Applications of pulse radiolysis to protein chemistry

Effects of radiation damage and inelastic scattering on single-particle imaging of hydrated proteins with an X-ray Free-Electron Laser

We present a computational case study of X-ray single-particle imaging of hydrated proteins on an example of 2-Nitrogenase-Iron protein covered with water layers of various thickness, using a start-to-end simulation platform and experimental parameters of the SPB/SFX instrument at the European X-ray Free-Electron Laser facility. The simulations identify an optimal thickness of the water layer at which the effective resolution for imaging the hydrated sample becomes significantly higher than for the non-hydrated sample. This effect is lost when the water layer becomes too thick. Even though the detailed results presented pertain to the specific sample studied, the trends which we identify should also hold in a general case. We expect these findings will guide future single-particle imaging experiments using hydrated proteins.

Hydrogen atom transfer in the radical cations of tryptophan-containing peptides AW and WA studied by mass spectrometry, infrared multiple-photon dissociation spectroscopy, and theoretical calculations

Two types of radical cations of tryptophan-the π-radical cation and the protonated tryptophan-N radical-have been studied in dipeptides AW and WA. The π-radical cation produced by removal of an electron during collision-induced dissociation of a ternary Cu(II) complex was only observed for the AW peptide. In the case of WA, only the ion corresponding to the loss of ammonia, [WA-NH₃] ^•+, was observed from the copper complex. Both protonated tryptophan-N radicals were produced by N-nitrosylation of the neutral peptides followed by transfer to the gas phase via electrospray ionization and subsequent collision-induced dissociation. The regiospecifically formed N^• species were characterized by infrared multiple-photon dissociation spectroscopy which revealed that the WA tryptophan-N^• radical remains the nitrogen radical, while the AW nitrogen radical rearranges into the π-radical cation. These findings are supported by the density functional theory calculations that suggest a relatively high barrier for the radical rearrangement (N^• to π) in WA (156.3 kJ mol^-1) and a very low barrier in AW (6.1 kJ mol^-1). The facile hydrogen atom migration in the AW system is also supported by the collision-induced dissociation of the tryptophan-N radical species that produces fragments characteristic of the tryptophan π-radical cation. Gas-phase ion-molecule reactions with n-propyl thiol have also been used to differentiate between the π-radical cations (react by hydrogen abstraction) and the tryptophan-N^• species (unreactive) of AW.

Protonation-modulated localization of excess electrons in histidine aqueous solutions revealed by ab initio molecular dynamics simulations: anion-centered versus cation-centered localization

In this work, we present an ab initio molecular dynamics simulation study on the interaction of an excess electron (EE) with histidine in its aqueous solution. Two different configurations of histidine (imidazole group protonated or not) are considered to reflect its different existing forms in neutral or slightly acidic surroundings. The simulation results indicate that localizations of EEs in different aqueous histidine solutions are quite different and are strongly affected by protonation of the side chain imidazole group and are thus pH-controlled. In neutral aqueous histidine solution, an EE localizes onto the carboxyl anionic group of the amino acid backbone after a relatively lengthy diffuse state, performing just like in an aliphatic amino acid solution. But in weakly acidic solution in which the side chain imidazole group is protonated, an EE undergoes a short lifetime diffuse state and finally localizes on the protonated imidazole group. We carefully examine these two different localization dynamics processes and analyze the competition between different dominating groups in their corresponding electron localization mechanisms. To explain the difference, we investigate the frontier molecular orbitals of these two systems and find that their energy levels and compositions are important to determine these differences. These findings can provide helpful information to understand the interaction mechanisms of low energy EEs with amino acids and even oligopeptides, especially with aromatic rings.

Intramolecular Electron Transfer in the Bacterial Two-Domain Multicopper Oxidase mgLAC

The kinetics of the intramolecular electron transfer process in mgLAC, a bacterial two-domain multicopper oxidase (MCO), were investigated by pulse radiolysis. The reaction is initiated by CO2(-) radicals produced in anaerobic, aqueous solutions of the enzyme by microsecond pulses of radiation. A sequence of pulses of CO2(-) radicals enables examination of the reductive half-cycle of the MCO catalysis. This is done by titrations of the Type 1 (T1) Cu(II) site and monitoring of the time course and amplitude of its reoxidation by internal electron transfer (ET) to the Type 3 site. Comparison of the internal ET kinetics observed for mgLAC with those of other MCOs studied by pulse radiolysis shows that they exhibit distinct reactivities. One main cause for the different reactivities is the broad range of T1 copper redox potentials, from the moderate potential of bacterial enzymes to the high potential of fungal laccases, and this possibly also reflects evolutionary quaternary structural adaptation of the MCO family to the wide range of reducing substrates that they oxidize while maintaining efficient reduction of the common substrate, molecular oxygen.

How protein structure affects redox reactivity: example of Human centrin 2

Human centrin 2 is a protein very sensitive to oxidative stress. Protein reactivity is unraveled by gamma radiolysis and electrochemical techniques.

Designed azurins show lower reorganization free energies for intraprotein electron transfer

Low reorganization free energies are necessary for fast electron transfer (ET) reactions. Hence, rational design of redox proteins with lower reorganization free energies has been a long-standing challenge, promising to yield a deeper understanding of the underlying principles of ET reactivity and to enable potential applications in different energy conversion systems. Herein we report studies of the intramolecular ET from pulse radiolytically produced disulfide radicals to Cu(II) in rationally designed azurin mutants. In these mutants, the copper coordination sphere has been fine-tuned to span a wide range of reduction potentials while leaving the metal binding site effectively undisrupted. We find that the reorganization free energies of ET within the mutants are indeed lower than that of WT azurin, increasing the intramolecular ET rate constants almost 10-fold: changes that are correlated with increased flexibility of their copper sites. Moreover, the lower reorganization free energy results in the ET rate constants reaching a maximum value at higher driving forces, as predicted by the Marcus theory.

Structure and reactivity of the distonic and aromatic radical cations of tryptophan

In this work, we regiospecifically generate and compare the gas-phase properties of two isomeric forms of tryptophan radical cations-a distonic indolyl N-radical (H3N(+) - TrpN(•)) and a canonical aromatic π (Trp(•+)) radical cation. The distonic radical cation was generated by nitrosylating the indole nitrogen of tryptophan in solution followed by collision-induced dissociation (CID) of the resulting protonated N-nitroso tryptophan. The π-radical cation was produced via CID of the ternary [Cu(II)(terpy)(Trp)](•2+) complex. CID spectra of the two isomeric species were found to be very different, suggesting no interconversion between the isomers. In gas-phase ion-molecule reactions, the distonic radical cation was unreactive towards n-propylsulfide, whereas the π radical cation reacted by hydrogen atom abstraction. DFT calculations revealed that the distonic indolyl radical cation is about 82 kJ/mol higher in energy than the π radical cation of tryptophan. The low reactivity of the distonic nitrogen radical cation was explained by spin delocalization of the radical over the aromatic ring and the remote, localized charge (at the amino nitrogen). The lack of interconversion between the isomers under both trapping and CID conditions was explained by the high rearrangement barrier of ca.137 kJ/mol. Finally, the two isomers were characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy in the ~1000-1800 cm(-1) region. It was found that some of the main experimental IR features overlap between the two species, making their distinction by IRMPD spectroscopy in this region problematic. In addition, DFT theoretical calculations showed that the IR spectra are strongly conformation-dependent.

First crystal structure of a fungal high-redox potential dye-decolorizing peroxidase: substrate interaction sites and long-range electron transfer

Dye-decolorizing peroxidases (DyPs) belong to the large group of heme peroxidases. They utilize hydrogen peroxide to catalyze oxidations of various organic compounds. AauDyPI from Auricularia auricula-judae (fungi) was crystallized, and its crystal structure was determined at 2.1 Å resolution. The mostly helical structure also shows a β-sheet motif typical for DyPs and Cld (chlorite dismutase)-related structures and includes the complete polypeptide chain. At the distal side of the heme molecule, a flexible aspartate residue (Asp-168) plays a key role in catalysis. It guides incoming hydrogen peroxide toward the heme iron and mediates proton rearrangement in the process of Compound I formation. Afterward, its side chain changes its conformation, now pointing toward the protein backbone. We propose an extended functionality of Asp-168, which acts like a gatekeeper by altering the width of the heme cavity access channel. Chemical modifications of potentially redox-active amino acids show that a tyrosine is involved in substrate interaction. Using spin-trapping experiments, a transient radical on the surface-exposed Tyr-337 was identified as the oxidation site for bulky substrates. A possible long-range electron transfer pathway from the surface of the enzyme to the redox cofactor (heme) is discussed.

Intramolecular electron transfer in laccases

Rate constants and activation parameters have been determined for the internal electron transfer from type 1 (T1) to type 3 (T3) copper ions in laccase from both the fungus Trametes hirsuta and the lacquer tree Rhus vernicifera, using the pulse radiolysis method. The rate constant at 298 K and the enthalpy and entropy of activation were 25 ± 1 s(-1), 39.7 ± 5.0 kJ·mol(-1) and -87 ± 9 J·mol(-1) ·K(-1) for the fungal enzyme and 1.1 ± 0.1 s(-1), 9.8 ± 0.2 kJ·mol(-1) and -211 ± 3 J·mol(-1) ·K(-1) for the tree enzyme. The initial reduction of the T1 site by pulse radiolytically produced radicals was direct in the case of T. hirsuta laccase, but occured indirectly via a disulfide radical in R. vernicifera. The equilibrium constant that characterizes the electron transfer from T1 to T3 copper ions was 0.4 for T. hirsuta laccase and 1.5 for R. vernicifera laccase, leading to full reduction of the T1 site occurring at 2.9 ± 0.2 electron equivalents for T. hirsuta and 4 electron equivalents for R. vernicifera laccase. These results were compared with each other and with those for the same process in other multicopper oxidases, ascorbate oxidase and Streptomyces coelicolor laccase, using available structural information and electron transfer theory.

Photo-oxidation of proteins

Photo-induced damage to proteins occurs via multiple pathways. Direct damage induced by UVB (λ 280-320 nm) and UVA radiation (λ 320-400 nm) is limited to a small number of amino acid residues, principally tryptophan (Trp), tyrosine (Tyr), histidine (His) and disulfide (cystine) residues, with this occurring via both excited state species and radicals. Indirect protein damage can occur via singlet oxygen ((1)O(2)(1)Δ(g)), with this resulting in damage to Trp, Tyr, His, cystine, cysteine (Cys) and methionine (Met) residues. Although initial damage is limited to these residues multiple secondary processes, that occur both during and after radiation exposure, can result in damage to other intra- and inter-molecular sites. Secondary damage can arise via radicals (e.g. Trp, Tyr and Cys radicals), from reactive intermediates generated by (1)O(2) (e.g. Trp, Tyr and His peroxides) and via molecular reactions of photo-products (e.g. reactive carbonyls). These processes can result in protein fragmentation, aggregation, altered physical and chemical properties (e.g. hydrophobicity and charge) and modulated biological turnover. Accumulating evidence implicates these events in cellular and tissue dysfunction (e.g. apoptosis, necrosis and altered cell signaling), and multiple human pathologies.

Electron transfer reactivity of type zero Pseudomonas aeruginosa azurin

Type zero copper is a hard-ligand analogue of the classical type 1 or blue site in copper proteins that function as electron transfer (ET) agents in photosynthesis and other biological processes. The EPR spectroscopic features of type zero Cu(II) are very similar to those of blue copper, although lacking the deep blue color, due to the absence of thiolate ligation. We have measured the rates of intramolecular ET from the pulse radiolytically generated C3-C26 disulfide radical anion to the Cu(II) in both type zero C112D/M121L and type 2 C112D Pseudomonas aeruginosa azurins in pH 7.0 aqueous solutions between 8 and 45 °C. We also have obtained rate/temperature (10-30 °C) profiles for ET reactions between these mutants and the wild-type azurin. Analysis of the rates and activation parameters for both intramolecular and intermolecular ET reactions indicates that the type zero copper reorganization energy falls in a range (0.9-1.1 eV) slightly above that for type 1 (0.7-0.8 eV), but substantially smaller than that for type 2 (>2 eV), consistent with XAS and EXAFS data that reveal minimal type zero site reorientation during redox cycling.

Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting

Hydroxyl radical-mediated protein footprinting is a convenient and sensitive technique for mapping solvent-accessible surfaces of proteins and examining the structure and dynamics of biological assemblies. In this study, the reactivities and tendencies to form easily detectable products for all 20 (common) amino acid side chains along with cystine are directly compared using various standards. Although we have previously reported on the oxidation of many of these residues, this study includes a detailed examination of the less reactive residues and better defines their usefulness in hydroxyl radical-mediated footprinting experiments. All 20 amino amides along with cystine and a few tripeptides were irradiated by gamma-rays, the products were analyzed by electrospray mass spectrometry, and rate constants of modification were measured. The reactivities of amino acid side chains were compared based on their loss of mass spectral signal normalized to the rate of loss for Phe or Pro that were radiolyzed simultaneously to serve as internal standards. In this way, accurate quantitation of relative rates could be assured. A reactivity order of amino acid side chains was obtained as Cys > Met > Trp > Tyr > Phe > cystine > His > Leu, Ile > Arg, Lys, Val > Ser, Thr, Pro > Gln, Glu > Asp, Asn > Ala > Gly. Ala and Gly are far too unreactive to be useful probes in typical experiments and Asp and Asn are unlikely to be useful as well. Although Ser and Thr are more reactive than Pro, which is known to be a useful probe, their oxidation products are not easily detectable. Thus, it appears that 14 of the 20 side chains (plus cystine) are most likely to be useful in typical experiments. Since these residues comprise approximately 65% of the sequence of a typical protein, the footprinting approach provides excellent coverage of the side-chain reactivity for proteins.

Radiolytic modification of sulfur-containing amino acid residues in model peptides: fundamental studies for protein footprinting

Protein footprinting based on hydroxyl radical-mediated modification and quantitative mass spectroscopic analysis is a proven technique for examining protein structure, protein-ligand interactions, and structural allostery upon protein complex formation. The reactive and solvent-accessible amino acid side chains function as structural probes; however, correct structural analysis depends on the identification and quantification of all the relevant oxidative modifications within the protein sequence. Sulfur-containing amino acids are oxidized readily and the mechanisms of oxidation are particularly complex, although they have been extensively investigated by EPR and other spectroscopic methods. Here we have undertaken a detailed mass spectrometry study (using electrospray ionization mass spectrometry and tandem mass spectrometry) of model peptides containing cysteine (Cys-SH), cystine (disulfide bonded Cys), and methionine after oxidation using gamma-rays or synchrotron X-rays and have compared these results to those expected from oxidation mechanisms proposed in the literature. Radiolysis of cysteine leads to cysteine sulfonic acid (+48 Da mass shift) and cystine as the major products; other minor products including cysteine sulfinic acid (+32 Da mass shift) and serine (-16 Da mass shift) are observed. Radiolysis of cystine results in the oxidative opening of the disulfide bond and generation of cysteine sulfonic acid and sulfinic acid; however, the rate of oxidation is significantly less than that for cysteine. Radiolysis of methionine gives rise primarily to methionine sulfoxide (+16 Da mass shift); this can be further oxidized to methionine sulfone (+32 Da mass shift) or another product with a -32 Da mass shift likely due to aldehyde formation at the gamma-carbon. Due to the high reactivity of sulfur-containing amino acids, the extent of oxidation is easily influenced by secondary oxidation events or the presence of redox reagents used in standard proteolytic digestions; when these are accounted for, a reactivity order of cysteine > methionine approximately tryptophan > cystine is observed.

Radiolytic Modification of Basic Amino Acid Residues in Peptides: Probes for Examining Protein−Protein Interactions

Protein footprinting utilizing hydroxyl radicals coupled with mass spectrometry has become a powerful technique for mapping the solvent accessible surface of proteins and examining protein-protein interactions in solution. Hydroxyl radicals generated by radiolysis or chemical methods efficiently react with many amino acid residue side chains, including the aromatic and sulfur-containing residues along with proline and leucine, generating stable oxidation products that are valuable probes for examining protein structure. In this study, we examine the radiolytic oxidation chemistry of histidine, lysine, and arginine for comparison with their metal-catalyzed oxidation products. Model peptides containing arginine, histidine, and lysine were irradiated using white light from a synchrotron X-ray source or a cesium-137 gamma-ray source. The rates of oxidation and the radiolysis products were primarily characterized by electrospray mass spectrometry including tandem mass spectrometry. Arginine is very sensitive to radiolytic oxidation, giving rise to a characteristic product with a 43 Da mass reduction as a result of the loss of guanidino group and conversion to gamma-glutamyl semialdehyde, consistent with previous metal-catalyzed oxidation studies. Histidine was oxidized to generate a mixture of products with characteristic mass changes primarily involving rupture of and addition to the imidazole ring. Lysine was converted to hydroxylysine or carbonylysine by radiolysis. The development of methods to probe these residues due to their high frequency of occurrence, their typical presence on the protein surface, and their frequent participation in protein-protein interactions considerably extends the utility of protein footprinting.

Re-evaluation of intramolecular long-range electron transfer between tyrosine and tryptophan in lysozymes. Evidence for the participation of other residues

One-electron oxidation of six different c-type lysozymes from hen egg white, turkey egg white, human milk, horse milk, camel stomach and tortoise was studied by gamma- and pulse-radiolysis. In the first step, one tryptophan side chain is oxidized to indolyl free radical, which is produced quantitatively. As shown already, the indolyl radical subsequently oxidizes a tyrosine side chain to the phenoxy radical in an intramolecular reaction. However this reaction is not total and its stoichiometry depends on the protein. Rate constants also vary between proteins, from 120 x s(-1) to 1000 x s(-1) at pH 7.0 and room temperature [extremes are hen and turkey egg white (120 x s(-1)) and human milk (1000 x s(-1))]. In hen and turkey egg white lysozymes we show that another reactive site is the Asn103-Gly104 peptidic bond, which gets broken radiolytically. Tryptic digestion followed by HPLC separation and identification of the peptides was performed for nonirradiated and irradiated hen lysozyme. Fluorescence spectra of the peptides indicate that Trp108 and/or 111 remain oxidized and that Tyr20 and 53 give bityrosine. Tyr23 appears not to be involved in the process. Thus new features of long-range intramolecular electron transfer in proteins appear: it is only partial and other groups are involved which are silent in pulse radiolysis.

Protection of radiation-induced protein damage by curcumin

Free radical reactions of lysozyme (Lz), tryptophan and disulfides were studied with curcumin, a lipid-soluble antioxidant from turmeric, in aqueous solution using a pulse radiolysis technique. The binding of curcumin with lysozyme was confirmed using absorption, fluorescence and stopped-flow techniques. The free radicals of curcumin generated after repairing radicals of disulfides, lysozyme and tryptophan absorb at 500-510 nm. Implication of this in evaluating the antioxidant behavior of curcumin in protecting proteins is discussed.

Generation and propagation of radical reactions on proteins

The oxidation of proteins by free radicals is thought to play a major role in many oxidative processes within cells and is implicated in a number of human diseases as well as ageing. This review summarises information on the formation of radicals on peptides and proteins and how radical damage may be propagated and transferred within protein structures. The emphasis of this article is primarily on the deleterious actions of radicals generated on proteins, and their mechanisms of action, rather than on enzymatic systems where radicals are deliberately formed as transient intermediates. The final section of this review examines the control of protein oxidation and how such damage might be limited by antioxidants.

Redox properties of protein disulfide bond in oxidized thioredoxin and lysozyme: a pulse radiolysis study

We have studied the one-electron reduction of oxidized Chlamydomonas reinhardtii thioredoxin and compared it to that of hen egg white lysozyme, using CO(2)(*) (-) free radicals as reductants. This comparison shows that the thioredoxin disulfide/thiol redox couple has different properties than that of lysozyme: the disulfide radical pK(a) is much lower (around 5 for small disulfides, 4.62 for lysozyme, <3 for thioredoxin). To get a better understanding of the modulation of the thioredoxin redox properties we have constructed the mutants W35A and D30A. Their reduction by pulse radiolysis indicates that W35 strongly controls both the disulfide radical acidity (the pK(a) in W35A is equal to ca. 4), and the thiol reactivity. Asp30 is also involved in the control of proton transfer to the disulfide free radical. In addition, its removal seems to increase the reduction potential of the thioredoxin thiyl/thiol couple. Overall, the reduction properties of thioredoxin confirm its nature as a unique reductant.

Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry

Radiolysis of peptide and protein solutions with high-energy X-ray beams induces stable, covalent modifications of amino acid residues that are useful for synchrotron protein footprinting. A series of 5-14 amino acid residue peptides of varied sequences were selected to study their synchrotron radiolysis chemistry. Radiolyzed peptide products were detected within 10 ms of exposure to a white light synchrotron X-ray beam. Mass spectrometry techniques were used to characterize radiolytic modification to amino acids cysteine (Cys), methionine (Met), phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), proline (Pro), histidine (His), and leucine (Leu). A reactivity order of Cys, Met >> Phe, Tyr, > Trp > Pro > His, Leu was determined under aerobic reaction conditions from MS/MS analysis of the radiolyzed peptide products. Radiolysis of peptides in 18O-labeled water under aerobic conditions revealed that oxygenated radical species from air and water both contribute to the modification of amino acid side chains. Cysteine and methionine side chains reacted with hydroxyl radicals generated from radiolysis of water as well as molecular oxygen. Phenylalanine and tyrosine residues were modified predominantly by hydroxyl radicals, and the source of modification of proline was exclusively through molecular oxygen.

Damage to hemoglobin by radiation-generated serum albumin radicals

We have studied the effects of the interaction of radiation generated human serum albumin radicals (HSA*) with human hemoglobin molecules (Hb). Diluted Hb aqueous solutions were irradiated under N2O or argon without HSA and in the presence of HSA. Analysis of Hb absorbance spectra in the visible range, cross-linking of HSA* radicals with Hb molecules and functional properties of Hb were investigated. The degree of Hb destruction estimated on the basis of changes in the absorption spectra indicated that the effectiveness of HSA* radicals generated under N2O for Hb destruction was approximately equal to that of *OH radicals. In this case mainly *OH radicals formed the secondary HSA* radicals. However, during the irradiation Hb + HSA under argon the presence of equivalent amounts of oxidizing and reducing products of water radiolysis lowers the degree of Hb destruction. Some reactions of HSA* radicals with Hb molecules lead to the formation of covalent bonds between the molecules of both proteins. The following types of hybrids could be distinguished: Hb monomer-HSA, Hb dimer-HSA and higher aggregates. Structural changes of Hb by HSA* radicals were reflected by alterations in the oxygen affinity (increase) and cooperativity (decrease) of Hb. The results obtained indicate that in the experimental systems studied, the HSA* radical reactions with Hb molecules are favoured over recombination reactions of HSA* radicals. On this basis one can suggest that in the studied systems Hb plays the role of an acceptor of radical energy located on HSA.

Protein cleavage by transition metal complexes bearing amino acid substituents

In this report, we describe protein damage by a series of metal complexes that mediate the formation of hydroxyl radical. The protein targets used are bovine serum albumin (BSA) and carboxypeptidase A (CPA). BSA contains several electrostatic, hydrogen bonding and hydrophobic binding sites for potential interaction with the metal complexes, and CPA contains a specific phenylalanine binding site. The data presented in this study show that aromatic side chain damage and backbone cleavage occur to similar extents with all the complexes. Reasonable levels of backbone cleavage specificity can be attained with relatively few recognition elements, despite the fact that a diffusible radical mediates cleavage. Incorporation of additional recognition elements can enlarge the set of cleavage sites. We show that the chemical environment of the cleavage reaction, manipulated by using different buffers, can dramatically affect the outcome of the cleavage reaction. Our work suggests that backbone cleavage site is determined by three factors: the binding sites of the metal complexes, the role of reactive sites on the protein backbone, and the influence of the chemical environment on the reaction.

Radiolysis of DNA in the presence of a protein studied by HPL-gel chromatography

The influence of bovine serum albumin (BSA) on the radiolysis of double-stranded DNA was studied by measuring the loss of highly polymerized DNA with HPL-gel chromatography. The scavenger capacity of BSA for OH.-radicals kBSA [BSA] was kept constant. at 7.8 x 10(5) s-1, when DNA (0.1 mg/ml) was irradiated under different gas conditions (air, N2 and N2O), at pH 7 and 5 and with different ionic conditions. The resulting protein radicals react with DNA producing DNA protein crosslinks and DNA double-strand breaks. The yield and the kind of DNA damage depend on the nature of the protein radicals and their association with DNA. High phosphate concentration prevents the association of BSA with DNA and causes a reduction of the protection by BSA against double-strand break-age of DNA. Radiolysis in the presence of BSA in perchlorate solution leads to more strand breakage and less protein crosslinking than in phosphate solution because perchlorate is more chaotropic than phosphate. Changing the pH from 7 to 5 increases the protection by BSA against DNA strand breakage.

Luminescence quenching by long range electron transfer: a probe of protein clustering and conformation at the cell surface

Quenching of luminescence from fluorescent and phosphorescent probes by nitroxide spin labels with a long range electron transfer (LRET) mechanism (44,45) has been tested as a tool to monitor association/clustering and conformational changes of cell surface proteins. The membrane proteins were labeled with monoclonal antibodies or Fab fragments conjugated with luminescent probes or water-soluble nitroxide spin labels. The method was tested as a probe of 3 different aspects of protein-protein association involving class I MHC molecules: (1) interaction between the heavy and light chains of the MHC molecules, (2) clustering, self-association of MHC molecules, (3) proximity of MHC molecules to transferrin receptors of fibroblasts or surface immunoglobulin molecules of B lymphoblasts. The extent of quenching upon increasing the fractional density of the quencher was sensitive for protein association in accordance with earlier immunoprecipitation and flow cytometric Förster-type energy transfer (FCET) data obtained on the same cells. These data suggest that the LRET quenching can be used as intra- or intermolecular ruler in a 0.5-2.5 nm distance range. This approach is simpler (measurements only on donor side) and faster than many other experimental techniques in screening physical association or conformational changes of membrane proteins by means of spectrofluorimetry, flow cytometry, or microscope based imaging.

Blue copper proteins as a model for investigating electron transfer processes within polypeptide matrices

Intramolecular long-range electron transfer (ET) processes have been investigated in two types of blue copper proteins; the single-copper protein, azurin and the multi-copper oxidase, ascorbate oxidase. These have several advantages for investigating the parameters that control the above reactions: (1) Their sole physiological role is mediating or catalyzing ET processes via the evolutionary optimized copper sites. (2) The three-dimensional structures of a considerable number of blue single copper containing proteins, e.g. azurins, and of ascorbate oxidase, have been determined at high resolution. (3) These proteins have no other cofactors except for the copper ions, thus the role of the polypeptide matrix can be addressed in a more straightforward manner. In azurins, the ET from the cystine (3-26) radical-ion produced by pulse-radiolytic reduction of this single disulfide bridge, to the Cu(II) ion bound at a distance of approximately 2.6 nm has been studied, in naturally occurring and in single-site mutated azurins. The role of changing specific amino acid residues on the internal long-range electron transfer (LRET) process and its potential pathways has been investigated. It is noteworthy that this process is most probably not part of the physiological function of azurin, hence, there has not been any evolutionary selection of structural elements for the reaction. Therefore, this provides a system for an unbiased examination of structural and chemical requirements for control of this process. By contrast, in blue copper oxidases, the internal ET from the electron uptake site from substrate to the O2 reduction site is part of these enzymes catalytic cycle, presumably optimized by selective pressure. We are investigating this internal ET in ascorbate oxidase and try to resolve the relation between this enzyme's distinct functional states and the internal ET rates. We conclude that in both types of proteins, the investigated LRET proceed primarily along covalent pathways, thus providing suitable systems where the parameters controlling the efficiency of these processes can be pursued.

Oxygen effect in the radiolysis of proteins. III. Haemoglobin

Radiolysis of haemoglobin was carried out in phosphate buffer under air, N2 or N2O and with and without ethanol. Radiation products were separated by SDS-PAGE. The loss of subunits and simultaneous aggregation and fragmentation of haemoglobin was measured, if OH-radicals were unscavenged. There was no sensitizing effect of oxygen on the degradation process. Radiation-induced fragmentation was not a random process, but produced specific fragments. The estimated molecular weights of these fragments gave further support to the assumption that the aminoacyl-proline peptide group is the preferential breaking site if OH radicals react with proteins in the presence of oxygen. In contrast with lactate dehydrogenase and bovine serum albumin such fragmentation was observed not only after aerobic radiolysis but also under anaerobic conditions. This difference must be caused by the Feporphyrin system which reacts with H2O2 under release of oxygen. If haemoglobin was irradiated under air the yield of aggregates was much lower than under N2O or N2.

Long range electron transfer along an alpha-helix

The many observations of long range electron transfer in proteins raises the question of whether a protein's structure can influence the rate or path of such transfers, and if so, then how. To answer these questions requires information on which of the various structural elements composing proteins support long range electron transfer. In this report, we present evidence for long range electron transfer along the alpha-helix of a synthetic leucine zipper dimer. We also present electron transfer rate data obtained with other helical peptides.

Long range electron transfer between tyrosine and tryptophan in hen egg-white lysozyme

The azide, dibromide and dichloride radicals oxidize one or more tryptophan side chains in hen egg-white lysozyme. The indolyl radical produced in this second-order 1-electron oxidation subsequently oxidizes a tyrosine side chain to the phenoxy radical in an intramolecular reaction with a rate constant of 130 +/- 10 s-1 at pH 7, 25 degrees C. The final indolyl and phenoxy equilibrium mixture then decays with a t1/2 approximately 2 s. The faster intramolecular reaction exhibits a pH dependence; on decreasing the pH from 9 the first-order rate constant increases to a maximum near pH 5.4 and then declines as the pH is lowered further. In contrast, the first-order rate constant for the intramolecular electron transfer between the tyrosine and tryptophan of the peptide trpH-pro-tyrOH remains unchanged between approx. pH 11 and 6.5 and then increases as the pH is lowered further. This difference in the observed pH dependence suggests that changes in structure or ionization state influence the protein electron transfer rate. We also discuss the radiation inactivation of lysozyme in light of these observations.

Intramolecular long-range electron transfer in the hemerythrin monomer: a pulse radiolysis study

The single sulfhydryl group (Cys-50) of the methemerythrin from Phascolosoma gouldii reacts with 5,5'dithiobis(2-nitrobenzoic acid) to form a mixed disulfide. The pulse radiolytically generated formate radical reduces this mixed disulfide to its radical anion. In turn, the disulfide radical anion reduces the protein two-iron center over a nominal distance of 13 A. The rate constant for this intramolecular electron transfer is approximately 15 s-1 at room temperature, pH 7. Between the two redox centers there is an equilibrium driving force of 0.78 V, measured by differential pulsed polarography.

Long-range intramolecular electron transfer in azurins

The Cu(II) sites of azurins, the blue single copper proteins, isolated from Pseudomonas aeruginosa and Alcaligenes spp. (Iwasaki) are reduced by CO2- radicals, produced by pulse radiolysis, in two distinct reaction steps: (i) a fast bimolecular phase, at the rates (5.0 +/- 0.8) x 10(8) M-1.s-1 (P. aeruginosa) and (6.0 +/- 1.0) x 10(8) M-1.s-1 (Alcaligenes); (ii) a slow unimolecular phase with specific rates of 44 +/- 7 s-1 in the former and 8.5 +/- 1.5 s-1 for the latter (all at 298 K, 0.1 M ionic strength). Concomitant with the fast reduction of Cu(II), the single disulfide bridge linking cysteine-3 to -26 in these proteins is reduced to the RSSR- radical ion as evidenced by its characteristic absorption band centered at 410 nm. This radical ion decays in a unimolecular process with a rate identical to that of the slow Cu(II) reduction phase in the respective protein, thus clearly suggesting that a long-range intramolecular electron transfer occurs between the RSSR- radicals and the Cu(II) site. The temperature dependence of the internal electron transfer process in both proteins was measured over the 4 degrees C to 42 degrees C range. The activation parameters derived are delta H* = 47.5 +/- 4.0 and 16.7 +/- 1.5 kJ.mol-1; and delta S not equal to = -56.5 +/- 7.0 and -171 +/- 18 J.K-1.mol-1, respectively. Using the Marcus theory, we found that the intramolecular electron transfer rates and their activation parameters observed for the two azurins correlate well with the distances between the reactive sites, their redox potential, and the nature of the separating medium. Thus, azurins with distinct structural and reactivity characteristics isolated from different bacteria or modified by site-directed mutagenesis can be used in comparing long-range electron transfer process between their conserved disulfide bridge and the Cu(II) sites.

Photo-induced electron ejection from the reduced copper of Pseudomonas aeruginosa azurin

The reduced form of Pseudomonas aeruginosa azurin exhibits an enhanced absorbance in the UV compared to that of the oxidized protein. This enhancement has also been observed for azurins from other bacterial species and for another type I copper protein, plastocyanin. Pulsed laser excitation of the reduced azurin in the region of enhanced absorbance at 308 nm results in single photon, rapid (less than 30 ns) oxidation of the copper center and formation of the hydrated electron with a quantum yield of 0.05. The hydrated electron reacts in the expected manner with scavengers such as nitrous oxide, oxygen, acetone and nitromethane. In the absence of scavengers, the electron reacts with the protein, including the disulfide bond, to form the disulfide radical anion, observed at 410 nm. The overall photophysical event involves a charge-transfer to solvent transition although the existence of intermediate states can not be excluded.

Parameters controlling the kinetics of ferric and ferrous hemeproteins reduction by hydrated electrons

To clarify the processes of hemeproteins reduction, three classes of these proteins (ferric, ferrous and desFe) were reduced by hydrated electrons generated by pulse radiolysis. Spectral and kinetic investigations were made on alpha hemoglobin chain and myoglobin. Human alpha chain has been chosen to avoid all ferric contaminations and horse ferric myoglobin to eliminate all ferrous protein fractions. We have successively studied the influences of: the iron presence, its oxidation state (II and III), the protein charge and the iron-ligand nature (H2O, OH-, N3- and CN-). For alpha human hemoglobin chain without metallic ion or with ferrous iron, the reduction rates are the same: 1.1 +/- 0.2.10(10) M-1.s-1. In the case of horse ferric myoglobin, the reduction rates depend principally on the protein charge (from pH 6.3 to pH 9.5, the reduction rate of Mb(FeIII)N3- decreases from 2.5 +/- 0.5.10(10) M-1.s-1 to 1.2 +/- 0.2.10(10) M-1.s-1) and are also modulated by the equilibrium constant of the hemeprotein-ligand association (1.2 +/- 0.2.10(10) M-1.s-1 for Mb(FeIII)N3- and 0.8 +/- 0.2.10(10) M-1.s-1 for Mb(FeIII)CN-, at pH 9.8).

Reactions of reducing radicals with ribonuclease

Radiation-induced reactions of hydrated electrons, formate- and ethanol radicals with ribonuclease were studied by pulse radiolysis and by electrophoresis. Initially formate radicals react rapidly and very specifically with the disulphide bonds of ribonuclease. This reaction leads to aggregation by intermolecular S-S-interchange, the process being more effective at pH 4, since formation and decay of S-S-.-radical anions increases with decreasing pH. With high doses additional unreducible aggregates are formed. Radical formation at the positively charged histidine residues seems to be involved. Hydrated electrons do not react as selectively as the formate radicals, but with several sites in native ribonuclease. Thus with low doses unreducible aggregates are formed. Electrophoresis shows that reaction of the electrons causes fragmentation of the peptide chain, when OH-radicals are scavenged. Very weak transient spectra and very little degradation result on reaction of ethanol radicals with ribonuclease.

Radiation-induced binding of methanol, ethanol and 1-butanol to haemoglobin

Aqueous solutions of haemoglobin were irradiated under N2 and under N2O in the presence of methanol, ethanol and 1-butanol, which were partly 14C-labelled. The amount of bound alcohol was measured after gel filtration on Sephadex G-100 and with sodium dodecyl sulphate on Sepharose 6B-CL. All alcohols became covalently linked to haemoglobin. After radiolysis under N2 the G values for the three different alcohols were very similar, but under N2O the yield of cross-linking of haemoglobin with 1-butanol is twice that of methanol or ethanol. The high degree of modification by butanol results in extensive dissociation to dimers. Possible mechanisms yielding covalent cross-links between alcohols and haemoglobin are discussed. The high G value for cross-linking with butanol suggests that butanol radicals can add very efficiently to double bonds.