Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams.

Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?

One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism of a metalloenzyme. Here, UV-Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects. UV-Vis absorption spectra of native crystals, as well as those soaked in 18 different radioprotectants, show dramatic metal reduction occurring in the first 60 s of irradiation with an X-ray beam from a third-generation synchrotron source. Among the tested radioprotectants only potassium hexacyanoferrate(III) seems to be capable of partially mitigating the rate of metal photoreduction at the concentrations used, but not to a sufficient extent that would allow a complete data set to be recorded from a fully oxidized crystal. On the other hand, analysis of the X-ray crystallographic data confirms ascorbate as an efficient protecting agent against radiation damage, other than metal centre reduction, and suggests further testing of HEPES and 2,3-dichloro-1,4-naphtoquinone as potential scavengers.

Molecular design of functional peptides by utilizing unnatural amino acids: toward artificial and photofunctional protein.

Unnatural amino acids are effective as building blocks to design functional peptides from the following two points: (1) utilization of rigid unnatural amino acids for the incorporated peptides to control the conformation to appear the function, and (2) incorporation of functional and unnatural amino acids into peptides resulting in appearance of the inherent functions. As a combined strategy, molecular design of artificial metalloproteins utilizing 5'-amino-2,2'-bipyridine-5-carboxilic acid (H-5Bpy-OH) as an unnatural amino acid is proposed. The peptide containing three residues of the unnatural amino acid would fold through coordination to a metal ion. In particular, ruthenium(II) ion would yield a ruthenium tris(bipyridine) derivative as the core complex of the artificial protein, which would appear the similar photochemical functions as that of ruthenium(II) tris(bipyridine) complex. The central complex could form two isomers, fac and mer. For selective synthesis of the mer complex, which is expected as the core complex in the artificial protein, dicyclohexylamide as a bulky group is introduced at the C-terminal of the unnatural amino acid to destabilize the fac complex due to steric hindrance. Furthermore, in order to know the photochemical properties and function of the protein mimics, ruthenium(II) tris(2,2'-bipyridine) complexes bearing amide groups at 5,5' positions have been synthesized as the model complexes. As a result, the direction of amide groups (RNHCO-or RCONH-) in ruthenium complexes is found to significantly affect the emission efficiency: the former reduces the quantum yield and the latter enhances it, respectively. The ruthenium(II) tris(5,5'-diamide-2,2'-bipyridine) complexes are also found to strongly bind with various anions [e.g., halogen ions (Cl-, Br-) and acetate anion] in acetonitrile and to detect these anions through the emission spectral changes under air. The molecular design of artificial protein is expected to develop new fields among peptide, organic, inorganic, and physical chemistry.

Modular synthesis of de novo-designed metalloproteins for light-induced electron transfer.

The design and chemical synthesis of two de novo four-helix bundle proteins is described; each protein has two bound cofactors. Their construction from purified peptides is based on the modular assembly of different amphiphilic helices by chemoselective coupling to a cyclic peptide template. In the hydrophobic interior of the antiparallel four-helix bundle these proteins contain a heme in a binding pocket with two ligating histidine residues. A ruthenium-tris(bipyridine) complex is covalently bound to different positions at the hydrophilic side of one of the heme-binding helices. Laser-induced electron transfer across the varied distance through this helix has been studied and compared with a pathway analysis. The UV-visible, CD, and mass spectra are consistent with the structure and orientation predetermined by the template.

Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold.

BACKGROUND: Nitrile hydratases are unusual metalloenzymes that catalyze the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alphabeta unit. We have determined the crystal structure of photoactivated iron-containing nitrile hydratase from Rhodococcus sp. R312 to 2.65 A resolution as a first step in the elucidation of its catalytic mechanism. RESULTS: The alpha subunit consists of a long N-terminal arm and a C-terminal domain that forms a novel fold. This fold can be described as a four layered structure, alpha-beta-beta-alpha, with unusual connectivities between the beta strands. The beta subunit also contains a long N-terminal extension, a helical domain, and a C-terminal domain that folds into a beta roll. The two subunits form a tight heterodimer that is the functional unit of the enzyme. The active site is located in a cavity at the subunit-subunit interface. The iron centre is formed by residues from the alpha subunit only-three cysteine thiolates and two mainchain amide nitrogen atoms are ligands. CONCLUSIONS: Nitrile hydratases contain a novel iron centre with a structure not previously observed in proteins; it resembles a hybrid of the iron centres of heme and Fe-S proteins. The low-spin electronic configuration presumably results in part from two Fe-amide nitrogen bonds. The structure is consistent with the metal ion having a role as a Lewis acid in the catalytic reaction.

Proximity of the manganese cluster of photosystem II to the redox-active tyrosine YZ.

Electron spin echo electron-nuclear double resonance (ESE-ENDOR) experiments performed on a broad radical electron paramagnetic resonance (EPR) signal observed in photosystem II particles depleted of Ca2+ indicate that this signal arises from the redox-active tyrosine YZ. The tyrosine EPR signal width is increased relative to that observed in a manganese-depleted preparation due to a magnetic interaction between the photosystem II manganese cluster and the tyrosine radical. The manganese cluster is located asymmetrically with respect to the symmetry-related tyrosines YZ and YD. The distance between the YZ tyrosine and the manganese cluster is estimated to be approximately 4.5 A. Due to this close proximity of the Mn cluster and the redox-active tyrosine YZ, we propose that this tyrosine abstracts protons from substrate water bound to the Mn cluster.

Ligand binding and protein dynamics in cupredoxins.

Type 1 copper sites bind nitric oxide (NO) in a photolabile complex. We have studied the NO binding properties of the type 1 copper sites in two cupredoxins, azurin and halocyanin, by measuring the temperature dependence of the ligand binding equilibria and the kinetics of the association reaction after photodissociation over a wide range of temperature (80-280 K) and time (10(-6)-10(2) s). In both proteins, we find nonexponential kinetics below 200 K that do not depend on the NO concentration. Consequently, this process is interpreted as geminate recombination. In azurin, the rebinding can be modeled with the Arrhenius law using a single pre-exponential factor of 10(8.3) s-1 and a Gaussian distribution of enthalpy barriers centered at 22 kJ/mol with a width [full width at half-maximum (FWHM)] of 11 kJ/mol. In halocyanin, a more complex behavior is observed. About 97% of the rebinding population can also be characterized by a Gaussian distribution of enthalpy barriers at 12 kJ/mol with a width of 6.0 kJ/mol (FWHM). The pre-exponential of this population is 1.6 x 10(12) s-1 at 100 K. After the majority population has rebound, a power-law phase that can be modeled with a gamma-distribution of enthalpy barriers is observed. Between 120 and 180 K, an additional feature that can be interpreted as a relaxation of the barrier distribution toward higher barriers shows up in the kinetics. Above 200 K, a slower, exponential rebinding appears in both cupredoxins. Since the kinetics depend on the NO concentration, this process is identified as bimolecular rebinding.(ABSTRACT TRUNCATED AT 250 WORDS)

Iron-sulfur centers as endogenous blue light sensitizers in cells: a study with an artificial non-heme iron protein.

The possible involvement of Fe-S clusters in photodynamic reactions as endogenous sensitizing chromophores in cells has been investigated, by using an artificial non-heme iron protein (ANHIP) derived from bovine serum albumin and ferredoxins isolated from spinach and a red marine algae. Ferredoxins and ANHIP, when exposed to visible light, generate singlet oxygen, as measured by the imidazole plus RNO method. Irradiation with intense blue light of the ANHIP-entrapped liposomes caused severe membrane-damage such as liposomal lysis and lipid peroxidation. In the presence of ANHIP, isocitrate dehydrogenase and fructose-1,6-diphosphatase were photoinactivated by blue light. However, all of these photosensitized reactions were significantly suppressed by a singlet oxygen (1O2) quencher, azide, but enhanced by a medium containing deuterium oxide. Further, the Fe-S proteins with the prosthetic groups destroyed did not initiate the blue light-induced reactions. In addition, the action spectrum for 1O2 generation from ANHIP was very similar to the visible absorption spectrum of Fe-S centers. The results obtained in this investigation appear consistent with the suggestion that Fe-S centers are involved in photosensitization in cells via a singlet oxygen mechanism.

Photophysics of metalloazurins.

The fluorescence lifetimes of Cu(II), Cu(I), Ag(I), Hg(II), Co(II), and Ni(II) azurin Pae from Pseudomonas aeruginosa and Cu(II), Cu(I), and Hg(II) azurin Afe from Alcaligenes faecalis were measured at 295 K by time-correlated single-photon counting. In addition, fluorescence lifetimes of Cu(II) azurin Pae were measured between 30 and 160 K and showed little change in value. Ultraviolet absorption difference spectra between metalloazurin Pae and apoazurin Pae were measured, as were the fluorescence spectra of metalloazurins. These spectra were used to determine the spectral overlap integral required for dipole-dipole resonance calculations. All metalloazurins exhibit a reduced fluorescence lifetime compared to their respective apoazurins. Forster electronic energy transfer rates were calculated for both metalloazurin Pae and metalloazurin Afe derivatives; both enzymes contain a single tryptophyl residue which is located in a different position in the two azurins. These azurins have markedly different fluorescence spectra, and electronic energy transfers occur from these two tryptophyl sites with different distances and orientations and spectral overlap integral values. Intramolecular distances and orientations were derived from an X-ray crystallographic structure and a molecular dynamic simulation of the homologous azurin Ade from Alcaligenes denitrificans, which contains both tryptophyl sites. Assignments were made of metal-ligand-field electronic transitions and of transition dipole moments and directions for tryptophyl residues, which accounted for the observed fluorescence quenching of Hg(II), Co(II), and Ni(II) azurin Pae and Cu(II) and Hg(II) azurin Afe. The fluorescence of azurin Pae is assigned as a 1Lb electronic transition, while that of azurin Afe is 1La. The marked fluorescence quenching of Cu(II) azurin Pae and Cu(I) azurin Pae and Afe is less well reproduced by our calculations, and long-range oxidative and reductive electron transfer, respectively, are proposed as additional quenching mechanisms. This study illustrates the application of Forster electronic energy transfer calculations to intramolecular transfers in structurally well characterized molecular systems and demonstrates its ability to predict observed fluorescence quenching rates when the necessary extensive structural, electronic transition assignment, and spectroscopic data are available. The agreement between Forster calculations and quenching rates derived from fluorescence lifetime measurements suggests there are limited changes in conformation between crystal structure and solution structures, with the exception of the tryptophyl residue of azurin Afe, where a conformation derived from a molecular simulation in water was necessary rather than that found in the crystal structure.

Physical mechanism for inactivation of metallo-enzymes by characteristic X-rays: analysis of the data of Jawad and Watt.

Table 1 summarizes the mean numbers of events and interactions of various types which we calculate to occur per single dihydro-orotic dehydrogenase enzyme when irradiated in solution with D37 = 99 Gy of 8.04 keV X-rays under the experimental conditions of Jawad and Watt (1986). There are clearly many orders or magnitude too few direct interactions of X-ray photons, or electrons, with the enzymes for these processes to be responsible for the mean of one inactivating event per enzyme which must occur at the D37 dose. Jawad and Watt (1986) concluded that the enzyme inactivation was predominantly due to direct interaction of an X-ray photon with a non-metal atom of the enzyme, but our analysis shows that this is not possible by five orders of magnitude. Of the possible mechanisms (a)-(d), the only one which remains feasible in this experimental system is the indirect action of radiolysis products from the solution (d). Diffusion distances of the order of 0.1 micron may be quite adequate for such inactivation. The situation would be very different for enzymes or other molecules within mammalian cells where diffusion distances are very much smaller (probably of the order of a few nanometres). Our analysis leaves unexplained the fairly small (20 per cent) change in effectiveness reported by Jawad and Watt (1986) for X-ray energy above, as compared to below, the K-absorption edge of Fe. The experimental observation is directly dependent on the accuracy of the dosimetry at these two energies; we have made no attempt to evaluate this.

[Effect of metronidazole and local irradiation of the tumor on paramagnetic metal complexes of the liver and tumor tissues]. / Vliianie metronidazola i lokal'nogo oblucheniia opukholi na paramagnitnye metallokompleksy tkanei pecheni i opukholi.

A study was made of changes in the intensity of the ESR signals in tissues of sarcoma-37 and liver of mice after radiation of the tumor, administration of metronidazole, and after the combined effect of the two factors. The most pronounced changes in the ESR signals were induced by metronidazole. An appreciable increase in the content of nitrosyl complexes in the tumor was noted after the combined effect of metronidazole and radiation which was indicative of the radiation-induced formation of a large number of metronidazole anion-radicals in the tumor.

Physical mechanism for inactivation of metallo-enzymes by characteristic X-rays.

Measurements have been made of the inactivation of the metallo-enzyme dihydro-oratic dehydrogenase in solution by characteristic X-rays at energies above and below the K absorption edge of the constituent iron atom. From the dose-survival curves and knowledge of the equilibrium electron spectrum generated by the X-ray 'field', inactivation cross-sections are deduced and expressed in terms of intrinsic efficiencies for the various proposed direct and indirect mechanisms of inactivation. It is concluded that the inactivation is caused by direct X-ray interaction in an area equivalent to about 30 per cent of the mean geometrical cross-section of the molecule, and is independent of whether the target is wet or dry. The contribution from Auger electron cascades, Coulomb charges etc. initiated by the inner-shell vacancy in the metal atom is negligible--possibly due to saturation effects. It seems that the presence of the metal atom simply serves to enhance the overall interaction probability with the molecule in a manner consistent with expectations from the photon absorption coefficients. No anomalously large damage is detected. These conclusions are supported by comparison with published results for other metallo-enzymes and bromine-loaded bacteria.

A resonance Raman study of native stellacyanin and its Ni(II) derivative. On the origin of the 450-nm electronic absorption.

The resonance Raman spectra of native stellacyanin and its Ni(II) derivative has been investigated. Raman intensity as a function of the exciting frequency shows minima at about 440--460 nm. Moreover, the resonance Raman spectra of the Ni(II) derivative indicate similar symmetry and nature of ligands, namely, one cysteine and at least one histidine.Optical electronegativity of the ligand involved in the intense visible absorption band of native stellacyanin and the corresponding transition of the Ni(lI) derivative confirm this assumption. The origin of the 450 nm band is also discussed.

Effects of laser radiation on Rhus vernicifera laccase, Type 2 Cu-depleted laccase, and stellacyanin.

Laser irradiation in the 450 nm region brings about irreversible changes in the copper sites of Rhus vernicifera lactase and its type 2 Cu-depleted derivative. The absorption band at 614 nm disappears after _ 2 hr of irradiation with a 200 mW laser beam; the amount of the paramagnetic detectable copper does not decrease, indicating no reduction of these types of copper. No apparent rearrangement of the protein backbone occurs, as ultaviolet dichroic spectra of the enzyme before and after the irradiation do not show appreciable differences. Stellacyanin is insensitive to laser radiation at any wavelength.

Hemerythrin's oxygen-binding reaction studied by laser photolysis.

The dioxygen--iron bond in oxyhemerythrin is shown to be photosensitive. The recombination reaction after photodissociation depends strongly on solvent viscosity. In water (eta = 1 centipoise or 1 x 10(-3) Pa . s) the recombination is monophasic and second-order in solvent oxygen concentration, with a bimolecular rate coefficient of 2.9 x 10(7) M-1 s-1. In a glycerol/water mixture (eta = 180 centipoise) a concentration-dependent geminate recombination process is also seen. This opens a class of proteins to study by flash photolysis.