Self-Assembled Peptide Nanofibers with Voltage-Regulated Inverse Photoconductance.

Inverse photoconductance is an uncommon phenomenon observed in selective low-dimensional materials, in which the electrical conductivity of the materials decreases under light illumination. The unique material property holds great promise for biomedical applications in photodetectors, photoelectric logic gates, and low-power nonvolatile memory, which remains a daunting challenge. Especially, tunable photoconductivity for biocompatible materials is highly desired for interfacing with biological systems but is less explored in organic materials. Here, we report nanofibers self-assembled with cyclo-tyrosine-tyrosine (cyclo-YY) having voltage-regulated inverse photoconductance and photoconductance. The peptide nanofibers can be switched back and forth by a bias voltage for imitating biological sensing in artificial vision and memory devices. A peptide optoelectronic resistive random access memory (PORRAM) device has also been fabricated using the nanofibers that can be electrically switched between long-term and short-term memory. The underlying mechanism of the reversible photoconductance is discussed in this paper. Due to the inherent biocompatibility of peptide materials, the reversible photoconductive nanofibers may have broad applications in sensing and storage for biotic and abiotic interfaces.

Radiolytic Oxidation of Two Inverse Dipeptides, Methionine-Valine and Valine-Methionine: A Joint Experimental and Computational Study.

The two inverse peptides methionine-valine (Met-Val) and valine-methionine (Val-Met) are investigated in an oxidative radiolysis process in water. The OH radical yields products with very different absorption spectra and concentration effects: Met-Val yields one main product with a band at about 400 nm and other products at higher energies; there is no concentration effect. Val-Met yields at least three products, with a striking concentration effect. Molecular simulations are performed with a combination of the Monte Carlo, density functional theory, and reaction field methods. The simulation of the possible transients enables an interpretation of the radiolysis: (1) Met-Val undergoes an H atom uptake leaving mainly a neutral radical with a 2-center-3-electron (2c-3e) SN bond, which cannot dimerize. Other radicals are present at higher energies. (2) Val-Met undergoes mainly an electron uptake leaving a cation monomer with a (2c-3e) SO bond and a cation dimer with a (2c-3e) SS bond. At higher energies, neutral radicals are possible. This cation monomer can transfer a proton toward a neutral peptide, leaving a neutral radical.

Epimerization of Alanyl-Alanine Induced by γ-Rays Irradiation in Aqueous Solutions.

Living organisms have homochiral L-amino acids in proteins and homochiral D-mononucleotides in nucleic acids. The chemical evolutionary process to protein homochirality has been discussed for many years. Although many scenarios have been proposed for homochirality in the monomeric compounds, homochirality in amino acids and mononucleotides does not always guarantee homochirality in polypeptides and polynucleotides. Integrated scenarios containing the pathways from monomer to polymer should be proposed because in the pathways oligomers and polymers as well as monomers racemize (or epimerize), degrade, and condense. This research addresses epimerization and degradation of dipeptides under γ-rays irradiation by a cobalt-60 (60Co) radiation source. The different rate constants of epimerization between diastereomeric dipeptides in the research suggest that the potential pathway toward homochirality could be much more complex.

Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features.

Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer.

Differential laser-induced perturbation Raman spectroscopy: a comparison with Raman spectroscopy for analysis and classification of amino acids and dipeptides.

Differential-laser induced perturbation spectroscopy (DLIPS) is a new spectral analysis technique for classification and identification, with key potential applications for analysis of complex biomolecular systems. DLIPS takes advantage of the complex ultraviolet (UV) laser­material interactions based on difference spectroscopy by coupling low intensity UV laser perturbation with a traditional spectroscopy probe. Here, we quantify the DLIPS performance using a Raman scattering probe in classification of basic constituents of collagenous tissues, namely, the amino acids glycine, L-proline, and L-alanine, and the dipeptides glycine­glycine, glycine­alanine and glycine­proline and compare the performance to a traditional Raman spectroscopy probe via several multivariate analyses. We find that the DLIPS approach yields an ~40% improvement in discrimination among these tissue building blocks. The effects of the 193-nm perturbation laser are further examined by assessing the photodestruction of targeted material molecular bonds. The DLIPS method with a Raman probe holds promise for future tissue diagnosis, either as a stand-alone technique or as part of an orthogonal biosensing scheme.

Long-lived coherences: improved dispersion in the frequency domain using continuous-wave and reduced-power windowed sustaining irradiation.

Long-lived coherences (LLC's) are detectable magnetisation modes with favourable relaxation times that translate as sharp resonances upon Fourier transform. The frequency domain of LLC's was previously limited to the range of J-couplings within pairs of homonuclear spins. LLC evolution at high magnetic fields needs to be sustained by radio-frequency irradiation. We show that LLC-based spectral dispersion can be extended beyond the J-couplings domain using adapted carrier offsets and introduce a new reduced-power sustaining method to preserve LLC's within the required range of offsets. Spectral resolution is enhanced as the natively narrow lines of LLC's are further dispersed, making them potential probes for the study of biomolecules featuring strong resonance overlap and for media where NMR spectroscopy is commonly hindered by line broadening.

Removal of amino acid, peptide and protein hydroperoxides by reaction with peroxiredoxins 2 and 3.

Prxs (peroxiredoxins) are a ubiquitous family of cysteine-dependent peroxidases that react rapidly with H2O2 and alkyl hydroperoxides and provide defence against these reactive oxidants. Hydroperoxides are also formed on amino acids and proteins during oxidative stress, and they too are a potential cause of biological damage. We have investigated whether Prxs react with amino acid, peptide and protein hydroperoxides, and whether the reactions are sufficiently rapid for these enzymes to provide antioxidant protection against these oxidants. Isolated Prx2, which is a cytosolic protein, and Prx3, which resides within mitochondria, were reacted with a selection of hydroperoxides generated by γ-radiolysis or singlet oxygen, on free amino acids, peptides and proteins. Reactions were followed by measuring the accumulation of disulfide-linked Prx dimers, via non-reducing SDS/PAGE, or the loss of the corresponding hydroperoxide, using quench-flow and LC (liquid chromatography)/MS. All the hydroperoxides induced rapid oxidation, with little difference in reactivity between Prx2 and Prx3. N-acetyl leucine hydroperoxides reacted with Prx2 with a rate constant of 4 × 10(4) M-1 · s-1. Hydroperoxides present on leucine, isoleucine or tyrosine reacted at a comparable rate, whereas histidine hydroperoxides were ~10-fold less reactive. Hydroperoxides present on lysozyme and BSA reacted with rate constants of ~100 M-1 · s-1. Addition of an uncharged derivative of leucine hydroperoxide to intact erythrocytes caused Prx2 oxidation with no concomitant loss in GSH, as did BSA hydroperoxide when added to concentrated erythrocyte lysate. Prxs are therefore favoured intracellular targets for peptide/protein hydroperoxides and have the potential to detoxify these species in vivo.

Mechanisms of UV photodissociation of small protonated peptides.

Photofragmentation of protonated dipeptides by 263 nm photons is investigated with an experimental technique based on the detection in coincidence of the ionic and neutral fragments. With this method, it is possible to determine whether the fragmentation takes place in one or several steps. The timing of these steps can also be evaluated. The interpretation of the various fragmentation pathways is tentatively developed along the same line as that previously proposed for tryptophan. The fragmentation can be explained by two types of mechanisms: internal conversions and direct fragmentations triggered by the migration of the photoactive electron on positive charged sites or on oxygen sites.

Phenyl radical-induced damage to dipeptides.

Laser-induced acoustic desorption (LIAD) incorporated with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) has been utilized to investigate phenyl radical-induced damage to dipeptides in the gas phase. On the basis of the product branching ratios measured for the reactions of two different positively charged phenyl radicals with 17 different dipeptides, the overall order of susceptibility to attack of the different sites in the dipeptides was determined to be heteroaromatic side chain approximately = S atom in SCH(3) group > H atom in SH group > H atom in CH group > aromatic side chain > S atom in SH group > NH(2) in side chain > N-terminal NH(2) > COOH in side chain approximately = C-terminal COOH. The amino acid sequence also influences the selectivity of these reactions. As expected, the ability of a phenyl radical to damage dipeptides increases as the electrophilicity of the phenyl radical increases.

Radiolytic one-electron reduction characteristics of tyrosine derivative caged by 2-oxopropyl group.

We employed X-irradiation to activate a caged amino acid with a 2-oxoalkyl group. We designed and synthesized tyrosine derivative caged by a 2-oxoalkyl group (Tyr(Oxo)) to evaluate its radiolytic one-electron reduction characteristics in aqueous solution. Upon hypoxic X-irradiation, Tyr(Oxo) released a 2-oxopropyl group to form the corresponding uncaged tyrosine. In addition, radiolysis of dipeptides containing Tyr(Oxo) revealed that the efficiency of radiolytic removal of 2-oxopropyl group increased significantly by the presence of neighboring aromatic amino acids.

Photolytic control and infrared probing of amide I mode in the dipeptide backbone-caged with the 4,5-dimethoxy-2-nitrobenzyl group.

Alanine dipeptide analog 1 backbone-caged with a photolabile linker, 4,5-dimethoxy-2-nitrobenzyl (DmNb), was synthesized. UV-pulse-induced photochemical reaction of 1 was monitored by Fourier transform IR absorption spectroscopy under a steady-state condition or in a fast-scan mode. Upon photolysis of 1, the amide I band is changed from a doublet to a singlet with concomitant line shape changes of several IR bands. The change of the amide I band is directly associated with the photocleavage of the covalent N-C bond connecting the backbone amide of 2 to DmNb. Therefore, IR spectroscopy is useful for directly probing the photocleavage of backbone-caged peptide 1 and the concurrent release of native peptide 2. In contrast, UV-vis spectroscopy probing the irradiation-induced structural change of the 2-nitrobenzyl moiety itself may not provide a clue directly relevant to the photocleavage of such N-C bond. Time-resolved IR spectra recorded in a fast-scan mode after pulsed UV irradiation of 1 reveal that such photocleavage occurs at least faster than a few seconds of our instrumental time resolution.

Usefulness of spectroscopy for biomedical engineering.

Modifications of phenylalanine amino acid after its exposure to near-infrared (NIR) radiation have been investigated using ATRFTIR (Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy). The process of amino acid aggregation after its exposure to NIR has been observed. A possible mechanism of amino acid dimer formation has been proposed with the help of theoretical calculations of quantum mechanics (MP2 and B3LYP/6-31 G* level) using the GAUSSIAN 03 package. The usefulness of spectroscopy for biomedical engineering is discussed. ATR-FTIR appears to be a powerful tool for measuring tissue damage in aqueous environments.

Statistical vs. non-statistical deactivation pathways in the UV photo-fragmentation of protonated tryptophan-leucine dipeptide.

The excited state dynamics of protonated tryptophan-leucine ions WLH+, generated in an electrospray source, is investigated by photo-induced fragmentation in the gas phase, using femtosecond laser pulses. Two main features arise from the experiment. Firstly, the initially excited pipi* state decays very quickly with 2 time constants of 1 and 10 ps. Secondly, the transient signals recorded on different fragments are not the same which indicates two competing primary fragmentation processes. One involves a direct dissociation from the excited state that gives evidence for a non-statistical deactivation path. The other is attributed to a statistical decay following internal conversion to the ground electronic surface.

Excited state dynamics and fragmentation channels of the protonated dipeptide H2N-Leu-Trp-COOH.

The excited state dynamics of the isolated and protonated peptide H(2)N-Leu-Trp-COOH are analyzed by fs pump-probe spectroscopy. The peptides are brought into the gas phase by electrospray ionization, and fs pump-probe excitation is detected by fragment ion formation. The pump laser addressed the excited pipi* state of the indole chromophore of the amino acid tryptophan. The subsequent excited state dynamics agreed with a biexponential decay with time constants of 500 fs and 10 ps. This is considerably shorter than the lifetime of neutral tryptophan in solution and in proteins, but similar to isolated, protonated tryptophan. Several models are discussed to explain the experimental results but the detailed quenching mechanism remains unresolved.

Rose Bengal-sensitized photooxidation of the dipeptides L-tryptophyl-L-phenylalanine, L-tryptophyl-L-tyrosine and L-tryptophyl-L-tryptophan: kinetics, mechanism and photoproducts.

The Rose Bengal-sensitized photooxidations of the dipeptides l-tryptophyl-l-phenylalanine (Trp-Phe), l-tryptophyl-l-tyrosine (Trp-Tyr) and l-tryptophyl-l-tryptophan (Trp-Trp) have been studied in pH 7 water solution using static photolysis and time-resolved methods. Kinetic results indicate that the tryptophan (Trp) moiety interacts with singlet molecular oxygen (O(2)((1)Delta(g))) both through chemical reaction and through physical quenching, and that the photooxidations can be compared with those of equimolecular mixtures of the corresponding free amino acids, with minimum, if any, influence of the peptide bond on the chemical reaction. This is not a common behavior in other di- and polypeptides of photooxidizable amino acids. The ratio between chemical (k(r)) and overall (k(t)) rate constants for the interaction O(2)((1)Delta(g))-dipeptide indicates that Trp-Phe and Trp-Trp are good candidates to suffer photodynamic action, with k(r)/k(t) values of 0.72 and 0.60, respectively (0.65 for free Trp). In the case of Trp-Tyr, a lower k(r)/k(t) value (0.18) has been found, likely as a result of the high component of physical deactivation of O(2)((1)Delta(g)) by the tyrosine moiety. The analysis of the photooxidation products shows that the main target for O(2)((1)Delta(g)) attack is the Trp group and suggests a much lower accumulation of kynurenine-type products, as compared with free Trp. This is possibly because of the occurrence of another accepted alternative pathway of oxidation that gives rise to 3a-oxidized hydrogenated pyrrolo[2,3-b]indoles.

Microwave enhanced Akabori reaction for peptide analysis.

The Akabori reaction, devised in 1952 for the identification of C-terminus amino acids, involves the heating of a linear peptide in the presence of anhydrous hydrazine in a sealed tube for several hours. We report here a modified Akabori reaction that rapidly identifies the C-terminus amino acid in a polypeptide including its amino acid sequence information at both the C-terminus and the N-terminus. This modified methodology demonstrates the fundamentals of microwave chemistry applied to bioanalytical problems. In this modified process, hydrazinolysis has been accelerated by the application of microwave irradiation. In our reaction, the linear peptide and hydrazine solution, contained in a loosely covered conical flask, was exposed to a few minutes of irradiation using an unmodified domestic microwave oven. While the classical Akabori reaction required several hours, the microwave assisted reaction takes just minutes. If dimethyl sulfoxide is added to dilute the reaction mixture, the process is retarded enough to allow aliquots of the reaction mixture to be drawn every few minutes over a period of about an hour in order to study the progress of hydrazinolysis. Reaction products were monitored by mass spectrometry-primarily FAB-MS. In addition to providing sequence information, the microwave enhanced Akabori reaction quickly detects the presence of arginine (Arg) by converting each Arg to ornithine (Orn). Furthermore, certain amino acids, containing beta-SH, CO2H, and CONH2 groups in their side chain, are susceptible to modification by hydrazine, thereby, providing rapid confirmation of the presence of these amino acid residues. In these preliminary studies, the following oligopeptides were analyzed to demonstrate the effectiveness of our approach; the dipeptide (Trp-Phe), the tripeptide (Tyr-Gly-Gly), the tetrapeptide (Pro-Phe-Gly-Lys), the heptapeptide (Ala-Pro-Arg-Leu-Arg-Phe-Tyr), and a N-terminal blocked tripeptide (N-acetyl-Met-Leu-Phe).

193 nm photolysis of aromatic and aliphatic dipeptides in aqueous solution: dependence of decomposition quantum yield on the amino acid sequence.

The values of molar absorption coefficient and quantum yields of photodecomposition and peptide bond scission were determined for a number of aromatic and aliphatic dipeptides under 193 nm laser irradiation in neutral argon-saturated aqueous solution. Under these conditions we could show that no dependence of the dipeptide decomposition quantum yield on the sequence of amino acid residues exists, neither for aromatic dipeptides nor for aliphatic ones.

Sensitized photooxidation of Di- and tripeptides of tyrosine.

This paper studies the dye-sensitized photooxidation of tyrosine (tyr) and tyr di- and tripeptides (tyr-tyr and tyr-tyr-tyr) mediated by singlet molecular oxygen (O2[1 delta g]) in alkaline media. Photooxidation quantum efficiencies (phi r) were obtained by determining the overall and reactive rate constants of interaction with the oxidative species, employing the time-resolved O2(1 delta g) phosphorescence detection method and static-photolysis actinometric method, respectively. The interaction of O2(1 delta g)-tyr derivatives occurs through an intermediate encounter complex with polar character. Ionization of the phenolic OH group of tyr derivatives and the polarity of the solvent favors the overall interaction. Nevertheless, phi r values decrease when changing from water to MeCN-water medium. This indicates that the reactive deactivation of the encounter complex, probably an entropy-controlled step, may be affected by solvent polarity in the same way as those processes in which charges are neutralized along the reaction pathway. Photooxidation quantum efficiencies indicate that the contribution to O2(1 delta g) physical quenching (a second alternative deactivation route for the encountered complex [O2(1 delta g)-tyr derivatives]) increases with the complexity of the peptide. As a result, the selfprotection of the peptidic entity against physical quenching also increases. The information obtained from the fractional consumption mol O2/mol tyr derivative (in tyr, the di- and tripeptides and the respective methyl ester of tyr and the tripeptide), together with the evolution (either consumption and/or generation) of primary amino groups upon photosensitized irradiation of the same compounds clearly indicates that the photooxidation of di- and tri-tyr peptides proceeds with the breakage of peptidic bonds. As a consequence, in the final balance each tyr unity behaves as an independent photooxidizable target.

Photolysis (193 nm) of aliphatic dipeptides in aqueous solution.

The photodecomposition of four aliphatic dipeptides containing valine and methionine was studied in neutral solution upon excitation at 193nm. The quantum yields of ionization and decomposition in Ar-saturated aqueous solution are phi(e)- = 0.06-0.16 and phi(d) = 0.06-0.16, respectively. Phi(d) is enhanced (0.08-0.28) under N2O, where the hydrated electrons are converted into OH radicals. A comparison of the phi(d) values of dipeptides with those of monomeric amino acids indicates efficient decomposition of the peptide bond (bond scission).