Orientation of the tyrosyl radical in Salmonella typhimurium class Ib ribonucleotide reductase determined by high field EPR of R2F single crystals

The R2 protein of class I ribonucleotide reductase (RNR) generates and stores a tyrosyl radical, located next to a diferric iron center, which is essential for ribonucleotide reduction and thus DNA synthesis. X-ray structures of class Ia and Ib proteins from various organisms served as bases for detailed mechanistic suggestions. The active site tyrosine in R2F of class Ib RNR of Salmonella typhimurium is located at larger distance to the diiron site, and shows a different side chain orientation, as compared with the tyrosine in R2 of class Ia RNR from Escherichia coli.No structural information has been available for the active tyrosyl radical in R2F. Here we report on high field EPR experiments of single crystals of R2F from S. typhimurium, containing the radical Tyr-105*. Full rotational pattern of the spectra were recorded, and the orientation of the g-tensor axes were determined, which directly reflect the orientation of the radical Tyr-105* in the crystal frame. Comparison with the orientation of the reduced tyrosine Tyr-105-OH from the x-ray structure reveals a rotation of the tyrosyl side chain, which reduces the distance between the tyrosyl radical and the nearest iron ligands toward similar values as observed earlier for Tyr-122* in E. coli R2. Presence of the substrate binding subunit R1E did not change the EPR spectra of Tyr-105*, indicating that binding of R2E alone induces no structural change of the diiron site. The present study demonstrates that structural and functional information about active radical states can be obtained by combining x-ray and high-field-EPR crystallography.     

Probing the secondary quinone (QB) environment in photosynthetic bacterial reaction centers by light-induced FTIR difference spectroscopy

The photoreduction of the secondary electron acceptor, QB, has been characterized by light-induced Fourier transform infrared difference spectroscopy of Rb. sphaeroides and Rp. viridis reaction centers. The reaction centers were supplemented with ubiquinone (UQ10 or UQ0). The QB- state was generated either by continuous illumination at very low intensity or by single flash in the presence of redox compounds which rapidly reduce the photooxidized primary electron donor P+. This approach yields spectra free from P and P+ contributions making possible the study of the microenvironment of QB and QB-. Assignments are proposed for the C...O vibration of QB- and tentatively for the C = O and C = C vibrations of QB.     

Orientation of the g-tensor axes of the Rieske subunit in the cytochrome bc1 complex

The orientation of the g-tensors of the Rieske iron-sulfur protein subunit was determined in a single crystal of the bovine mitochondrial cytochrome bc1 complex with stigmatellin in the Qo quinol binding site. The g-tensor principal axes are skewed with respect to the Fe-Fe and S-S atom direction in the 2Fe2S cluster, which is allowed by the lack of rigorous symmetry of the cluster. The asymmetric unit in the crystal is the active dimer, and the g-tensor axes have slightly different orientations relative to the iron-sulfur cluster in the two halves of the dimer. The g approximately 1.79 axis makes an average angle of 30 degrees with respect to the Fe-Fe direction and the g approximately 2.024 axis an average angle of 26 degrees with respect to the S-S direction. This assignment of the g-tensor axis directions indicates that conformations of the Rieske protein are likely the same in the cytochrome bc1 and b6f complexes and that the extent of motion of the Rieske head domain during the catalytic cycle has been highly conserved during evolution of these distantly related complexes.     

Electron spin polarization in photosynthesis and the mechanism of electron transfer in photosystem I. Experimental observations.

Transient electron paramagnetic resonance (EPR) methods are used to examine the spin populations of the light-induced radicals produced in spinach chloroplasts, photosystem I particles, and Chlorella pyrenoidosa. We observe both emission and enhanced absorption within the hyperfine structure of the EPR spectrum of P700+, the photooxidized reaction-center chlorophyll radical (Signal I). By using flow gradients or magnetic fields to orient the chloroplasts in the Zeeman field, we are able to influence both the magnitude and sign of the spin polarization. Identification of the polarized radical and P700+ is consistent with the effects of inhibitors, excitation light intensity and wavelength, redox potential, and fractionation of the membranes. The EPR signal of the polarized P700+ radical displays a 30% narrower line width than P700+ after spin relaxation. This suggests a magnetic interaction between P700+ and its reduced (paramagnetic) acceptor, which leads to a collapse of the P700+ hyperfine structure. Narrowing of the spectrum is evident only in the spectrum of polarized P700+, because prompt electron transfer rapidly separates the radical pair. Evidence of cross-relaxation between the adjacent radicals suggests the existence of an exchange interaction. The results indicate that polarization is produced by a radical pair mechanism between P700+ and the reduced primary acceptor of photosystem I. The orientation dependence of the spin polarization of P700+ is due to the g-tensor anisotropy of the acceptor radical to which it is exchange-coupled. The EPR spectrum of P700+ is virtually isotropic once the adjacent acceptor radical has passed the photoionized electron to a later, more remote acceptor molecule. This interpretation implies that the acceptor radical has g-tensor anisotropy significantly greater than the width of the hyperfine field on P700+ and that the acceptor is oriented with its smallest g-tensor axis along the normal to the thylakoid membranes. Both the ferredoxin-like iron-sulfur centers and the X- species observed directly by EPR at low temperatures have g-tensor anisotropy large enough to produce the observed spin polarization; however, studies on oriented chloroplasts show that the bound ferredoxin centers do not have this orientation of their g tensors. In contrast, X- is aligned with its smallest g-tensor axis predominantly normal to the plane of the thylakoid membranes. This is the same orientation predicted for the acceptor radical based on analysis of the spin polarization of P700+, and indicates that the species responsible for the anisotropy of the polarized P700+ spectrum is probably X-. The dark EPR Signal II is shown to possess anisotropic hyperfine structure (and possibly g-tensor anisotropy), which serves as a good indicator of the extent of membrane alignment.     

The involvement of iron and ubiquinone in electron transfer reactions mediated by reaction centers from photosynthetic bacteria.

Reaction centers from Rhodopseudomonas sphaeroides strain R-26 were prepared with varying Fe and ubiquinone (Q) contents. The photooxidation of P-870 to P-870+ was found to occur with the same quantum yield in Fe-depleted reaction centers as in control samples. The kinetics of electron transfer from the initial electron acceptor (I) to Q also were unchanged upon Fe removal. We conclude that Fe has no measurable role in the primary photochemical reaction. The extent of secondary reaction from the first quinone acceptor (QA) to the second quinone acceptor (QB) was monitored by the decay kinetics of P-870+ after excitation of reaction centers with single flashes in the absence of electron donors, and by the amount of P-870 photooxidation that occurred on the second flash in the presence of electron donors. In reaction centers with nearly one iron and between 1 and 2 ubiquinones per reaction center, the amount of secondary electron transfer is proportional to the ubiquinone content above one per reaction center. In reaction centers treated with LiClO4 and o-phenanthroline to remove Fe, the amount of secondary reaction is decreased and is proportional to Fe content. Fe seems to be required for the secondary reaction. In reaction centers depleted of Fe by treatment with SDS and EDTA, the correlation between Fe content and secondary activity is not as good as that found using LiClO4. This is probably due in part to a loss of primary photochemical activity in samples treated with SDS; but the correlation is still not perfect after correction for this effect. The nature of the back reaction between P-870+ and Q-B was investigated using stopped flow techniques. Reaction centers in the P-870+ Q-B state decay with a 1-s half-time in both the presence and absence of o-phenanthroline, an inhibitor of electron transfer between Q-B and QB. This indicates that the back reaction between P-870+ and Q-A is direct, rather than proceeding via thermal repopulation of Q-A. The P-870+ Q-B state is calculated to lie at least 100 mV in free energy below the P-870+ Q-A state.     

Orientation of the tyrosyl D, pheophytin anion, and semiquinone Q(A)(*)(-) radicals in photosystem II determined by high-field electron paramagnetic resonance

The radical forms of two cofactors and an amino acid in the photosystem II (PS II) reaction center were studied by using high-field EPR both in frozen solution and in oriented multilayers. Their orientation with respect to the membrane was determined by using one-dimensionally oriented samples. The ring plane of the stable tyrosyl radical, Y(D)(*), makes an angle of 64 degrees +/- 5 degrees with the membrane plane, and the C-O direction is tilted by 72 degrees +/- 5 degrees in the plane of the radical compared to the membrane plane. The semiquinone, Q(A)(*)(-), generated by chemical reduction in samples lacking the non-heme iron, has its ring plane at an angle of 72 degrees +/- 5 degrees to the membrane plane, and the O-O axis is tilted by 21 degrees +/- 5 degrees in the plane of the quinone compared to the membrane plane. This orientation is similar to that of Q(A)(*)(-) in purple bacteria reaction centers except for the tilt angle which is slightly bigger. The pheophytin anion was generated by photoaccumulation under reducing conditions. Its ring plane is almost perpendicular to the membrane with an angle of 70 degrees +/- 5 degrees with respect to the membrane plane. This is very similar to the orientation of the pheophytin in purple bacteria reaction centers. The position of the g tensor with respect to the molecule is tentatively assigned for the anion radical on the basis of this comparison. In this work, the treatment of orientation data from EPR spectroscopy applied to one-dimensionally oriented multilayers is examined in detail, and improvements over previous approaches are given.     

A study of protein structure changes during hydration by diffuse X-ray scattering. I. The intensity and the shape of "10-angstrom" maximum

The angle dependencies of diffuse x-ray scattering intensities were studied in a wide range of angles from 3 to 80 degrees for water-soluble and membrane proteins with a different structural organization: alpha-helical protein myoglobin, alpha-helical protein serum albumen, alpha + beta protein lysozyme, and transmembrane proteins of photosynthetic reaction centers (RC) from purple bacteria Rhodobacter sphaeroides, and Blastochlorii (Rhodopseudomonas) viridis containing cytocrome c, situated out side the membrane, and for H and L+M subunits of membrane protein of reaction center from Rb. sphaeroides for various hydration degrees. The hydration/dehydration process was studied for water-soluble proteins (within hydration range from h = 0.05 to h = 1). The hydration/dehydration process appears to be reversible. All water-soluble proteins show a 10 angstroms peak, and proteins of reaction center do not show this peak. A quantitative comparable study of the behaviour for of the 10 angstroms peak different proteins the degree of lysozyme hydration increases from h = 0.05 to h = 0.45, the protein structure slightly changes (most probably the motifoffolding), the structure of myoglobin in solution is slightly different from the structure in crystal. By taking into account the changes in the shape and intensity of the 10 angstroms peak only, it is impossible to make the conclusion about structural changes in other proteins studied. A correlation between the structural changes observed and dynamic and functional properties of proteins is discussed.     

Crystallization and electron paramagnetic resonance characterization of the complex of photosystem I with its natural electron acceptor ferredoxin

The formation of a transient complex between photosystem I and ferredoxin is involved in the process of ferredoxin photoreduction in oxygenic photosynthetic organisms. Reduced ferredoxin is an essential redox intermediate involved in many assimilatory processes and is necessary for the reduction of NADP(+) to NADPH. Single crystals from a complex of photosystem I with ferredoxin were grown using PEG 400 and CaCl(2) as precipitation agents. The crystals diffract x-rays to a resolution of 7-8 A. The space group was determined to be orthorhombic with the unit cell dimensions a = 194 A, b = 208 A, and c = 354 A. The crystals contain photosystem I and ferredoxin in a 1:1 ratio. Electron paramagnetic resonance (EPR) measurements on these crystals are reported, where EPR signals of the three [4Fe-4S] clusters F(A), F(B), F(X), and the [2Fe-2S] cluster of ferredoxin were detected. From the EPR spectra observed at three particular orientations of the crystal in the magnetic field, the full orientation pattern of the F g-tensor was simulated. This simulation is consistent with the presence of 12 magnetically inequivalent F clusters per unit cell with the C(3) axis of the PSI trimers oriented at (23 degrees, 72 degrees, 77 degrees ) to the unit cell axes.     

Transmembrane orientation of reaction centers in proteoliposomes from Rhodopseudomonas sphaeroides

The photochemical reaction centers from Rhodopseudomonas sphaeroides were reconstituted with soybean phospholipids into liposomes by the cholate-dialysis method. The transmembrane orientation of the reaction centers in the proteoliposomes and the morphology of the vesicles were investigated. The orientation was determined by the reduction of externally added cytochrome c after its photooxidation by a flash. The structure of the vesicles was examined by electron microscope. Discontinuous sucrose density gradient centrifugation yielded several proteoliposome fractions with different vesicular sizes and reaction-center orientations. The proportion of the reaction centers that exposed their cytochrome c reacting sites to the outside of the vesicles increased from 45 to 85% with an increase of the vesicular size. The proportion also depended on the ionic composition of the dialysis buffer. The optimal ionic environment during the dialysis (100 mM NaCl or 2.5 mM MgSO4) gave a liposome yield of 25-30% with a highly asymmetric orientation (greater than 60%). Entrapping of cytochrome c molecules into the phospholipid vesicles had little effect on the orientation of the reaction centers.     

Kinetics of electron transfer between the primary and the secondary electron acceptor in reaction centers from Rhodopseudomonas sphaeroides.

Photoreduction of the two ubiquinone molecules, UQ1 and UQ2, bound to purified reaction center from Rhodopseudomonas sphaeroides induces different absorption band shifts of bacteriochlorophyll and bacteriopheophytin molecules depending on which ubiquinone is photoreduced. This allows us to study electron transfer between UQ1 and UQ2 directly by absorption spectrometry. The results support a model in which electrons are transferred one by one from UQ1 to UQ2 with a half-time 200 micro seconds, and two by two from fully reduced UQ2 to the secondary acceptor pool.     

Photochemical Electron Transport in Photosynthetic Reaction Centers from Rhodopseudomonas spheroides: II. Interaction with external Electron Donors and Acceptors and a Reevaluation of Some Spectroscopic Data

Photochemical reaction centers prepared from Rhodopseudomonas spheroides were treated with reduced cytochrome c (cyt c), and in some cases with ubiquinone (UQ), and illuminated. The light-induced oxidation of cy and reduction of UQ were observed, and also the variations in fluorescence of P870. These observations indicated that each reaction center contains a primary photochemical electron acceptor capable of holding just one electron. Depending on the method of preparation, the reaction centers may also contain secondary electron acceptor pools consisting mainly of UQ. The role of native UQ as an electron acceptor could be duplicated by added UQ. The yield of P870 fluorescence increased by a factor of 3-4, at most, during illumination of reaction centers in the presence of an electron donor such as reduced cyt. This suggests that the quantum efficiency for the primary photoact is about 0.7, rather than 0.9-1.0 as concluded in the past from optical absorption measurements. The apparent quantum efficiency for the oxidation of cyt by illuminated reaction centers can be increased by the addition of UQ and is decreased at higher concentrations of the detergent lauryl dimethylamine oxide (LDAO). These treatments do not affect the quantum efficiency of P870 oxidation, measured in the absence of cyt.     

Turnover of ubiquinone-0 at the acceptor side of photosynthetic reaction center

The steady-state operation of photosynthetic reaction center from Rhodobacter sphaeroides was investigated by measuring the rate of cytochrome photo-oxidation under intensive continuous illumination (808 nm, 5 W cm(-2)). The native quinone UQ(10) in Q(B) binding site of the reaction center was substituted by tailless UQ(0) and the binding parameters and the turnover rate of the UQ(0) was studied to test the recently discovered light-intensity dependent acceptor side effect (Gerencsér and Maróti 2006). The binding parameters of UQ(0) (k (on) = 2.1 x 10(5) M(-1) s(-1) and k (off) = 100 s(-1)) were characteristic to the RC exposed to high light-intensity. The dissociation constant (K (D) = 480 muM) determined under high light intensity is 2-3 times larger than that determined from flash-experiments. The light-intensity dependent acceleration of cytochrome turnover measured on reaction center of inhibited proton binding was independent of the type of the quinone and was sensitive only to the size ("pressure") of the quinone pool. The dissociation constants of different types of semiquinones show similarly high (several orders of magnitude) increase in the modified conformation of the Q(B) binding pocket due to high intensity of illumination. This result indicates the exclusive role of the quinone headgroup in the binding of semiquinone to different conformations of the protein.     

Powder and single-crystal electron paramagnetic resonance studies of yeast cytochrome c peroxidase and its peroxide and its peroxide compound, Compound ES

Electron paramagnetic resonance absorption spectrum of ferric cytochrome c peroxidase exhibited a mixture of high- and low-spin compounds. The principal values and the eigenvectors of the g-tensor for the low-spin species were determined by single-crystal EPR spectroscopy at 77 K. The powder EPR spectra of the peroxide compound, Compound ES, were measured at S-, X-, and Q-band microwave frequencies. Careful examination at 77 K showed a narrow free radical-like signal at g = 2.004 with hyperfine structures accompanied by a broad signal spreading on both low- and high-field sides. Single-crystal EPR analyses of Compound ES clearly demonstrated that there exist at least two different radical species: one is isotropic with hyperfine structure at g = 2.004 and the other exhibits an axially symmetric signal at 5 K and broad signal centered at g = 2.004 at 77 K, respectively. The principal values and the eigenvectors of the g-tensor for the axially symmetric signal were determined: g(parallel) = 2.034 and g(perpendicular) = 2.006, 1.999. The orientation of the unique axis (g(parallel)) was found to be identical to that of the heme normal. A new radical signal with complicated hyperfine structures in the g = 2.004 region was observed upon illumination of Compound ES at both 5 and 77 K. The photoinduced species grew effectively by the illumination light around 500 nm. On warming to -80 degrees C, the photoinduced signal was reversibly brought back to the original radical species of Compound ES via an intermediate species. From these results, we have proposed the possible sites for the free radical centers in Compound ES.     

Conformation of the c552:aa3 electron transfer complex in Paracoccus denitrificans studied by EPR on oriented samples

The EPR spectral parameters of aa(3) oxidase and cyt c(552) from Paracoccus denitrificans were studied in purified oxidase and enriched cyt c(552). The orientation of the g-tensors of hemes a and c(552) were determined on partially ordered membranes, enriched cyt c(552) and a c(552):aa(3) subcomplex. The known correlation of g-tensor to molecular axes in histidine/methionine ligated hemes permits us to position cyt c(552) with respect to the parent membrane. Taken together with previous data on the interaction surface between aa(3) oxidase and cyt c(552), these results allow us to arrive at a single conformation for the c(552):aa(3) electron transfer complex.     

Photosystem II single crystals studied by transient EPR: the light-induced triplet state

Transient electron paramagnetic resonance (TR EPR) at 9.8 GHz has been used to study the light-induced triplet state in single crystals of Photosystem II (PS II). The crystals were grown from a solution of PS II core complexes from the thermophilic cyanobacterium Synechococcus elongatus. The core complexes contain at least 17 subunits, including the water-oxidizing complex, and 32 chlorophyll a molecules per PS II complex. The PS II complexes are active in light-induced electron transfer and water oxidation. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with four dimers of PS II complexes per unit cell. Laser excitation was used to generate the recombination triplet state in PS II which was then studied by EPR at low temperatures (10 K). The crystal spectra show the same magnitude of the zero-field splitting (ZFS) values D, E as spectra obtained earlier for the triplet state of PS II in frozen solution. The orientation of the ZFS tensor D of the triplet state with respect to the crystallographic axes has been deduced from the analysis of angular-dependent EPR spectra. Knowledge of the orientation of the D tensor component perpendicular to the plane of the chlorophyll (D(Z)) allows an assignment on which chlorophyll of the reaction centre the triplet state is localized at low temperatures. Furthermore, the orientation of the D(X) and D(Y) components of the D tensor yielded the in-plane orientation of the respective chlorophyll in the reaction centre providing first experimental evidence for the orientation of this molecule in the PS II.     

Preliminary x-ray investigation of an orthorhombic crystal form of human plasma albumin.

An orthorhombic form of single crystals of human plasma albumin, suitable for x-ray diffraction studies, has been grown with ammonium sulfate from protein solutions purified from fresh frozen single donor plasma as well as from a commercial sample of plasma albumin. The space group is P2(1)2(1)2 with 12 molecules in the unit cell. The cell dimensions are: a = 133.3 +/- 1.2 A, b = 274.8 +/- 3.3 A,, and c = 58.02 +/- 0.02 A.     

Volume contraction on photoexcitation of the reaction center from Rhodobacter sphaeroides R-26: internal probe of dielectrics.

Reaction centers of Rhodobacter sphaeroides undergo a approximately 20 A3/mole volume contraction in < 50 ns after excitation. The rapid volume change is tentatively assigned to electrostriction. From its magnitude, we infer that the effective dielectric coefficient is 10-15 if the compressibility of the reaction center is similar to that of globular proteins. The volume contraction is not sensitive to replacement of the natural ubiquinone at the QA site by other quinones or to the occupancy of the QB site. The quenching caused by pressure on the reaction centers most likely occurs on a faster time scale than that of electron transfer.     

Participation of inorganic phosphates as electron donors in the primary reactions of photosynthesis in Rhodobacter sphaeroides

The formation of ATP during photophosphorylation in chromatophores from purple nonsulfur bacterium Rhodobacter sphaeroides in the presence of phenazine methosulfate and without exogenous electron carriers under constant illumination and by the action of single light flashes was studied. It was shown that the photoinduced transport of electrons to the exogenous electron acceptor depends on phosphate. It was assumed that phosphate ions are electron donors in the reaction center P870; by the action of light, P870 converts the phosphate ion HPO4(2-) into anion radical HPO4-.. In the difference EPR spectra "light minus darkness" at 77 K, an asymmetrical doublet signal with a weak low-field line was observed. The signal had a g-tensor of about 2.014 and a hyperfine coupling constant of about 2.5 mT and belongs probably to the phosphate anion radical.     

Photochemical Electron Transport in Photosynthetic Reaction Centers from Rhodopseudomonas spheroides: III. Effects of Orthophenanthroline and Other Chemicals

Reaction centers from Rhodopseudomonas spheroides mediate the photochemical oxidation of cytochrome c (cyt c), and show a time-varying fluorescence of P870. Analyses of these effects indicate that the reaction centers contain a primary photochemical electron acceptor capable of holding one electron. Native or added ubiquinone (UQ) can act as a secondary electron acceptor. Orthophenanthroline (o-phen) blocks electron transfer from primary to secondary acceptors, and allows the primary acceptor to be exhibited in the foregoing experiments. Other chelators (with the possible exception of 8-hydroxyquinoline) and dichlorophenyldimethylurea (DCMU) are without apparent effect on reaction centers. o-Phen also inhibits the primary photochemical act in reaction centers; this effect is prevented by the presence of UQ. 2-n-Nonyl-4-hydroxyquinoline-N-oxide (NQNO) inhibits the primary photochemistry in reaction centers but does not affect secondary electron transfer.     

Linear dichroism and the orientation of reaction centers of Rhodopseudomonas sphaeroides in dried gelatin films.

Aqueous mixtures of reaction centers of Rhodopseudomonas sphaeroides and gelatin were dried to form thin films. Following hydration, these films were stretched as much as two to three times their original length. Polarized absorption spectra showing linear dichroism were obtained for both unstretched and stretched films, with the planes and stretching axes of the films mounted in various geometries relative to the electric vector of the measuring beam. These data were analyzed in terms of the following model: Reaction centers possess an axis of symmetry that is fixed in relation to the reaction center structure. In unstretched films this axis is confined to the film plane and oriented at random within the plane. In stretched films the symmetry axis is aligned with the direction of stretching. In both preparations reaction centers are distributed randomly with respect to rotation about the axis of symmetry. The data are consistent with this model when the analysis acknowledges less than perfect orientation. For perfect orientation in a stretched film the model predicts uniaxial symmetry about the axis of stretching. The approach to this condition was examined with films stretched to different extents. Extrapolation yielded dichroic ratios for the ideal case of perfect orientation, and allowed calculation of the angles between the axis of symmetry and the various optical transition dipoles in the reaction center. This treatment included the two absorption bands of the bacteriochlorophyll 'special pair' (photochemical electron donor) in the Qx region, at 600 and 630 nm, which we were able to resolve in light minus dark difference spectra.