NetWheels: A web application to create high quality peptide helical wheel and net projections

Mól, Alan Ribeiro; Castro, Mariana S.; Fontes, Wagner

doi:10.1101/416347

Cited by 68 publications

(46 citation statements)

References 12 publications

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“…Amphipaseek and Heliquest confidently predict that the C-terminus of AAV2 MAAP contains an amphipathic, membrane-binding α-helix (aa 96-116) (see Fig 3 and Table 1). Fig 4 depicts this region as a helical wheel representation [31]. As expected, it is clearly divided into a hydrophobic face (bottom) and polar face (top), the latter having a high positive net charge (+6).…”

Section: Bothmentioning

confidence: 60%

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Sequence Properties of the MAAP Protein and of the VP1 Capsid Protein of Adeno-Associated Viruses

Karlin¹

2020

Preprint

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Adeno-associated viruses (AAVs, genus dependoparvovirus) are promising gene therapy vectors. In strains AAV1-12, the capsid gene VP1 encodes a recently discovered protein, MAAP, in an overlapping frame.MAAP binds the cell membrane by an unknown mechanism. We discovered that MAAP is also encoded in bovine AAV and in porcine AAVs (which have shown promise for gene transfer into muscle tissues), in which it is probably translated from a non-canonical start codon. MAAP is predicted to be mostly disordered except for a predicted C-terminal, membrane-binding amphipathic α-helix. MAAP has a highly unusual composition. In particular, it lacks internal methionines, and is devoid of tyrosines in most strains.Unexpectedly, we discovered that the N-terminus of VP1 also lacks several amino acids. In all AAVs that encode MAAP, the first 200 aas of VP1 are devoid of internal methionines, probably owing to a selection against ATG codons that could prevent translation of MAAP and of capsid isoforms (VP2, VP3). The Nterminus of VP1 also lacks cysteines, likely to avoid the formation of disulfide bridges when it becomes exposed outside of the capsid during post-endocytic trafficking. Finally, the region common to VP1 and VP2 lacks tyrosine in the vast majority of AAVs that encode MAAP. Avoiding these "forbidden" aas in MAAP and VP1 when creating recombinant AAV capsids might increase the efficiency of capsid design. Conversely, the presence of "forbidden" aas in some rare strains probably indicates that they have unusual properties that could help us understand the viral cycle.Preprints (www.preprints.org) | NOT PEER-REVIEWED |

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Section: Bothmentioning

confidence: 60%

“…The helix is predicted as "potential" membrane-binding amphipathic α-helix if 0.68 <D <1.34, and as "reliable" if D≥1.34 [30]. We also used Heliquest to plot helical wheel representations (reviewed in [31]).…”

Section: Prediction Of Protein Structural Featuresmentioning

confidence: 99%

Sequence Properties of the MAAP Protein and of the VP1 Capsid Protein of Adeno-Associated Viruses

Karlin¹

2020

Preprint

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“…4 Predicted amphiphilic α-helices in Sp-CTx α- and β-subunits. Two potential amphiphilic α-helices were predicted by Helical Wheel Projections by Schiffer-Edmundson [ 39 , 40 ]. Residues are colored according to their chemical character as follows: acidic (blue), basic (red), uncharged polar (green) and nonpolar (yellow).…”

Section: Resultsmentioning

confidence: 99%

“…The amphiphilicity, α-helices, glycosylation sites and peptide signal sequences in Sp-CTx were analyzed by the programs PSIPRED Protein Sequence Analysis Workbench (UCL Department of Computer Science), NETNGLYC ( http://www.cbs.dtu.dk/services/NetNGlyc ) and SignalP 4.0 [ 38 ], respectively. Cytolytic sites in α-helices were predicted by designing a Helical Wheel as described by Schiffer & Edmundson [ 39 ] and using the program ( http://lbqp.unb.br/NetWheels ) [ 40 ].…”

Section: Methodsmentioning

confidence: 99%

Sequence analysis of the cDNA encoding for SpCTx: a lethal factor from scorpionfish venom (Scorpaena plumieri)

Costa

Lima

Figueiredo

et al. 2018

J Venom Anim Toxins Incl Trop Dis

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BackgroundLethal factors are multifunctional oligomeric proteins found in the venomous apparatus of Scorpaeniformes fish. These toxins elicit not only an array of biological responses in vitro but also cardiovascular disorders and strong hemolytic, nociceptive and edematogenic activities in vivo. This work describes the cloning and molecular identification of two toxin subunits, denominated Sp-CTx-α and Sp-CTx-β, from scorpionfish venom (Scorpaena plumieri).MethodsThe primary structures were deduced after cDNA amplification by PCR with primers from conserved sequences described in Scorpaeniformes toxins. Following DNA sequencing and bioinformatic analysis, the tridimensional structures of both subunits were modeled.ResultsThe translated sequences (702 amino acids, each subunit) show homology with other lethal factors, while alignment between Sp-CTx-α and Sp-CTx-β shows 54% identity. The subunits lack N-terminal signal sequences and display masses of approximately 80 kDa each. Both Sp-CTx subunits display a B30.2/SPRY domain at the C-terminal region with typically conserved motifs as described in these toxins. Secondary structure prediction identified six α-helices 18 residues long in both α and β subunits, some of them amphiphilic with their N-terminal flanked by many basic residues, creating a cationic site associated with the cytolytic activity of these toxins. Antimicrobial potential sites were identified in Sp-CTx and share some features with other peptides presenting variable and broad-spectrum activity. A phylogenetic tree built to represent these toxins supports the proximity between scorpionfish, lionfish and stonefish.ConclusionThe study identified a putative toxin protein whose primary structure is similar to other fish toxins and with potential for production of antivenom against scorpionfish envenomation in Brazil. As a prelude to structure-function studies, we propose that the toxin is structurally related to pore-forming marine toxins.Electronic supplementary materialThe online version of this article (10.1186/s40409-018-0158-7) contains supplementary material, which is available to authorized users.

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“…The BLAST software (http://blast.ncbi.nlm.nih.gov/Blast.cgi) [20] and The Antimicrobial Peptide Database (APD, http://aps.unmc.edu/AP/database/query_input.php) were used to search for peptide sequence similarity; Expasy pI/Mw tool (http://web.expasy.org/compute_pi) [21] was used to determine the theoretical mass for the peptide; multiple sequence alignment was performed using Clustal Omega program (http://www.ebi.ac.uk/Tools/msa/clustalo/) [22]; helical wheel projection of the peptide was obtained using NetWheels software (www.lbqp.unb.br/NetWheels/) [23]; I-Tasser server was used to predict its secondary structure (https://zhanglab.ccmb.med.umich.edu/I-TASSER/) [24]; and the hydrophobic ratio and GRAVY (Grand Average of Hydropathy) were determined by APD3: Antimicrobial Peptide Calculator and Predictor (http://aps.unmc.edu/AP/prediction/prediction_main. php) [25].…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Biological Properties of a Novel Multifunctional Host Defense Peptide from the Skin Secretion of the Chaco Tree Frog, Boana raniceps

et al. 2020

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In recent years, the number of new antimicrobial drugs launched on the market has decreased considerably even though there has been an increase in the number of resistant microbial strains. Thus, antimicrobial resistance has become a serious public health problem. Amphibian skin secretions are a rich source of host defense peptides, which generally are cationic and hydrophobic molecules, with a broad-spectrum of activity. In this study, one novel multifunctional defense peptide was isolated from the skin secretion of the Chaco tree frog, Boana raniceps. Figainin 2 (1FLGAILKIGHALAKTVLPMVTNAFKPKQ28) is cationic and hydrophobic, adopts an α-helical structure in 50% (v/v) trifluoroethanol (TFE), and is thermally stable. This peptide exhibited activity against Gram-negative and Gram-positive pathogenic bacteria arboviruses, T. cruzi epimastigotes; however, it did not show activity against yeasts. Figainin 2 also showed antiproliferative activity on cancer cells, is moderately active on human erythrocytes, and activates the oxidative burst in human neutrophils.

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NetWheels: A web application to create high quality peptide helical wheel and net projections

Cited by 68 publications

References 12 publications

Sequence Properties of the MAAP Protein and of the VP1 Capsid Protein of Adeno-Associated Viruses

Sequence Properties of the MAAP Protein and of the VP1 Capsid Protein of Adeno-Associated Viruses

Sequence analysis of the cDNA encoding for SpCTx: a lethal factor from scorpionfish venom (Scorpaena plumieri)

Biological Properties of a Novel Multifunctional Host Defense Peptide from the Skin Secretion of the Chaco Tree Frog, Boana raniceps

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