhombeatus venom was compared to Bothrops asper and Bothrops atrox, and the effectiveness of antivenoms from the National Institute of Health of Colombia (INS) and Antivipmyn-Tri (AVP-T) of Mexico were analyzed. Protein profiles were studied with sodium dodecyl [...] Read more.
The protein profile of Bothrops rhombeatus venom was compared to Bothrops asper and Bothrops atrox, and the effectiveness of antivenoms from the National Institute of Health of Colombia (INS) and Antivipmyn-Tri (AVP-T) of Mexico were analyzed. Protein profiles were studied with sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) and reverse-phase high-performance liquid chromatography (RP-HPLC). The neutralizing potency and the level of immunochemical recognition of the antivenoms to the venoms were determined using Western blot, affinity chromatography, and enzyme-linked immunosorbent assay (ELISA). Bands of phospholipase A2 (PLA2), metalloproteinases (svMPs) I, II, and III as well as serine proteinases (SPs) in the venom of B. rhombeatus were recognized by SDS-PAGE. With Western blot, both antivenoms showed immunochemical recognition towards PLA2 and svMP. INS showed 94% binding to B. rhombeatus venom and 92% to B. asper while AVP-T showed 90.4% binding to B. rhombeatus venom and 96.6% to B. asper. Both antivenoms showed binding to PLA2 and svMP, with greater specificity of AVP-T towards B. rhombeatus. Antivenom neutralizing capacity was calculated by species and mL of antivenom, finding the following for INS: B. asper 6.6 mgV/mL, B. atrox 5.5 mgV/mL, and B. rhombeatus 1.3 mgV/mL. Meanwhile, for AVP-T, the following neutralizing capacities were found: B. asper 2.7 mgV/mL, B. atrox 2.1 mgV/mL, and B. rhombeatus 1.4 mgV/mL. These results show that both antivenoms presented similarity between calculated neutralizing capacities in our trial, reported in a product summary for the public for the B. asper species; however, this does not apply to the other species tested in this trial. Full article
(This article belongs to the Special Issue Proteomic Analysis and Functional Characterization of Venom)
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7 pages, 529 KiB  
Communication
Preliminary Insights of Brazilian Snake Venom Metalloproteomics
by Bruna Cavecci-Mendonça, Karen Monique Luciano, Tauane Vaccas, Laudicéia Alves de Oliveira, Eloisa Fornaro Clemente, Bruno Cesar Rossini, José Cavalcante Souza Vieira, Luciana Curtolo de Barros, Ilka Biondi, Pedro de Magalhães Padilha and Lucilene Delazari dos Santos
Toxins 2023, 15(11), 648; https://doi.org/10.3390/toxins15110648 - 10 Nov 2023
Cited by 1 | Viewed by 1086
Abstract
Snakebite envenoming is one of the most significantly neglected tropical diseases in the world. The lack of diagnosis/prognosis methods for snakebite is one of our motivations to develop innovative technological solutions for Brazilian health. The objective of this work was to evaluate the [...] Read more.
Snakebite envenoming is one of the most significantly neglected tropical diseases in the world. The lack of diagnosis/prognosis methods for snakebite is one of our motivations to develop innovative technological solutions for Brazilian health. The objective of this work was to evaluate the protein and metallic ion composition of Crotalus durissus terrificus, Bothrops jararaca, B. alternatus, B. jararacussu, B. moojeni, B. pauloensis, and Lachesis muta muta snake venoms. Brazilian snake venoms were subjected to the shotgun proteomic approach using mass spectrometry, and metal ion analysis was performed by atomic spectrometry. Shotgun proteomics has shown three abundant toxin classes (PLA2, serine proteases, and metalloproteinases) in all snake venoms, and metallic ions analysis has evidenced that the Cu2+ ion is present exclusively in the L. m. muta venom; Ca2+ and Mg2+ ions have shown a statistical difference between the species of Bothrops and Crotalus genus, whereas the Zn2+ ion presented a statistical difference among all species studied in this work. In addition, Mg2+ ions have shown 42 times more in the C. d. terrificus venom when compared to the average concentration in the other genera. Though metal ions are a minor fraction of snake venoms, several venom toxins depend on them. We believe that these non-protein fractions are capable of assisting in the development of unprecedented diagnostic devices for Brazilian snakebites. Full article
(This article belongs to the Special Issue Proteomic Analysis and Functional Characterization of Venom)
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20 pages, 2233 KiB  
Article
Exosome Liberation by Human Neutrophils under L-Amino Acid Oxidase of Calloselasma rhodostoma Venom Action
by Suzanne N. Serrath, Adriana S. Pontes, Mauro V. Paloschi, Milena D. S. Silva, Jéssica A. Lopes, Charles N. Boeno, Carolina P. Silva, Hallison M. Santana, Daniel G. Cardozo, Andrey V. E. Ugarte, João G. S. Magalhães, Larissa F. Cruz, Sulamita S. Setubal, Andreimar M. Soares, Bruna Cavecci-Mendonça, Lucilene D. Santos and Juliana P. Zuliani
Toxins 2023, 15(11), 625; https://doi.org/10.3390/toxins15110625 - 25 Oct 2023
Viewed by 1638
Abstract
L-Amino acid oxidase (LAAO) is an enzyme found in snake venom that has multifaceted effects, including the generation of hydrogen peroxide (H2O2) during oxidative reactions, leading to various biological and pharmacological outcomes such as apoptosis, cytotoxicity, modulation of platelet [...] Read more.
L-Amino acid oxidase (LAAO) is an enzyme found in snake venom that has multifaceted effects, including the generation of hydrogen peroxide (H2O2) during oxidative reactions, leading to various biological and pharmacological outcomes such as apoptosis, cytotoxicity, modulation of platelet aggregation, hemorrhage, and neutrophil activation. Human neutrophils respond to LAAO by enhancing chemotaxis, and phagocytosis, and releasing reactive oxygen species (ROS) and pro-inflammatory mediators. Exosomes cellular nanovesicles play vital roles in intercellular communication, including immune responses. This study investigates the impact of Calloselasma rhodostoma snake venom-derived LAAO (Cr-LAAO) on human neutrophil exosome release, including activation patterns, exosome formation, and content. Neutrophils isolated from healthy donors were stimulated with Cr-LAAO (100 μg/mL) for 3 h, followed by exosome isolation and analysis. Results show that Cr-LAAO induces the release of exosomes with distinct protein content compared to the negative control. Proteomic analysis reveals proteins related to the regulation of immune responses and blood coagulation. This study uncovers Cr-LAAO’s ability to activate human neutrophils, leading to exosome release and facilitating intercellular communication, offering insights into potential therapeutic approaches for inflammatory and immunological disorders. Full article
(This article belongs to the Special Issue Proteomic Analysis and Functional Characterization of Venom)
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24 pages, 7247 KiB  
Article
Multilevel Comparison of Indian Naja Venoms and Their Cross-Reactivity with Indian Polyvalent Antivenoms
by Archana Deka, Siddharth Bhatia, Vishal Santra, Omesh K. Bharti, Hmar Tlawmte Lalremsanga, Gerard Martin, Wolfgang Wüster, John B. Owens, Stuart Graham, Robin Doley and Anita Malhotra
Toxins 2023, 15(4), 258; https://doi.org/10.3390/toxins15040258 - 01 Apr 2023
Cited by 5 | Viewed by 2516
Abstract
Snake envenoming is caused by many biological species, rather than a single infectious agent, each with a multiplicity of toxins in their venom. Hence, developing effective treatments is challenging, especially in biodiverse and biogeographically complex countries such as India. The present study represents [...] Read more.
Snake envenoming is caused by many biological species, rather than a single infectious agent, each with a multiplicity of toxins in their venom. Hence, developing effective treatments is challenging, especially in biodiverse and biogeographically complex countries such as India. The present study represents the first genus-wide proteomics analysis of venom composition across Naja species (N. naja, N. oxiana, and N. kaouthia) found in mainland India. Venom proteomes were consistent between individuals from the same localities in terms of the toxin families present, but not in the relative abundance of those in the venom. There appears to be more compositional variation among N. naja from different locations than among N. kaouthia. Immunoblotting and in vitro neutralization assays indicated cross-reactivity with Indian polyvalent antivenom, in which antibodies raised against N. naja are present. However, we observed ineffective neutralization of PLA2 activities of N. naja venoms from locations distant from the source of immunizing venoms. Antivenom immunoprofiling by antivenomics revealed differential antigenicity of venoms from N. kaouthia and N. oxiana, and poor reactivity towards 3FTxs and PLA2s. Moreover, there was considerable variation between antivenoms from different manufacturers. These data indicate that improvements to antivenom manufacturing in India are highly desirable. Full article
(This article belongs to the Special Issue Proteomic Analysis and Functional Characterization of Venom)
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14 pages, 2325 KiB  
Article
Function Prediction of Peptide Toxins with Sequence-Based Multi-Tasking PU Learning Method
by Yanyan Chu, Huanhuan Zhang and Lei Zhang
Toxins 2022, 14(11), 811; https://doi.org/10.3390/toxins14110811 - 21 Nov 2022
Viewed by 1445
Abstract
Peptide toxins generally have extreme pharmacological activities and provide a rich source for the discovery of drug leads. However, determining the optimal activity of a new peptide can be a long and expensive process. In this study, peptide toxins were retrieved from Uniprot; [...] Read more.
Peptide toxins generally have extreme pharmacological activities and provide a rich source for the discovery of drug leads. However, determining the optimal activity of a new peptide can be a long and expensive process. In this study, peptide toxins were retrieved from Uniprot; three positive-unlabeled (PU) learning schemes, adaptive basis classifier, two-step method, and PU bagging were adopted to develop models for predicting the biological function of new peptide toxins. All three schemes were embedded with 14 machine learning classifiers. The prediction results of the adaptive base classifier and the two-step method were highly consistent. The models with top comprehensive performances were further optimized by feature selection and hyperparameter tuning, and the models were validated by making predictions for 61 three-finger toxins or the external HemoPI dataset. Biological functions that can be identified by these models include cardiotoxicity, vasoactivity, lipid binding, hemolysis, neurotoxicity, postsynaptic neurotoxicity, hypotension, and cytolysis, with relatively weak predictions for hemostasis and presynaptic neurotoxicity. These models are discovery-prediction tools for active peptide toxins and are expected to accelerate the development of peptide toxins as drugs. Full article
(This article belongs to the Special Issue Proteomic Analysis and Functional Characterization of Venom)
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