Antimicrobial peptides from amphibian skin: What do they tell us?

Simmaco, Maurizio; Mignogna, Giuseppina; Barra, Donatella

doi:10.1002/(sici)1097-0282(1998)47:6<435::aid-bip3>3.0.co;2-8

Cited by 399 publications

(173 citation statements)

References 103 publications

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“…They are simply implemented to produce a workable load of suggested peptide antibiotics expected to have high TI and good antibacterial activity against Gram-negative bacterium. On the basis of these restrictions, the algorithm selected the following peptides out of 8 × 10 29 possible ones: GLKGLLGKALKGIGKHIGKAQGC; GLKGLLGKALGEAKGLLGKHKGC; GITQGVLKGIGKHVGKALKGIGC; GIGKHVGKALKGLKGLLKGLGEC; GIGKHVGKALKGVKGLLKGLGEC; GIGKHVGKALGELKGLLKGLKGC; GIGKHVGKALKGLKGLLKGLGES; adepantin 1 Six of these sequences end with a cysteine residue, which may be a vestige from the so-called "Rana-box", a cysteinebridged stretch present at the C-terminus of many frogderived helical antimicrobial peptides, 8,27 which is not correlated with increased activity or selectivity. 27 This likely means that restriction 6 has to be modified.…”

Section: Sequence Moments and The D-descriptormentioning

confidence: 99%

Computational Design of Highly Selective Antimicrobial Peptides

Juretić

Vukičević

Ilić

et al. 2009

J. Chem. Inf. Model.

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We have created a structure-selectivity database (AMPad) of frog-derived, helical antimicrobial peptides (AMPs), in which the selectivity was determined as a therapeutic index (TI), and then used the novel concept of sequence moments to study the lengthwise asymmetry of physicochemical peptide properties. We found that the cosine of the angle between two sequence moments obtained with different hydrophobicity scales, defined as the D-descriptor, identifies highly selective peptide antibiotics. We could then use this descriptor to predict TI changes after point mutations in known AMPs, and to aid the prediction of TI for de noVo designed AMPs. In combination with an amino acid selectivity index, a motif regularity index and other statistical rules extracted from AMPad, the D-descriptor enabled construction of the AMP-Designer algorithm. A 23 residue, glycine-rich, peptide suggested by the algorithm was synthesized and the activity and selectivity tested. This peptide, adepantin 1, is less than 50% identical to any other AMP, has a potent antibacterial activity against the reference organism, E. coli, and has a significantly greater selectivity (TI > 200) than the best AMP present in the AMPad database (TI ) 125).

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Section: Sequence Moments and The D-descriptormentioning

confidence: 99%

Computational Design of Highly Selective Antimicrobial Peptides

Juretić

Vukičević

Ilić

et al. 2009

J. Chem. Inf. Model.

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“…The second class includes linear peptides with an over-representation of a single amino acid, such as histatin 5 (Oppenheim et al, 1988). The third class comprises peptides with loop structures connected by one disulphide bridge, such as the brevinins from frog skin (Simmaco et al, 1998). The fourth class includes peptides with two or more disulphide bonds.…”

Section: Introductionmentioning

confidence: 99%

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

Wang

et al. 2006

Molecular Immunology

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“…It was successfully applied to all five peptides while reduction/carboxamidomethylation failed in the case of brevinin-1Ra, despite all variations of reaction conditions. (J Am Soc Mass Spectrom 2008, 19, 479 -487) © 2008 American Society for Mass Spectrometry A skin secretion produced by granular skin glands of anurans in response to a variety of stimuli contains biologically active peptides [1][2][3][4]. Our interest was focused on the Rana genus containing a notable array of common frogs spread around the territory of Eurasia and America.…”

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confidence: 99%

“…Our interest was focused on the Rana genus containing a notable array of common frogs spread around the territory of Eurasia and America. A major part of ranid peptides has a disulfide cycle at the C-terminus [1,5]. This peculiarity, called "Rana box" [6], complicates sequencing of these peptides.…”

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confidence: 99%

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Oxidation versus carboxamidomethylation of s-s bond in ranid frog peptides: Pro and contra for de novo MALDI-MS sequencing

Samgina

Artemenko

Gorshkov

et al. 2008

J. Am. Soc. Mass Spectrom.

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Five natural peptides isolated from ranid skin secretions of European frog species of Rana ridibunda and Rana arvalis (molecular masses 3516, 26743516, , 26363516, , 18743516, , and 1810 were studied by MALDI-TOF/TOF to compare two procedures of disulfide bond cleavage: (1) performic oxidation and (2) reduction/carboxamidomethylation. The processes are relevant for the elucidation of the amino acid sequence inside the seven-member cystine ring at the C-terminus. The results clearly demonstrated that oxidation of the disulfide bond led to notably higher abundances of b-and y-ions, corresponding to the C-terminal peptide bonds, than reduction/carboxamidomethylation. This conclusion is true for all five peptides studied. Besides that, the oxidation procedure is simpler than carboxamidomethylation, as it is a one-step process with no purification required. The oxidation is more reproducible. The results were similar each time the peptide was subjected to the process. It was successfully applied to all five peptides while reduction/carboxamidomethylation failed in the case of brevinin-1Ra, despite all variations of reaction conditions. (J Am Soc Mass Spectrom 2008, 19, 479 -487) © 2008 American Society for Mass Spectrometry A skin secretion produced by granular skin glands of anurans in response to a variety of stimuli contains biologically active peptides [1][2][3][4]. Our interest was focused on the Rana genus containing a notable array of common frogs spread around the territory of Eurasia and America. A major part of ranid peptides has a disulfide cycle at the C-terminus [1,5]. This peculiarity, called "Rana box" [6], complicates sequencing of these peptides. The amino acid sequence inside the cycle is practically unattainable by means of mass spectrometry without preliminary chemical derivatization. There is only one communication on direct sequence identification inside the C-terminus disulfide cycle using ESI MS/MS in the negative ion mode. It deals with some bioactive peptides isolated from genus Crinia (Australia) and with brevinin-1E R. ridibunda, (Russia) [7]. In this case, a combination of the positive and negative mass spectra has produced complete sequences for all the investigated peptides. Unfortunately not all peptides give reasonable negative ion spectra.Mass spectrometric sequencing of disulfide containing peptides requires preliminary modification of the S-S bond. There are two general methods to cleave this bond: (1) reduction followed by the alkylation of cysteines [8 -10]; (2) oxidation with performic acid [11]. The first procedure is traditionally used to break S-S bonds in proteins with associated polypeptide chains before their enzymatic digestion. We applied it for the skin peptides of the Rana genus with an internal disulfide cycle [12,13]. Reduction of the S-S bond followed by carboxamidomethylation allows reliable sequencing at the C-terminus. LTQ FTICR mass spectrometric results completely match those obtained by Edman degradation.Performic oxidation is a well-known method for the cl...

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Antimicrobial peptides from amphibian skin: What do they tell us?

Cited by 399 publications

References 103 publications

Computational Design of Highly Selective Antimicrobial Peptides

Computational Design of Highly Selective Antimicrobial Peptides

NK-lysin of channel catfish: Gene triplication, sequence variation, and expression analysis

Oxidation versus carboxamidomethylation of s-s bond in ranid frog peptides: Pro and contra for de novo MALDI-MS sequencing

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