INFLUENCE OF THE LOCATION OF TRYPTOPHANYL RESIDUES IN PROTEINS ON THEIR PHOTOSENSITIVITY

The environmental effect on Trp residues photolysis was investigated on four proteins containing a single Trp residue in environments of various polarities: glucagon (exposed residue), nuclease (partially buried residue), RNase T₁ (fully buried residue) and melittin (exposed or partially buried residue depending on the salt concentration). Direct photolysis was performed in neutral N₂-saturated phosphate solution at 20°C using 302 nm monochromatic light. Tryptophan loss was monitored by both absorption and fluorescence spectroscopy and by amino acid analysis. The results suggest that tryptophan photodegradation depends on the location of the residue in the protein, with regard to the exposure to the aqueous medium and to the neighbouring amino acids in the primary amino acid sequence and in the three dimensional structure. Photochemical products were not analysed but fluorescence spectra indicate that they vary with protein.     

LC-MS/MS Analysis and Comparison of Oxidative Damages on Peptides Induced by Pathogen Reduction Technologies for Platelets

Pathogen reduction technologies (PRT) are photochemical processes that use a combination of photosensitizers and UV-light to inactivate pathogens in platelet concentrates (PCs), a blood-derived product used to prevent hemorrhage. However, different studies have questioned the impact of PRT on platelet function and transfusion efficacy, and several proteomic analyses revealed possible oxidative damages to proteins. The present work focused on the oxidative damages produced by the two main PRT on peptides. Model peptides containing residues prone to oxidation (tyrosine, histidine, tryptophane, and cysteine) were irradiated with a combination of amotosalen/UVA (Intercept process) or riboflavin/UVB (Mirasol-like process). Modifications were identified and quantified by liquid chromatography coupled to tandem mass spectrometry. Cysteine-containing peptides formed disulfide bridges (R-SS-R, ?2 Da; favored following amotosalen/UVA), sulfenic and sulfonic acids (R-SOH, +16 Da, R-SO₃H, +48 Da, favored following riboflavin/UVB) upon treatment and the other amino acids exhibited different oxidations revealed by mass shifts from +4 to +34 Da involving different mechanisms; no photoadducts were detected. These amino acids were not equally affected by the PRT and the combination riboflavin/UVB generated more oxidation than amotosalen/UVA. This work identifies the different types and sites of peptide oxidations under the photochemical treatments and demonstrates that the two PRT may behave differently. The potential impact on proteins and platelet functions may thus be PRT-dependent.

Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions

Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).     

Photooxidized products of recombinant alpha A-crystallin and W9F mutant

Human lenses contain many photosensitizers that absorb light at wavelengths above 300 nm, most notably UVA light (320-400 nm). Kynurenine (Kyn) and 3-hydroxykynurenine (HK), two of the best-known photosensitizers in the human lens, may play a significant role in photooxidation-related changes in lens proteins, such as conformational change and aggregation. In vitro irradiation experiments with proteins indicate that the Trp residue (with maximal absorption at 295 nm) is more susceptible to photooxidation by UVB light (280-320 nm) than by UVA light, but most UVB light below 300 nm is screened by the cornea and little reaches the lens, especially the nuclear region where nuclear color develops. Therefore, if photooxidation is an important contributor to nuclear color or nuclear cataract, it must arise from a photosensitized reaction. In the present study, we use recombinant alpha A- and its Trp-deficient mutant W9F as models to study the effects of UVA irradiation in the presence of HK or Kyn and of UVB (300 nm) irradiation on alpha-crystallins. alpha A-crystallin showed a large decrease in Trp fluorescence and a large increase in non-Trp (blue) fluorescence after the HK-sensitized or 300 nm photooxidation. For the W9F mutant, a smaller decrease in protein fluorescence (lambda ex at 280 nm) and a smaller increase in blue fluorescence than for the wild-type alpha A-crystallin were observed. A decrease in the near-UV CD was also observed for both photooxidized alpha A and the W9F mutant. The effect of Kyn sensitization is smaller than that of HK sensitization. A study of chaperone-like activity indicated that only 300 nm photooxidized alpha A and the W9F mutant increased the ability to protect insulin from dithiothreitol-induced aggregation. Thus, sensitized photooxidation can occur in amino acids other than Trp by UVA in the presence of HK or Kyn with effects similar to, albeit smaller than, those of direct UVB (300 nm) photooxidation.     

Quenching of the Singlet and Triplet Excited States of Pterin by Amino Acids

Unconjugated oxidized pterins accumulate in the skin of patients suffering from vitiligo and, under UVA irradiation, photosensitize the oxidation of amino acids. In this work, we study the interaction of the singlet and triplet excited states of pterin (Ptr), the parent compound of oxidized pterins, with four oxidizable amino acids: tryptophan (Trp), tyrosine (Tyr), histidine (His) and methionine (Met). Steady‐state and time‐resolved fluorescence measurements and laser flash photolysis experiments were performed to investigate the quenching of the Ptr excited states by the amino acids in aqueous solution. The singlet excited states of Ptr are quenched by Met mainly via a dynamic process and by Trp via a combination of dynamic and static processes. His does not quench singlet excited states of Ptr, and quenching by Tyr could not be investigated due to the low solubility of this amino acid. The triplet excited states of Ptr are quenched by the four studied amino acids, and the corresponding bimolecular quenching rate constants are in the range of diffusion controlled limit. The assessment of the results in the context of the Ptr‐photosensitization of amino acids suggests that triplet excited state of Ptr is the species that initiates the photochemical processes.     

Boosting the Peroxidase‐like Activity of Cobalt Ions by Amino Acid‐based Biological Species and Its Applications

Enzyme mimics have been widely used as alternatives to natural enzymes, owing to their high stability and low cost. However, the activity and atom economy of enzyme mimics still need to be improved. Herein, we report the boosting effects of amino acids, peptides and proteins on the peroxidase‐like activity of Co²⁺. Among 20 amino acids, tryptophan (Trp) enhanced the activity of Co²⁺ approximately 8 times and was identified as the best stimulator. The study revealed the synergy of amino acids‐based species and HCO₃^? for efficient catalysis. Co²⁺ is proposed to bind simultaneously to HCO₃^? and Trp, and to form a ternary catalyst which facilitates the generation of reactive oxygen species. Based on the selective boosting by Trp, a simple and low‐cost Co²⁺ sensor with high sensitivity was developed, which showed a linear range of 10–300 μM and a limit of detection of 0.4 μM for Co²⁺.     

Quantitation of the Reactive Oxygen Species Generated by the UVA Irradiation of Ascorbic Acid-Glycated Lens Proteins

The oxidation products of ascorbic acid rapidly glycate proteins and produce protein-bound, advanced glycation endproducts. These endproducts can absorb UVA light and cause the photolytic oxidation of proteins (Ortwerth, Linetsky and Olesen, Photochem. Photobiol . 62, 454–463, 1995), which is mediated by the formation of reactive oxygen species. A dialyzed preparation of calf lens proteins, which had been incubated for 4 weeks with 20 mM ascorbic acid in air, was irradiated for 1 h with 200 mW/ cm² of absorbed UVA light (λ > 338 nm), and the concentration of individual oxygen free radicals was measured. Superoxide anion attained a level of 76 μ M as determined by the superoxide dismutase (SOD)-depen-dent increase in hydrogen peroxide formation and of 52 μ M by the SOD-inhibitable reduction of cytochrome c. Hydrogen peroxide formation increased linearly to 81 μM after 1 h. Neither superoxide anion nor hydrogen peroxide, however, could account for the UVA photolysis of Trp and His seen in this system.
Singlet oxygen levels approached 1.0 mM as measured by the oxidation of histidine, which was consistent with singlet oxygen measurements by the bleaching of N,N- dimethyl-4-nitrosoaniline. High concentrations of sodium azide, a known singlet oxygen quencher, inhibited the photolytic destruction of both His and Trp. Little or no protein damage could be ascribed to hydroxyl radical based upon quenching experiments with added mannitol. Therefore, superoxide anion and H₂O₂ were generated by the UVA irradiation of ascorbate advanced glycation endproducts, however, the major reactive oxygen species formed was singlet oxygen.     

An E.P.R. study of peptides after U.V. irradiation

Abstract— Various peptides of Gly, Ala, Phe, Tyr, and Trp have been irradiated with U.V. light in the solid state or in frozen aqueous solution. The radicals produced were studied by E.P.R. spectroscopy at low temperature and at room temperature. Radicals seem to occur preferentially on Gly or Ala when in the C-terminal position and there is evidence for a photosensitization of these amino acids by aromatic amino acids.     

Analysis of photo-oxidized amino acids in tryptic peptides of calf lens gamma-II crystallin.

Insoluble and crosslinked proteins and increased pigmentation in the eye lens are features of aging and cataracts. Determining the amino acids which are involved in insolubilization, crosslinking and visible light scattering will shed light on the mechanisms by which cataracts form. Calf lens gamma-II crystallin was irradiated at 295 nm, digested and separated into tryptic peptides. Additional tryptic peptides were found in the digest of irradiated gamma-II which were not present in the dark control digest. These peptides were identified by amino acid sequencing and shown to correspond to expected tryptic fragments of the protein, indicating more facile digestion in the UV-irradiated protein than in dark controls. Amino acid analysis of the irradiated protein and peptides showed losses of histidine, methionine and cysteine residues as compared to control samples. Tryptophan, which is not detected by amino acid analysis, was also found to be reactive since losses in its fluorescence intensity were observed after irradiation. Some of the photochemically active amino acids had lower than expected responses in amino acid sequencing experiments. This suggested specific sites of photochemical activity in the various peptides. The evidence for peptide crosslinks is also discussed.     

Comparative studies of photophysical and photochemical properties of solketal substituted platinum(II) and zinc(II) phthalocyanine sets

A complete set of platinum(II) solketal substituted phthalocyanines has been synthesized and characterized. To evaluate their potential as Type II photosensitizers for photodynamic therapy, comparative studies of their photophysical and photochemical properties with analogous zinc(II) series have been achieved: electronic absorption, fluorescence quantum yields, lifetimes, and fluorescence quenching by benzoquinone, as well as singlet oxygen generation and photodegradation. It appears that platinum(II) phthalocyanines are worth being used as Type II photosensitizers, as they exhibit good singlet oxygen generation and appropriate photodegradation.     

A laser flash photolysis study of amino acids and dipeptides using 4-nitroquinoline 1-oxide as a photosensitizer: The pH dependence

The pH effects on the photochemical reaction of amino acids and related dipeptides with 4-nitroquinoline 1-oxide (4NQO) as a photosensitizer have been investigated by laser flash photolysis. The obtained kinetic parameters show that the electron transfer from Tryptophan (Trp), Tyrosine (Tyr) as well as dipeptides containing Trp and/or Tyr residue to triplet 4NQO (^T4NQO) are efficient, but inefficient from methionine (Met) and dipeptides containing neither Trp nor Tyr. The result was supported by the calculated values of the free energy change from measured oxidation potentials for the electron transfer. It was demonstrated that Trp and Tyr residues are initial reaction sites with ^T4NQO, while Tyr/O^? radical may be final species for Trp-Tyr dipeptide. In acidic aqueous solutions, the self-quenching rate constants of ^T4NQO and the rate constants of electron transfer from amino acids to ^T4NQO decrease with decreasing pH. In alkaline solutions, amino acids are easily oxidized by 4NQO under irradiation of laser pulse, and no transient absorption signal was observed.     

ANALYSIS OF PHOTO-OXIDIZED AMINO ACIDS IN TRYPTIC PEPTIDES OF CALF LENS γ-II CRYSTALLIN

Insoluble and crosslinked proteins and increased pigmentation in the eye lens are features of aging and cataracts. Determining the amino acids which are involved in insolubilization, crosslinking and visible light scattering will shed light on the mechanisms by which cataracts form. Calf lens γ-II crystallin was irradiated at 295 nm, digested and separated into tryptic peptides. Additional tryptic peptides were found in the digest of irradiated γ-II which were not present in the dark control digest. These peptides were identified by amino acid sequencing and shown to correspond to expected tryptic fragments of the protein, indicating more facile digestion in the UV-irradiated protein than in dark controls. Amino acid analysis of the irradiated protein and peptides showed losses of histidine. methionine and cysteine residues as compared to control samples. Tryptophan, which is not detected by amino acid analysis, was also found to be reactive since losses in its fluorescence intensity were observed after irradiation. Some of the photochemically active amino acids had lower than expected responses in amino acid sequencing experiments. This suggested specific sites of photochemical activity in the various peptides. The evidence for peptide crosslinks is also discussed.     

Riboflavin photodegradation and photosensitizing effects are highly dependent on oxygen and ascorbate concentrations

Riboflavin (RF) is a normal component of the eye lens which triggers a strong photosensitizing activity when exposed to light. Upon irradiation with short wavelength radiations below 400 nm, RF-photosensitized damage may occur. However, vitamin C is present at high concentrations in the normal lens and plays an important role in inhibiting these photosensitization processes. An in vitro simple model was used with the objective of understanding better the relationships between vitamin C and oxygen concentrations on the mechanisms of RF-mediated photodegradation of tryptophan (Trp), a target particularly sensitive to photo-oxidation. Under nitrogen, the RF decomposition reached its maximal value, and vitamin C and Trp photo-oxidation was negligible. When increasing oxygen pressure, RF photodegradation dropped and vitamin C photo-oxidation strongly increased and was maximal at 100% O2. RF-induced photodegradation of Trp first increased with oxygen concentration, up to 40 microM O2, and then decreased. RF and Trp degradation were significantly protected by vitamin C so that no more than 20% of the substrates concentration were oxidized in the presence of vitamin C higher than 0.8 mM. From our results we conclude that in the specific conditions of the normal lens, the high vitamin C concentration (2 mM) is compatible with the UVA radiation hazard, despite the presence of RF. However, if lenticular vitamin C decreases below 0.8 mM, photodegradation of RF may occur and Trp may therefore be photo-oxidized by a Type-I mechanism.     

Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N‐formyl‐L‐valinamide and N‐formyl‐L‐phenylalaninamide

Employing introductory (3‐21G RHF) and medium‐size (6‐311++G** B3LYP) ab initio calculations, complete conformational libraries, containing as many as 27 conformers, have been determined for diamide model systems incorporating the amino acids valine (Val) and phenylalanine (Phe). Conformational and energetic properties of these libraries were analyzed. For example, significant correlation was found between relative energies from 6‐311++G** B3LYP and single‐point B3LYP/6‐311++G**//RHF/3‐21G calculations. Comparison of populations of molecular conformations of hydrophobic aromatic and nonaromatic residues, based on their ab initiorelative energies, with their natural abundance indicates that, at least for the hydrophobic core of proteins, the conformations of Val (Ile, Leu) and Phe (Tyr, Trp) are controlled by the local energetic preferences of the respective amino acids. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 732–751, 2001     

H-bonding cooperativity and energetics of alpha-helix formation of five 17-amino acid peptides

Five peptides, each containing 17 amino acids, have been completely geometrically optimized in their alpha-helical and beta-strand forms using a mixed DFT/AM1 procedure. B3LYP/D95** was used for the entire helical structures, while AM1 was initially used to optimize the side chains, followed by reoptimization at the DFT level. The energetic and structural results show (1) that the helices are favored over the strands by 29.5 to 37.4 kcal/mol; (2) that alkyl groups on the amino acid side chains favor helix formation even in the absence of solvent; (3) that C-H...O hydrogen bonds contribute to the relative stability of the helices that contain amino acids (val, leu and ile) with beta-hydrogens in their alkyl side chains; (4) that formation of these helices entails approximately 6.6 kcal/mol of strain within the backbone per hydrogen bond; and (5) that H-bond cooperativity is essential for the alpha-helix to become more stable than a corresponding beta-strand. This last observation strongly suggests that pairwise potentials are inadequate for modeling of peptides and proteins.     

PHOTOCHEMICAL ADDITION OF AMINO ACIDS AND PEPTIDES TO DNA

Abstract— The quantum yields for photochemical addition of twenty of the amino acids commonly occurring in proteins to denatured calf thymus DNA have been determined in deoxygenated phosphate buffer at λ 254 nM and pH 7 using a fluorescamine assay technique. Fifteen were found to be reactive, with cysteine, lysine, phenylalanine, tryptophan and tyrosine being the most reactive. Alanine, aspartic acid, glutamic acid, serine and threonine were unreactive. Analogous quantum yields for a series of eighteen peptides of the form glycyl X (X being one of the commonly occurring amino acids) were also determined, along with the corresponding quantum yields for L-alanyl-L-alanine, L-alanyl-L-tryptophan, L-seryl-L-seryl-L-serine, L-threonyl-L-threonyl-L-threonine, and L-cystine- bis -glycine. All of the peptides were found to be reactive. The modified amino acids N^ε-methyllysine, N^ε, N^ε, N^ε-trimethyllysine and N^ε-acetyllysine, all occurring in minor amounts in the histone group of chromosomal proteins, were also found to be reactive as was N^α-acetyllysine. The quantum yields for photoaddition of a selected group of amino acids and peptides to denatured DNA and native DNA are compared. In some cases higher quantum yields for photoaddition to denatured DNA are observed while in other cases the reverse is true. The effect of oxygen on the quantum yields for photoaddition of selected peptides to DNA was examined. While for most systems studied the amount of reaction in aerated systems was less than in deoxygenated systems, in the case of glycyl-L-phenylalanine the reverse was true.     

Thermogravimetric analysis of photodegraded acrylic coated lime wood

A series of experiments were carried out to investigate the photodegradation of lime wood (Tilia cordata Mill.) coated with acrylic copolymer during artificial UV/Vis light irradiation for 600 h. Photodegradation of the Paraloid B72 films and Paraloid B72 treated lime wood samples was evaluated by thermogravimetry throughout the irradiation period of 100 h. The results obtained indicate a shifting of the DTG maxima to lower temperatures, which may be related to a decrease in the stability of the copolymer and wood during photodegradation. The decrease of weight loss with increasing time of exposure was observed, while the global kinetic parameters for the main peak increases when increasing exposure time of wood to the UV light. Even when the surface of the wood was covered with a thin layer of acrylic resin, some photodegradation reactions of the wood surface occurred. The modifications in the wood structure may be influenced by the newly formed structures from acrylic resin photodegradation.     

丙酮三重态与含芳香氨基酸肽的物理化学过程

用激光闪光光解瞬态吸收光谱研究了水溶液中含芳香氨基酸残基肽的光敏化反应过程.结果表明,在丙酮存在的含色氨酸残基肽(Trp-Gly,n-f-Met-Trp,Trp-Phe)体系的光解,丙酮三重态与Trp分别通过三重态-三重态(T-T)激发能转移和电子转移生成Trp激发三重态和N中心自由基(Trp/N^·);丙酮三重态仅与含酪氨酸残基肽(Phe-Tyr)通过电子转移生成Tyr酚氧自由基(Tyr/O^·).在色氨酰酪氨酸(Trp-Tyr)与丙酮的光解体系中,观察到分子内的电子转移,即由Trp/N^·-Tyr→Trp-Tyr/O^·自由基的生成过程     

Evaluation of protein, peptide, and amino acid retention on C5 hydride-based stationary phases

A pentyl (C5) stationary phase is synthesized on a hydride surface using both 100 and 300 A silica particles. The aqueous normal phase properties of these new phases are evaluated using amino acids at high concentrations of ACN in the mobile phase containing 0.1% formic acid. The RP properties of the materials are tested by using peptides and proteins in order to evaluate the effect of pore size on retention. Comparisons of retention as well as efficiencies and peak symmetry with a C18 phase are used to determine the influence of the hydrophobic properties of the bonded material. An evaporative light scattering detector (ELSD) is used in all phases of the study and compared with UV detector for gradient elution of proteins.     

Solid-Phase Peptide Modification via Deaminative Photochemical Csp3-Csp3 Bond Formation Using Katritzky Salts

Introduction of unnatural amino acids can significantly improve the binding affinity and stability of peptides. Commercial availability of such amino acids is limited, and their synthesis is a long and tedious process. We here describe a method that allows the functionalization of peptides directly on solid-support by converting lysine residues to Katritzky salts, and subjecting them to a photochemical Giese reaction under mild reaction conditions. The method avoids the need for amino acid synthesis and instead offers a late-stage modification route for rapid peptide diversification. While numerous modification approaches at the lysine amine have been described, this work provides the first example of deaminative functionalization of peptides at lysine. The two-step protocol is compatible with various substrates, lysine analogues, resins, and all proteinogenic amino acids. Finally, by leveraging solid-phase modification, this protocol facilitates the functionalization of longer peptides as was demonstrated using biologically relevant peptides of up to 15 amino acids.