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Darin R Rokyta - One of the best experts on this subject based on the ideXlab platform.
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functional characterizations of venom phenotypes in the eastern diamondback rattlesnake Crotalus adamanteus and evidence for expression driven divergence in toxic activities among populations
Toxicon, 2016Co-Authors: Mark J Margres, Elda E Sanchez, Montamas Suntravat, Robert Walls, Sara Lucena, Darin R RokytaAbstract:Phenotypes frequently vary across and within species. The connection between specific phenotypic effects and function, however, is less understood despite being essential to our understanding of the adaptive process. Snake venoms are ideal for identifying functionally important phenotypic variation because venom variation is common, and venoms can be functionally characterized through simple assays and toxicity measurements. Previous work with the eastern diamondback rattlesnake (Crotalus adamanteus) used multivariate statistical approaches to identify six unique venom phenotypes. We functionally characterized hemolytic, gelatinase, fibrinogenolytic, and coagulant activity for all six phenotypes, as well as one additional venom, to determine if the statistically significant differences in toxin expression levels previously documented corresponded to differences in venom activity. In general, statistical differences in toxin expression predicted the identified functional differences, or lack thereof, in toxic activity, demonstrating that the statistical approach used to characterize C. adamanteus venoms was a fair representation of biologically meaningful differences. Minor differences in activity not accounted for by the statistical model may be the result of amino-acid differences and/or post-translational modifications, but overall we were able to link variation in protein expression levels to variation in function as predicted by multivariate statistical approaches.
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phenotypic integration in the feeding system of the eastern diamondback rattlesnake Crotalus adamanteus
Molecular Ecology, 2015Co-Authors: Mark J Margres, Kenneth P Wray, Margaret Seavy, James J Mcgivern, Dragana Sanader, Darin R RokytaAbstract:Selection can vary geographically across environments and temporally over the lifetime of an individual. Unlike geographic contexts, where different selective regimes can act on different alleles, age-specific selection is constrained to act on the same genome by altering age-specific expression. Snake venoms are exceptional traits for studying ontogeny because toxin expression variation directly changes the phenotype; relative amounts of venom components determine, in part, venom efficacy. Phenotypic integration is the dependent relationship between different traits that collectively produce a complex phenotype and, in venomous snakes, may include traits as diverse as venom, head shape and fang length. We examined the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus) across environments and over the lifetime of individuals and used a genotype–phenotype map approach, protein expression data and morphological data to demonstrate that: (i) ontogenetic effects explained more of the variation in toxin expression variation than geographic effects, (ii) both juveniles and adults varied geographically, (iii) toxin expression variation was a result of directional selection and (iv) different venom phenotypes covaried with morphological traits also associated with feeding in temporal (ontogenetic) and geographic (functional) contexts. These data are the first to demonstrate, to our knowledge, phenotypic integration between multiple morphological characters and a biochemical phenotype across populations and age classes. We identified copy number variation as the mechanism driving the difference in the venom phenotype associated with these morphological differences, and the parallel mitochondrial, venom and morphological divergence between northern and southern clades suggests that each clade may warrant classification as a separate evolutionarily significant unit.
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linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake Crotalus adamanteus
Journal of Proteomics, 2014Co-Authors: Mark J Margres, Kenneth P Wray, Margaret Seavy, James J Mcgivern, Kate Calvin, Darin R RokytaAbstract:Abstract Understanding the molecular basis of the phenotype is key to understanding adaptation, and the relationship between genes and specific traits is represented by the genotype–phenotype map. The specialization of the venom-gland towards toxin production enables the use of transcriptomics to identify a large number of loci that contribute to a complex phenotype (i.e., venom), while proteomic techniques allow verification of the secretion of the proteins produced by these loci, creating a genotype–phenotype map. We used the extensive database of mRNA transcripts generated by the venom-gland transcriptome of Crotalus adamanteus along with proteomic techniques to complete the genotype–phenotype map for the C. adamanteus venom system. Nanospray LC/MS E analysis of a whole venom sample identified evidence for 52 of the 78 unique putative toxin transcript clusters, including 44 of the 50 most highly expressed transcripts. Tandem mass spectrometry and SDS-PAGE of reversed-phase high-performance liquid chromatography fractions identified 40 toxins which clustered into 20 groups and represented 10 toxin families, creating a genotype–phenotype map. By using the transcriptome to understand the proteome we were able to achieve locus-specific resolution and provide a detailed characterization of the C. adamanteus venom system. Biological significance Identifying the mechanisms by which genetic variation presents itself to the sieve of selection at the phenotypic level is key to understanding the molecular basis of adaptation, and the first step in understanding this relationship is to identify the genetic basis of the phenotype through the construction of a genotype–phenotype map. We used the high-throughput venom-gland transcriptomic characterization of the eastern diamondback rattlesnake ( C. adamanteus ) and proteomic techniques to complete and confirm the genotype–phenotype map, providing a detailed characterization of the C. adamanteus venom system.
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the venom gland transcriptome of the eastern diamondback rattlesnake Crotalus adamanteus
BMC Genomics, 2012Co-Authors: Darin R Rokyta, Mark J Margres, Alan R Lemmon, Karalyn AronowAbstract:Snake venoms have significant impacts on human populations through the morbidity and mortality associated with snakebites and as sources of drugs, drug leads, and physiological research tools. Genes expressed by venom-gland tissue, including those encoding toxic proteins, have therefore been sequenced but only with relatively sparse coverage resulting from the low-throughput sequencing approaches available. High-throughput approaches based on 454 pyrosequencing have recently been applied to the study of snake venoms to give the most complete characterizations to date of the genes expressed in active venom glands, but such approaches are costly and still provide a far-from-complete characterization of the genes expressed during venom production. We describe the de novo assembly and analysis of the venom-gland transcriptome of an eastern diamondback rattlesnake (Crotalus adamanteus) based on 95,643,958 pairs of quality-filtered, 100-base-pair Illumina reads. We identified 123 unique, full-length toxin-coding sequences, which cluster into 78 groups with less than 1% nucleotide divergence, and 2,879 unique, full-length nontoxin coding sequences. The toxin sequences accounted for 35.4% of the total reads, and the nontoxin sequences for an additional 27.5%. The most highly expressed toxin was a small myotoxin related to crotamine, which accounted for 5.9% of the total reads. Snake-venom metalloproteinases accounted for the highest percentage of reads mapping to a toxin class (24.4%), followed by C-type lectins (22.2%) and serine proteinases (20.0%). The most diverse toxin classes were the C-type lectins (21 clusters), the snake-venom metalloproteinases (16 clusters), and the serine proteinases (14 clusters). The high-abundance nontoxin transcripts were predominantly those involved in protein folding and translation, consistent with the protein-secretory function of the tissue. We have provided the most complete characterization of the genes expressed in an active snake venom gland to date, producing insights into snakebite pathology and guidance for snakebite treatment for the largest rattlesnake species and arguably the most dangerous snake native to the United States of America, C. adamanteus. We have more than doubled the number of sequenced toxins for this species and created extensive genomic resources for snakes based entirely on de novo assembly of Illumina sequence data.
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a high throughput venom gland transcriptome for the eastern diamondback rattlesnake Crotalus adamanteus and evidence for pervasive positive selection across toxin classes
Toxicon, 2011Co-Authors: Darin R Rokyta, Kenneth P Wray, Alan R Lemmon, Emily Moriarty Lemmon, Brian S CaudleAbstract:Despite causing considerable human mortality and morbidity, animal toxins represent a valuable source of pharmacologically active macromolecules, a unique system for studying molecular adaptation, and a powerful framework for examining structure-function relationships in proteins. Snake venoms are particularly useful in the latter regard as they consist primarily of a moderate number of proteins and peptides that have been found to belong to just a handful of protein families. As these proteins and peptides are produced in dedicated glands, transcriptome sequencing has proven to be an effective approach to identifying the expressed toxin genes. We generated a venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) using Roche 454 sequencing technology. In the current work, we focus on transcripts encoding toxins. We identified 40 unique toxin transcripts, 30 of which have full-length coding sequences, and 10 have only partial coding sequences. These toxins account for 24% of the total sequencing reads. We found toxins from 11 previously described families of snake-venom toxins and have discovered two putative, previously undescribed toxin classes. The most diverse and highly expressed toxin classes in the C. adamanteus venom-gland transcriptome are the serine proteinases, metalloproteinases, and C-type lectins. The serine proteinases are the most abundant class, accounting for 35% of the toxin sequencing reads. Metalloproteinases are the most diverse; 11 different forms have been identified. Using our sequences and those available in public databases, we detected positive selection in seven of the eight toxin families for which sufficient sequences were available for the analysis. We find that the vast majority of the genes that contribute directly to this vertebrate trait show evidence for a role for positive selection in their evolutionary history.
Vance G Nielsen - One of the best experts on this subject based on the ideXlab platform.
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characterization of l amino acid oxidase derived from Crotalus adamanteus venom procoagulant and anticoagulant activities
International Journal of Molecular Sciences, 2019Co-Authors: Vance G NielsenAbstract:Snake venom enzymes of the L-amino acid oxidase (LAAO) class are responsible for tissue hemorrhage, edema, and derangement of platelet function. However, what role, if any, these flavoenzymes play in altering plasmatic coagulation have not been well defined. Using coagulation kinetomic analyses (thrombelastograph-based), it was determined that the LAAO derived from Crotalus adamanteus venom displayed a procoagulant activity associated with weak clot strength (no factor XIII activation) similar to thrombin-like enzymes. The procoagulant activity was not modified in the presence of reduced glutathione, demonstrating that the procoagulant activity was likely due to deamination, and not hydrogen peroxide generation by the LAAO. Further, unlike the raw venom of the same species, the purified LAAO was not inhibited by carbon monoxide releasing molecule-2 (CORM-2). Lastly, exposure of the enzyme to phenylmethylsulfonyl fluoride (PMSF) resulted in the LAAO expressing anticoagulant activity, preventing contact activation generated thrombin from forming a clot. In sum, this investigation for the first time characterized the LAAO of a snake venom as both a fibrinogen polymerizing and an anticoagulant enzyme acting via oxidative deamination and not proteolysis as is the case with thrombin-like enzymes (e.g., serine proteases). Using this thrombelastographic approach, future investigation of purified enzymes can define their biochemical nature.
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carbon monoxide inhibits the anticoagulant activity of phospholipase a2 purified from Crotalus adamanteus venom
Journal of Thrombosis and Thrombolysis, 2019Co-Authors: Vance G NielsenAbstract:Snake venom contains a myriad of classes of enzyme which have been investigated for medicinal and toxinological purposes, including phospholipase A2 (PLA2), which is responsible for anticoagulant, myotoxic and neurotoxic effects. Given the importance of PLA2, the purposes of the present investigation were to characterize the coagulation kinetic behavior of a PLA2 purified from Crotalus adamanteus venom (Ca-PLA2) in human plasma with thrombelastography and determine if carbon monoxide could inhibit its activity. Coagulation kinetics were determined in human plasma with a range of Ca-PLA2 activity (0–2 U/ml) via thrombelastography. Then, using carbon monoxide releasing molecule-2 or its inactivated molecule (0 or 100 µM), the vulnerability of Ca-PLA2 activity to carbon monoxide mediated inhibition was assessed. Lastly, the inhibitory response of Ca-PLA2 activity to exposure to carbon monoxide releasing molecule-2 (0–100 µM) was determined. Ca-PLA2 activity degraded the velocity of clot growth and clot strength in an activity dependent, exponential manner. Carbon monoxide inhibited Ca-PLA2 activity in a concentration dependent fashion, with loss of detectable activity at 100 µM of carbon monoxide releasing molecule-2. These findings, while preliminary, open the possibility that other PLA2 contained in snake venom with multiple toxicities (e.g., myotoxin, neurotoxin) may be heme bearing and CO-inhibitable, which have profound potential basic and clinical science implications.
Mark J Margres - One of the best experts on this subject based on the ideXlab platform.
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functional characterizations of venom phenotypes in the eastern diamondback rattlesnake Crotalus adamanteus and evidence for expression driven divergence in toxic activities among populations
Toxicon, 2016Co-Authors: Mark J Margres, Elda E Sanchez, Montamas Suntravat, Robert Walls, Sara Lucena, Darin R RokytaAbstract:Phenotypes frequently vary across and within species. The connection between specific phenotypic effects and function, however, is less understood despite being essential to our understanding of the adaptive process. Snake venoms are ideal for identifying functionally important phenotypic variation because venom variation is common, and venoms can be functionally characterized through simple assays and toxicity measurements. Previous work with the eastern diamondback rattlesnake (Crotalus adamanteus) used multivariate statistical approaches to identify six unique venom phenotypes. We functionally characterized hemolytic, gelatinase, fibrinogenolytic, and coagulant activity for all six phenotypes, as well as one additional venom, to determine if the statistically significant differences in toxin expression levels previously documented corresponded to differences in venom activity. In general, statistical differences in toxin expression predicted the identified functional differences, or lack thereof, in toxic activity, demonstrating that the statistical approach used to characterize C. adamanteus venoms was a fair representation of biologically meaningful differences. Minor differences in activity not accounted for by the statistical model may be the result of amino-acid differences and/or post-translational modifications, but overall we were able to link variation in protein expression levels to variation in function as predicted by multivariate statistical approaches.
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phenotypic integration in the feeding system of the eastern diamondback rattlesnake Crotalus adamanteus
Molecular Ecology, 2015Co-Authors: Mark J Margres, Kenneth P Wray, Margaret Seavy, James J Mcgivern, Dragana Sanader, Darin R RokytaAbstract:Selection can vary geographically across environments and temporally over the lifetime of an individual. Unlike geographic contexts, where different selective regimes can act on different alleles, age-specific selection is constrained to act on the same genome by altering age-specific expression. Snake venoms are exceptional traits for studying ontogeny because toxin expression variation directly changes the phenotype; relative amounts of venom components determine, in part, venom efficacy. Phenotypic integration is the dependent relationship between different traits that collectively produce a complex phenotype and, in venomous snakes, may include traits as diverse as venom, head shape and fang length. We examined the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus) across environments and over the lifetime of individuals and used a genotype–phenotype map approach, protein expression data and morphological data to demonstrate that: (i) ontogenetic effects explained more of the variation in toxin expression variation than geographic effects, (ii) both juveniles and adults varied geographically, (iii) toxin expression variation was a result of directional selection and (iv) different venom phenotypes covaried with morphological traits also associated with feeding in temporal (ontogenetic) and geographic (functional) contexts. These data are the first to demonstrate, to our knowledge, phenotypic integration between multiple morphological characters and a biochemical phenotype across populations and age classes. We identified copy number variation as the mechanism driving the difference in the venom phenotype associated with these morphological differences, and the parallel mitochondrial, venom and morphological divergence between northern and southern clades suggests that each clade may warrant classification as a separate evolutionarily significant unit.
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linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake Crotalus adamanteus
Journal of Proteomics, 2014Co-Authors: Mark J Margres, Kenneth P Wray, Margaret Seavy, James J Mcgivern, Kate Calvin, Darin R RokytaAbstract:Abstract Understanding the molecular basis of the phenotype is key to understanding adaptation, and the relationship between genes and specific traits is represented by the genotype–phenotype map. The specialization of the venom-gland towards toxin production enables the use of transcriptomics to identify a large number of loci that contribute to a complex phenotype (i.e., venom), while proteomic techniques allow verification of the secretion of the proteins produced by these loci, creating a genotype–phenotype map. We used the extensive database of mRNA transcripts generated by the venom-gland transcriptome of Crotalus adamanteus along with proteomic techniques to complete the genotype–phenotype map for the C. adamanteus venom system. Nanospray LC/MS E analysis of a whole venom sample identified evidence for 52 of the 78 unique putative toxin transcript clusters, including 44 of the 50 most highly expressed transcripts. Tandem mass spectrometry and SDS-PAGE of reversed-phase high-performance liquid chromatography fractions identified 40 toxins which clustered into 20 groups and represented 10 toxin families, creating a genotype–phenotype map. By using the transcriptome to understand the proteome we were able to achieve locus-specific resolution and provide a detailed characterization of the C. adamanteus venom system. Biological significance Identifying the mechanisms by which genetic variation presents itself to the sieve of selection at the phenotypic level is key to understanding the molecular basis of adaptation, and the first step in understanding this relationship is to identify the genetic basis of the phenotype through the construction of a genotype–phenotype map. We used the high-throughput venom-gland transcriptomic characterization of the eastern diamondback rattlesnake ( C. adamanteus ) and proteomic techniques to complete and confirm the genotype–phenotype map, providing a detailed characterization of the C. adamanteus venom system.
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the venom gland transcriptome of the eastern diamondback rattlesnake Crotalus adamanteus
BMC Genomics, 2012Co-Authors: Darin R Rokyta, Mark J Margres, Alan R Lemmon, Karalyn AronowAbstract:Snake venoms have significant impacts on human populations through the morbidity and mortality associated with snakebites and as sources of drugs, drug leads, and physiological research tools. Genes expressed by venom-gland tissue, including those encoding toxic proteins, have therefore been sequenced but only with relatively sparse coverage resulting from the low-throughput sequencing approaches available. High-throughput approaches based on 454 pyrosequencing have recently been applied to the study of snake venoms to give the most complete characterizations to date of the genes expressed in active venom glands, but such approaches are costly and still provide a far-from-complete characterization of the genes expressed during venom production. We describe the de novo assembly and analysis of the venom-gland transcriptome of an eastern diamondback rattlesnake (Crotalus adamanteus) based on 95,643,958 pairs of quality-filtered, 100-base-pair Illumina reads. We identified 123 unique, full-length toxin-coding sequences, which cluster into 78 groups with less than 1% nucleotide divergence, and 2,879 unique, full-length nontoxin coding sequences. The toxin sequences accounted for 35.4% of the total reads, and the nontoxin sequences for an additional 27.5%. The most highly expressed toxin was a small myotoxin related to crotamine, which accounted for 5.9% of the total reads. Snake-venom metalloproteinases accounted for the highest percentage of reads mapping to a toxin class (24.4%), followed by C-type lectins (22.2%) and serine proteinases (20.0%). The most diverse toxin classes were the C-type lectins (21 clusters), the snake-venom metalloproteinases (16 clusters), and the serine proteinases (14 clusters). The high-abundance nontoxin transcripts were predominantly those involved in protein folding and translation, consistent with the protein-secretory function of the tissue. We have provided the most complete characterization of the genes expressed in an active snake venom gland to date, producing insights into snakebite pathology and guidance for snakebite treatment for the largest rattlesnake species and arguably the most dangerous snake native to the United States of America, C. adamanteus. We have more than doubled the number of sequenced toxins for this species and created extensive genomic resources for snakes based entirely on de novo assembly of Illumina sequence data.
Charlotte L Ownby - One of the best experts on this subject based on the ideXlab platform.
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systemic hemorrhage induced by proteinase h from Crotalus adamanteus eastern diamondback rattlesnake venom
Toxicon, 1997Co-Authors: Steffan G Anderson, Charlotte L OwnbyAbstract:Abstract The systemic effects of a purified hemorrhagic toxin, proteinase H, from Crotalus adamanteus venom, were studied. Female, white CD-1 mice were injected intravenously with proteinase H and tissue samples were obtained at 1, 3 and 24 hr after injection. Hemorrhage was observed grossly within 1 hr in several internal organs including the stomach and small intestine, the heart and the lungs. Surface discolorations thought to be petechial hemorrhages were observed in the kidneys. The livers of treated animals were visibly swollen and darkened and lobules were accentuated. Tissue samples were taken from the stomach, duodenum, heart, lungs, liver and kidneys and prepared for observation by light and electron microscopy. Frank hemorrhage was observed by light microscopy in the walls of the stomach and duodenum, in the myocardium and in the lungs. Pulmonary hemorrhage was severe, with involvement of nearly all of the pulmonary tissue within 3 hr. At doses of 5 μg/g, hepatic degeneration was observed by 3 hr. Renal glomeruli were noticeably swollen and the lumena of the proximal convoluted tubules indistinct. Closer examination by electron microscopy revealed that the endothelial cells comprising the fenestrated glomerular capillaries remained intact but signs of degeneration (i.e. cytoplasmic swelling and mitochondrial swelling) were observed. Proteinase H induces systemic hemorrhage in the heart, lungs, stomach and small intestine, renal glomerulonephropathy and hepatic degeneration.
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pathogenesis of hemorrhage induced by proteinase h from eastern diamondback rattlesnake Crotalus adamanteus venom
Toxicon, 1997Co-Authors: Steffan G Anderson, Charlotte L OwnbyAbstract:Abstract The pathogenesis of hemorrhage of a purified hemorrhagic toxin, proteinase H from Crotalus adamanteus venom, was studied. Female, white CD-1 mice were injected intramuscularly with sublethal doses of the hemorrhagic toxin and tissue samples were obtained at 10 min, 1, 3 and 24 hr following injection. Severe local hemorrhage was observed grossly within 10 min. Hemorrhage was observed in the connective tissue of skeletal muscle and within adjacent adipose tissue. Many larger vessels were congested with erythrocytes and platelets. By 3 hr inflammatory cell infiltration was observed and necrosis of some muscle cells was evident. Transmission electron microscopy showed that the capillary endothelium was ruptured, leading to hemorrhage per rhexis . Capillary basal laminae were disorganized and often wholly or partially absent.
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Citrate is a major component of snake venoms.
Toxicon, 1992Co-Authors: Michael A Freitas, Paul W. Geno, L.w. Sumner, M.e. Cooke, S.a. Hudiburg, Ivan I. Kaiser, Charlotte L Ownby, George V. OdellAbstract:Abstract Citrate has been identified as a major component of snake venoms by gas liquid chromatography and mass spectrometry. The venoms of Bothrops asper, Crotalus atrox, Crotalus viridis viridis, Crotalus adamanteus, Sistrurus miliarius barbouri, Crotalus horridus horridus, Agkistrodon contortrix mokasen, Agkistrodon contortrix contortrix and Agkistrodon piscivorus piscivorus contain citrate at concentration levels which can serve as effective buffers. Calcium, magnesium, zinc, iron, sodium and potassium salts of citrate would be constituents of venom.
Dietrich Mebs - One of the best experts on this subject based on the ideXlab platform.
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Cross-neutralization of thrombin-like enzymes in snake venoms by polyvalent antivenoms
Toxicon, 2002Co-Authors: Ina Claus, Dietrich MebsAbstract:Abstract I. Claus and D. Mebs . Cross-neutralization of thrombin-like enzymes in snake venoms by polyvalent antivenoms. Toxicon 27, 1397–1399, 1989.—Five polyvalent antivenoms (Crotalidae; Orient, North, Central and South Africa) were tested for their ability to neutralize the thrombin-like activity of snake venoms ( Bitis gabonica, Agkistrodon acutus, Bothrops asper, B. atrox, Crotalus adamanteus ). Considerable cross-neutralization was observed. Anti-coagulase antibodies were isolated from an antivenom by affinity chromatography using a purified enzyme from Bitis gabonica venom. These antibodies neutralized the activity of most snake venom coagulant enzymes.
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amino acid sequence of a myotoxin from venom of the eastern diamondback rattlesnake Crotalus adamanteus
Toxicon, 1991Co-Authors: Yuji Samejima, Y Aoki, Dietrich MebsAbstract:Y. Samejima, Y. Aoki and D. Mebs. Amino acid sequence of a myotoxin from venom of the eastern diamondback rattlesnake (Crotalus adamanteus). Toxicon29, 461–468, 1991.—The complete amino acid sequence of a myotoxin isolated from Crotalus adamanteus venom (CAM-toxin) was determined. The total number of amino acid residues was 45, giving a mol. wt of 5202. The amino acid sequence was compared with those of previously determined Crotalus myotoxins. The CAM-toxin shows a surprisingly close relationship to those of peptide c (C. v. helleri), myotoxin a (C. v. viridis), crotamine (C. d. terrificus), myotoxin I and II (C. v. concolor) with homologies of approximately 98, 83, 90, 95 and 91%, respectively. The hydropathy profile of the CAM-toxin is almost identical to peptide c and myotoxin I, as can be assumed from the sequence homology. Despite the absence of any close sequence homology with the myotoxic phospholipase A2 enzymes, CAM-toxin contains a similar cationic myotoxic region at residues 2–10 as found in the other five myotoxic peptides.