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. A force field and a Gaussian 3D-QSAR model were built to screen for potential antioxidants from tripeptide fragments covering all sequences of tryptophyllin L database. Among those, PWY(NH2 ) corresponding tryptophyllin L 4.1 was predicted to have the highest 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical cation (ABTS+ ·) scavenging capability. Two newly designed peptides PYW and PYW(NH2 ) together with PWY(NH2 ), tryptophyllin L 4.1, and the reference peptide PWY were synthesized and subjected to two antioxidant assays including ABTS scavenging and ferric reducing antioxidant power assays. Although the experimental TEAC values of the five peptides were roughly similar to those from predictions, the activity order was not in agreement with the predictions. The dissimilarities were accounted by the difference in the experimental procedures, the deviation of modelling regression, and the synergetic effect of structural and experimental features. The ABTS radical scavenging assays revealed that all the tested peptides were strong ABTS+ · scavengers with the antioxidant capabilities approximately twice as high as trolox and higher than glutathione. The ferric reducing activities of the peptides were, on the other hand, much weaker than that of trolox suggesting different antioxidant mechanisms inserted by trolox and the peptides. This work was a demonstration that 3D-QSAR methods can be employed in conjunction with experimental methods to effectively detect and design antioxidant peptides.

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 review then describes, in more depth, the negative-ion cleavages of the post-translational groups Kyn, isoAsp, pyroglu, disulfides, phosphates, and sulfates. Particular emphasis is devoted to disulfides (both intra- and intermolecular) and phosphates because of the extensive and spectacular anion chemistry shown by these groups. © 2016 Wiley Periodicals, Inc. Mass Spec Rev.

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. In this work, we demonstrate that the broad-spectrum amphibian AMP uperin 3.5, which has a random-coil structure in solution but adopts an α-helical structure in membrane-like environments, forms amyloid fibrils rapidly in solution at neutral pH. These fibrils are cytotoxic to model neuronal cells in a similar fashion to those formed by the proteins implicated in neurodegenerative diseases. The addition of small quantities of 2,2,2-trifluoroethanol accelerates fibril formation by uperin 3.5, and is correlated with a structural stabilisation induced by this co-solvent. Uperin 3.5 fibril formation and the associated cellular toxicity are inhibited by the polyphenol (-)-epigallocatechin-3-gallate (EGCG). Furthermore, EGCG rapidly dissociates fully formed uperin 3.5 fibrils. Ion mobility-mass spectrometry reveals that uperin 3.5 adopts various oligomeric states in solution. Combined, these observations imply that the mechanism of membrane permeability by uperin 3.5 is related to its fibril-forming properties.

The membrane-active amphibian peptide caerin 1.8 inhibits fibril formation of amyloid ß1-42.

The amphibian host-defense peptide caerin 1.8 [(1)GLFKVLGSV(10)AKHLLPHVVP(20)VIAEKL(NH2)] inhibits fibril formation of amyloid ß 1-42 [(1)DAEFRHDSG(10)YEVHHQKLVF(20)FAEDVGSNKG(30)AIIGLMVGGV(40)VIA] [Aß42] (the major precursor of the extracellular fibrillar deposits of Alzheimer's disease). Some truncated forms of caerin 1.8 also inhibit fibril formation of Aß42. For example, caerin 1.8 (1-13) [(1)GLFKVLGSV(10)AKHL(NH2) and caerin 1.8 (22-25) [KVLGSV(10)AKHLLPHVVP(20)VIAEKL(NH2)] show 85% and 75% respectively of the inhibition activity of the parent caerin 1.8. The synthetic peptide KLVFFKKKKKK is a known inhibitor of Aß42 fibril formation, and was used as a standard in this study. Caerin 1.8 is the more effective fibril inhibitor. IC50 values (± 15%) are caerin 1.8 (75 µM) and KLVFFKKKKKK (370 µM). MALDI mass spectrometry shows the presence of a small peak corresponding to a protonated 1:1 adduct [caerin 1.8/Aß42]H(+). Molecular dynamics simulation suggests that both hydrogen bonding and hydrophobic interactions between Aß42 and caerin 1.8 facilitate the formation of a 1:1 complex in water. Fibril formation from Aß42 has been proposed to be based around the (16)KLVF(20)F region of Aß42; this region in the 1:1 complex is partially blocked from attachment of a further molecule of Aß42.

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. These peptides also inhibited the transfer of HIV by dendritic cells (DCs) to T cells when added up to 8h after virus exposure. Here we report on the anti-HIV activity of 18 additional structurally related caerin 1 family peptides in comparison with our previous best candidate caerin 1.9. Nine peptides were equally effective or more effective in the inhibition of T cell infection and disruption of the HIV envelope as caerin 1.9. Of those nine peptides, three peptides (caerin 1.2, caerin 1.10, and caerin 1.20) exhibited excellent inhibition of HIV infectivity at low concentrations (12-25µM) and limited toxicity against target T cells and endocervical epithelial cells. There was a direct correlation between the effectiveness of the peptides in disruption of the viral envelope and their capacity to inhibit infection. Thus, several additional caerin 1 family peptides inhibit HIV infection have limited toxicity for vaginal epithelial cells, and would be good candidates for inclusion in microbicide formulations.

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. Five disulfide-containing peptides were identified, three intermolecular and two intramolecular disulfide-containing peptides. The [M-H](-) anions of the intermolecular disulfides undergo facile cleavage of the disulfide units to produce fragment peptides. In negative-ion collision-induced dissociation (CID) these source-formed anions undergo backbone cleavages, which provide sequencing information. The two intramolecular disulfides were converted proteolytically into intermolecular disulfides, which were identified as outlined above. CONCLUSIONS: The positions of the five disulfide groups in ricin D may be determined by characteristic negative-ion cleavage of the disulfide groups, while sequence information may be determined using the standard negative-ion backbone cleavages of the resulting cleaved peptides. Negative-ion mass spectrometry can also be used to provide partial sequencing information for other peptides (i.e. those not containing Cys) using the standard negative-ion backbone cleavages of these peptides.

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 1.8, dahlein 5.6, and a synthetic modification of citropin 1.1, interact with CaM to inhibit NO signaling. Isothermal titration calorimetry was used to determine thermodynamic parameters of the binding interactions and revealed that all the peptides bind to CaM in a similar fashion, with the peptide encapsulated between the two lobes of CaM. Ion mobility-mass spectrometry was used to investigate the changes in collision cross section that occur as a result of complexation, providing additional evidence for this binding mode. Finally, nuclear magnetic resonance spectroscopy was used to track chemical shift changes upon binding. The results obtained confirm that these complexes adopt canonical collapsed structures and demonstrate the strength of the interaction between the peptides and CaM. An understanding of these molecular recognition events provides insights into the underlying mechanism of the amphibian host-defense system.

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. A combination of (31)P and (2)H solid state NMR studies of each of these three peptides in eukaryotic phospholipid models at 25°C shows that rothein 1 does not interact with the membrane at all. In contrast, both of the cyclic disulfides signiferin 1 and riparin 1.1 interact with phospholipid head groups and partially penetrate into the upper leaflet of the model bilayer, but to different extents. These interactions are not sufficiently effective to cause disruption of the lipid bilayer since the peptides are not antimicrobial, anticancer, antifungal nor active against enveloped viruses.

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. RESULTS: Previously, it has been shown that a peptide containing a Tyr sulfate group shows [(M-H)(-) -SO3] as the base peak. Only a small peak was observed corresponding to HOSO3(-) (formed following rearrangement of the sulfate). A Ser sulfate-containing peptide, in contrast, shows pronounced peaks due to cleavage product anions [(M-H)(-)-SO3] and HOSO3(-). Theoretical calculations at the CAM-B3LYP/6-311++g(d,p) level of theory suggest that rearrangement of a Ser sulfate to give C-terminal CO2SO3H is energetically unfavourable in comparison with fragmentation of the intact Ser sulfate to yield [(M-H)(-)-SO3] and HOSO3(-). [(M-H)(-)-H2SO4] anions are not observed in the spectra of peptides containing Ser sulfate, presumably because HOSO3(-) is a relatively weak gas-phase base (ΔGacid = 1265 kJ mol(-1)). CONCLUSIONS: Experimental and theoretical data suggest that [(M-H)(-)-SO3] and HOSO3(-) product anions (from a peptide with a C-terminal Ser sulfate) are formed from the serine sulfate anion accompanied by specific proton transfer. CID MS/MS/MS data for an [(M-H)(-)-SO3] ion of an underivatised sulfate-containing peptide will normally allow the determination of the amino acid sequence of that peptide. The one case we have studied where that is not the case is GLS(SO3H)GDA(OH), where the peptide contains Ser sulfate and Asp, where the diagnostic Asp cleavages are competitive with the Ser sulfate cleavages.

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. The basic backbone cleavages of [(M-H)-SO3](-) allowed the sequence of the peptide to be determined. Rearrangement reactions involving the formation of HOSO3(-) and [(M-H)-H2SO4](-) yielded minor peaks with relative abundances ≤ 10% and ≤ 2%, respectively. CONCLUSIONS: The mass spectra of the [M-H](-) and [(M-H)-SO3](-) anions of peptides containing tyrosine sulfate allowed the position of the tyrosine sulfate group to be determined, together with the amino acid sequence of the peptide.

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. Theoretical calculations were used to describe the energetics of the cross-linker fragmentations as well as several low-energy side-chain-induced fragmentations which compete with disulfide cleavages. RESULTS: Altering the spacer arm length of the cross-linker, such that there is one methylene group less than in DSP, results in a more facile cleavage process, whilst the opposite is true when a methylene group is added. Of the low-energy side-chain-induced fragmentations studied, only those from aspartic acid compete significantly with those of the cross-linker disulfide. CONCLUSIONS: Low-energy cleavage processes from aspartic acid that compete with cross-linker fragmentations occur in the negative ion MS/MS spectra of the cross-linked peptides, irrespective of the spacer arm length. Other fragmentation pathways do not significantly interfere with low-energy disulfide cleavage, making the presence of additional product ions in the MS/MS spectrum diagnostic for the presence of aspartic acid.

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 1.1 isomers, and antimicrobial activity for the two isomers of citropin 1.1), and (iii) 3D structures in water, trifluoroethanol-d(3)/water (1:1) and DPC micelles as determined by 2D nuclear magnetic resonance spectroscopy. Proteolytic cleavage with trypsin was identical for each pair of Asp/isoAsp isomers. Cleavage with chymotrypsin was the same for the Crinia angiotensin and uperin 1.1 isomeric pairs, but different for the two Asp/isoAsp citropin 1.1 isomers. Chymotrypsin cleaved at Phe3 (adjacent to Asp4) for citropin 1.1, but not at Phe3 (adjacent to isoAsp4) for isoAsp citropin 1.1. The smooth muscle activity of the isoAsp isomer of Crinia angiotensin 11 was less than that of the Asp isomer. The smooth muscle activity of isoAsp3-uperin 1.1 is greater than that of the Asp isomer at low concentration (<10(-9)M) but no different from the Asp isomer at concentrations>10(-9) M. Citropin 1.1 is a wide-spectrum antibiotic against Gram positive organisms, while the isoAsp isomer is inactive against the test pathogens Staphylococcus aureus and Bacillus subtilis. The observed changes in activity are accompanied by changes in the 3D structures of isomers as determined by 2D nuclear magnetic resonance spectroscopy.

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.

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 ß' ion proposed earlier is incorrect. Backbone cleavage ß' 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. CONCLUSIONS: The calculations suggest that RNH(-) ions are formed by S(N)i cyclisation processes involving either (i) the C-terminal CO(2)(-) or C-terminal [CONH](-) as appropriate, or (ii) an enolate ion [-NHC(-)(Y)-] cyclising at the backbone CH of the -CH(X)- group. Concomitant C-N bond cleavage then liberates an RNH(-) ion, processes which can occur along the peptide backbone.

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. This approach is based around the facile cleavages of disulfide bonds in the negative mode, and allows identification of cross-linked products based on their characteristic fragmentations. MS(3) analysis of the cross-linked peptides allows for their sequencing and identification, with residue specific location of cross-linking sites. We demonstrate the applicability of the commercially available cystine based cross-linking reagent dithiobis(succinimidyl) propionate (DSP) and identify cross-linked peptides from ubiquitin. In each instance, the characteristic fragmentation behavior of the cross-linked species is described. The data presented here indicate that this negative ion approach may be a useful tool to characterize the structures of proteins and protein complexes, and provides the basis for the development of high throughput negative ion MS chemical cross-linking strategies.

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. The reaction rates including hydrogen tunnelling effects have been calculated for these gas phase reactions at temperatures from 300 K to 0 K using Wenzel-Kramers-Brillouin (WKB) and Eckart methods. The Eckart method has been found to be unsatisfactory for the last two systems listed above, because it significantly underestimates the width of the reaction barriers for the interconversions. The calculations at all-electron CCSD(T)/CBS level of theory indicate that the barriers for all reactions (forward and reverse) are greater than 100 kJ mol(-1), meaning that the chemical reactivity of the reactants is limited in the absence of hydrogen tunnelling. Hydrogen tunnelling, in some cases, enhance rates of reaction by more than 100 orders of magnitude at low temperature, and around 2 orders of magnitude at room temperature, compared to results obtained from canonical variational transition state theory. Tunnelling corrected reaction rates suggest that some of these isomerisation reactions may occur in interstellar media.

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. The interaction of :CH(2) with the 5 C-H bond of uracil may form thymine in an energetically favourable reaction, but competing reactions where :CH(2) reacts with double bonds and other CH and NH bonds of uracil, reduce the effectiveness of this synthesis. The reaction between the hydrated propional enolate anion and isocyanic acid may produce thymine, in a reaction sequence where ΔG(reaction)(298 K) is -22 kJ mol(-1) and the maximum energy requirement (barrier to the first transition state) is only 47 kJ mol(-1).

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. The reverse reaction, namely transfer of a phosphate group from pSer or pThr to Tyr, is energetically unfavourable in comparison. pSer can transfer phosphate to a non-phosphorylated Ser. The non-rearranged [M-H](-) species yields more abundant product anions than its rearranged counterpart. If a peptide containing any or all of Ser, Thr and Tyr is not completely phosphorylated, negative-ion cleavages can determine the number of phosphated residues, and normally the positions of Ser, Thr and Tyr, but not which specific residues are phosphorylated. This is in accord with comments made earlier by Lehmann and coworkers.

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. This reaction is aided by the intermediacy of an H-bonded intermediate in which the nucleophilic and electrophilic reaction centres are held in proximity in order for the S(N)i cyclisation/cleavage to proceed. The ΔG(reaction) is +184 kJ mol(-1) with the barrier to the S(N)i transition state being +240 kJ mol(-1) at the HF/6-31 + G(d)//AM1 level of theory. A similar phosphate rearrangement from pTyr to side chain CO(2)(-) (of Asp or Glu) may also occur for energised peptide [M-H](-) anions. The reaction is favourable: ΔG(reaction) is -44 kJ mol(-1) with a maximum barrier of +21 kJ mol(-1) (to the initial transition state) when Asp and Tyr are adjacent. The rearranged species R(1)-Tyr-NHCH(CH(2)CO(2)PO(3)H(-))COR(2) (R(1) = CHO; R(2) = OCH(3)) may undergo an S(N)i six-centred cyclisation/cleavage reaction to form the product anion R(1)-Tyr(NH(-)). This process has a high energy requirement [ΔG(reaction) = +224 kJ mol(-1), with the barrier to the S(N)i transition state being +299 kJ mol(-1)].