Virtual screening and rational design of antioxidant peptides based on tryptophyllin L structures isolated from the Litoria rubella frog.

Discovery of natural antioxidants has been carried out for decades relying mainly on experimental approaches that are commonly associated with time and cost demanding biochemical assays. The maturation of quantitative structure activity relationship (QSAR) modelling has provided an alternative approach for searching and designing antioxidant compounds with alleviated costs. As a contribution to this approach, this work aimed to establish a fragment-based 3D-QSAR procedure to discover and design potential antioxidants based on tryptophyllin L structures isolated from the red tree frog Litoria rubella.

Antioxidant activities of major tryptophyllin L peptides: A joint investigation of Gaussian-based 3D-QSAR and radical scavenging experiments.

The red tree frog Litoria rubella from Australia has been studied for several decades showing that their dorsal skin glands secrete a number of small peptides containing a Pro-Trp sequence, known as tryptophyllin L peptides. Although peptides from many genera of Australian frogs have been reported to possess a variety of biological activities, the bioactivities of this peptide family have remained to be discovered. In this study, we investigated the antioxidant potency of a number of tryptophyllin L peptides for the first time using a joint statistical and experimental approach in which predictions based on Gaussian three-dimensional quantitative structure-activity relationship (3D-QSAR) models were employed to guide an in vitro experimental investigation.

Negative ion cleavages of (M-H) anions of peptides. Part 3. Post-translational modifications.

It is now 25 years since we commenced the study of the negative-ion fragmentations of peptides and we have recently concluded this research with investigations of the negative-ion chemistry of most post-translational functional groups. Our first negative-ion peptide review (Bowie, Brinkworth, & Dua, 2002) dealt with the characteristic backbone fragmentations and side-chain cleavages from (M-H) ions of underivatized peptides, while the second (Bilusich & Bowie, 2009) included negative-ion backbone cleavages for Ser and Cys and some initial data on some post-translational groups including disulfides. This third and final review provides a brief summary of the major backbone and side chain cleavages outlined before (Bowie, Brinkworth, & Dua, 2002) and describes the quantum mechanical hydrogen tunneling associated with some proton transfers in enolate anion/enolate systems.

The Amyloid Fibril-Forming Properties of the Amphibian Antimicrobial Peptide Uperin 3.5.

The amphibian skin is a vast resource for bioactive peptides, which form the basis of the animals' innate immune system. Key components of the secretions of the cutaneous glands are antimicrobial peptides (AMPs), which exert their cytotoxic effects often as a result of membrane disruption. It is becoming increasingly evident that there is a link between the mechanism of action of AMPs and amyloidogenic peptides and proteins.

The membrane-active amphibian peptide caerin 1.8 inhibits fibril formation of amyloid β1-42.

The amphibian host-defense peptide caerin 1.8 [(1)GLFKVLGSV(10)AKHLLPHVVP(20)VIAEKL(NH2)] inhibits fibril formation of amyloid β 1-42 [(1)DAEFRHDSG(10)YEVHHQKLVF(20)FAEDVGSNKG(30)AIIGLMVGGV(40)VIA] [Aβ42] (the major precursor of the extracellular fibrillar deposits of Alzheimer's disease). Some truncated forms of caerin 1.

Inhibition of HIV infection by caerin 1 antimicrobial peptides.

The major mode of transmission of the human immunodeficiency virus (HIV) is by sexual intercourse. In the effort to halt the spread of HIV, one measure that holds great promise is the development of effective microbicides that can prevent transmission. Previously we showed that several amphibian antimicrobial peptides (AMPs) completely inhibit HIV infection of T cells while maintaining good viability of the T cell targets.

The identification of disulfides in ricin D using proteolytic cleavage followed by negative-ion nano-electrospray ionization mass spectrometry of the peptide fragments.

Rationale: To use negative-ion nano-electrospray ionization mass spectrometry of peptides from the tryptic digest of ricin D, to provide sequence information; in particular, to identify disulfide position and connectivity.

Methods: Negative-ion fragmentations of peptides from the tryptic digest of ricin D was studied using a Waters QTOF2 mass spectrometer operating in MS and MS(2) modes.

Results: Twenty-three peptides were obtained following high-performance liquid chromatography and studied by negative-ion mass spectrometry covering 73% of the amino-acid residues of ricin D.

Structural analysis of calmodulin binding by nNOS inhibitory amphibian peptides.

Calmodulin (CaM) is a ubiquitous protein in nature and plays a regulatory role in numerous biological processes, including the upregulation of nitric oxide (NO) synthesis in vivo. Several peptides that prevent NO production by interacting with CaM have been isolated in the cutaneous secretions of Australian amphibians, and are thought to serve as a defense mechanism against predators. In this work, we probe the mechanism by which three of these peptides, namely, caerin 1.

The investigation of membrane binding by amphibian peptide agonists of CCK2R using (31)P and (2)H solid-state NMR.

It has been proposed that some neuropeptides may be anchored to the cell membranes prior to attaching to the adjacent active sites of transmembrane receptors. The three amphibian skin neuropeptides signiferin 1 [RLCIPYIIPC(OH)] (smooth muscle active and immunomodulator), riparin 1.1 [[RLCIPVIFPC(OH)] (immunomodulator) and rothein 1 [SVSNIPESIGF(OH)] (immunomodulator) act via CCK2 transmembrane receptors.

Fragmentations of [M-H]- anions of peptides containing Ser sulfate. A joint experimental and theoretical study.

Rationale: To determine the negative-ion cleavages from [M-H](-) ions of Ser sulfate-containing peptides using experiment and theory in concert.

Methods: Fragmentations were explored using a Waters QTOF2 mass spectrometer in negative-ion electrospray mode, together with calculations at the CAM-B3LYP/6-311++g(d,p) level of theory. Peptides used in this study were: GS(SO3H)(OH) 1 GS(SO3H)(OCH3) 1a GAVS(SO3H)(OH) 2 GAVS(SO3H)(OCH3) 2a GLS(SO3H)(GVA(OH) 3 GLS(SO3H)GDA(OH) 4 GLS(SO3H)GS(SO3H)A(OH) 5.

Fragmentations of [M-H]- anions of peptides containing tyrosine sulfate. Does the sulfate group rearrange? A joint experimental and theoretical study.

Rationale: To investigate the fragmentations in the negative-ion electrospray mass spectra of peptides containing tyrosine sulfate.

Methods: Possible fragmentation mechanisms were explored using a Waters QTOF2 tandem mass spectrometer in concert with calculations at the CAM-B3LYP/6-311++g(d,p) level of theory.

Results: The major negative ion formed in the ESI-MS of peptides containing tyrosine sulfate is [(M-H)-SO3](-) and this process normally yields the base peak of the spectrum.

Negative ion fragmentations of disulfide-containing cross-linking reagents are competitive with aspartic acid side-chain-induced cleavages.

Rationale: It has been shown that the disulfide moiety in the chemical cross-linking reagent dithiobis(succinimidyl)propionate (DSP), which is similar in structure to the natural cystine disulfide, cleaves preferentially to the peptide backbone in the negative ion mode. However, the tandem mass (MS/MS) spectra of peptides in the negative ion mode are often dominated by products arising from low-energy, side-chain-induced processes, which may compete with any facile cross-linker fragmentations and complicate identification of chemical cross-links in a complex mixture.

Methods: Two disulfide-containing crosslinking reagents similar to DSP, but with varying spacer arm lengths, were synthesized and the MS/MS spectra of several model peptides cross-linked with these reagents were investigated.

Structural and activity changes in three bioactive anuran peptides when Asp is replaced by isoAsp.

The Asp and isoAsp isomers of three bioactive peptides, Crinia angiotensin 11 [APGDRIYHPF(OH)], uperin 1.1 [pEADPNAFYGLM(NH(2))] and citropin 1.1 [GLFDVIKKVASVIGGL(NH(2))] were tested for changes in (i) susceptibility towards proteolytic cleavage, (ii) activity (smooth muscle activity for Crinia angiotensin 11 and uperin 1.

Backbone fragmentations of [M-H]- anions from peptides. Reinvestigation of the mechanism of the beta prime cleavage.

Rationale: An experimental study has shown that the structure of a β' ion proposed earlier is incorrect. Backbone cleavage β' anions have structures R(NH(-)) from systems [[RNHCH(X)CONHCH(Y)CO(2)H (or C-terminal CONH(2))-H](-) (where R is the rest of the peptide molecule and X and Y represent the α side chains of the individual amino acid residues).

Methods: Ab initio calculations were carried out at the CAM-B3LYP/6-311++g(d,p) level of theory.

Host-defense peptides of Australian anurans. Part 2. Structure, activity, mechanism of action, and evolutionary significance.

A previous review summarized research prior to 2004 carried out on the bioactive host-defense peptides contained in the skin secretions of Australian anurans (frogs and toads). This review covers the extension of that research from 2004 to 2012, and includes membrane-active peptides (including antibacterial, anticancer, antifungal and antiviral peptides) together with the mechanisms by which these peptides interact with model membranes, peptides that may be classified as "neuropeptides" (including smooth muscle active peptides, opioids and immunomodulators) and peptides which inhibit the formation of nitric oxide from neuronal nitric oxide synthase. The review discusses the outcome of cDNA sequencing of signal-spacer-active peptides from an evolutionary viewpoint, and also lists those peptides for which activities have not been found to this time.

A negative ion mass spectrometry approach to identify cross-linked peptides utilizing characteristic disulfide fragmentations.

Chemical cross-linking combined with mass spectrometry (MS) is an analytical tool used to elucidate the topologies of proteins and protein complexes. However, identification of the low abundance cross-linked peptides and modification sites amongst a large quantity of proteolytic fragments remains challenging. In this work, we present a strategy to identify cross-linked peptides by negative ion MS for the first time.

Pheromones, attractants and other chemical cues of aquatic organisms and amphibians.

This review covers the subject of pheromones, attractants and other chemical cues of aquatic invertebrates, fishes and amphibians (including salamanders and anurans). Major topics include the sex pheromones of gastropods, salamanders and a giant tree frog, and the conspecific attraction of sperm to ova of some of the organisms and animals described in this review.

Hydrogen tunnelling influences the isomerisation of some small radicals of interstellar importance. A theoretical investigation.

Hydrogen atom isomerisations within five radical systems (i.e., CH(3)˙NH/˙CH(2)NH; CH(3)O˙/˙CH(2)OH; ˙CH(2)SH/CH(3)S˙; CH(3)CO(2)˙/˙CH(2)CO(2)H; and HOCH(2)CH(2)O˙/HO˙CHCH(2)OH) have been studied via quantum-mechanical hydrogen tunnelling through reaction barriers.

Can cytosine, thymine and uracil be formed in interstellar regions? A theoretical study.

This theoretical study investigates possible synthetic routes to cytosine, uracil and thymine in the gas phase from precursor molecules that have been detected in interstellar media. Studies at the CCSD(T)/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory suggest that: The reactions between :CCCNH and :CCCO with monosolvated urea may constitute viable interstellar syntheses of cytosine and uracil. No low energy equilibration between cytosine and uracil has been demonstrated.

Can collision-induced negative-ion fragmentations of [M-H](-) anions be used to identify phosphorylation sites in peptides?

A joint experimental and theoretical investigation of the fragmentation behaviour of energised [M-H](-) anions from selected phosphorylated peptides has confirmed some of the most complex rearrangement processes yet to be reported for peptide negative ions. In particular: pSer and pThr (like pTyr) may transfer phosphate groups to C-terminal carboxyl anions and to the carboxyl anion side chains of Asp and Glu, and characteristic nucleophilic/cleavage reactions accompany or follow these rearrangements. pTyr may transfer phosphate to the side chains of Ser and Thr.

Diagnostic di- and triphosphate cyclisation in the negative ion electrospray mass spectra of phosphoSer peptides.

It has been shown previously that [M-H](-) anions of small peptides containing two phosphate residues undergo cyclisation of the phosphate groups, following collision-induced dissociation (CID), to form a characteristic singly charged anion A (H3P2O7(-), m/z 177). In the present study it is shown that the precursor anions derived from the diphosphopeptides of caerin 1.1 [GLLSVLGSVAKHVLPHVVPVIAEHL(NH2)] and frenatin 3 [GLMSVLGHAVGNVLGGLFKPKS(OH)] also form the characteristic product anion A (m/z 177).

Diagnostic cyclisation reactions which follow phosphate transfer to carboxylate anion centres for energised [M-H]- anions of pTyr-containing peptides.

The low-energy negative ion phosphoTyr to C-terminal -CO(2)PO(3)H(2) rearrangement occurs for energised peptide [M-H](-) anions even when there are seven amino acid residues between the pTyr and C-terminal amino acid residues. The rearranged C-terminal -CO(2)PO(2)H(O(-)) group effects characteristic S(N)i cyclisation/cleavage reactions. The most pronounced of these involves the electrophilic central backbone carbon of the penultimate amino acid residue.

An unusual kynurenine-containing opioid tetrapeptide from the skin gland secretion of the Australian red tree frog Litoria rubella. Sequence determination by electrospray mass spectrometry.

The Kyn-containing peptide FP-Kyn-L(NH(2)) is an unusual minor component of the skin peptide profile of the Australian red tree frog Litoria rubella collected from an area within a 20 kilometre radius of Alice Springs in central Australia. The structure was determined by electrospray mass spectrometry and synthesis. The major component of the skin secretion is the analogous tryptophyllin peptide FPWL(NH(2)).

Histidine-containing host-defence skin peptides of anurans bind Cu2+. An electrospray ionisation mass spectrometry and computational modelling study.

Anuran peptides which contain His, including caerin 1.8 (GLFKVLGSVAKHLLPHVVPVIAEKL-NH(2)), caerin 1.2 (GLLGVLGSVAKHVLPHVVPVIAEHL-NH(2)), Ala(15) maculatin 1.

Studies of cyclization reactions of linear cumulenes and heterocumulenes using the neutralization-reionization procedure and/or ab initio calculations.

A number of linear cumulenes and heterocumulenes have been made by charge stripping of anions of known bond connectivity in the source of a mass spectrometer. Some of these reactive molecules have been identified in interstellar molecular clouds. The structures of these neutrals may be investigated by reionization to a decomposing positive ion [the neutralization-reionization technique ((-)NR(+))], and/or by ab initio calculations.