Investigation of the Mn Binding Site in Cytochrome c Oxidase from Paracoccus denitrificans by High-Frequency EPR

Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics

During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated.

Theory of solid effect and cross effect dynamic nuclear polarization with half-integer high-spin metal polarizing agents in rotating solids

Detailed theoretical description of high-spin properties of metal polarizing agents, especially Gd³⁺, for solid effect and cross effect DNP.

Multifrequency pulsed electron paramagnetic resonance on metalloproteins

Metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (EPR) spectroscopy can be a powerful tool for studying protein structure and function. Dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. Hyperfine spectroscopy can be used to measure the interaction between an unpaired electron spin and nuclear spins within a distance of 0.8 nm; it therefore permits the characterization of the local structure of the paramagnetic center's ligand sphere with very high precision. In this Account, we review our laboratory's recent applications of both dipolar and hyperfine pulsed EPR methods to metalloproteins. We used pulsed dipolar relaxation methods to investigate the complex of cytochrome c and cytochrome c oxidase, a noncovalent protein-protein complex involved in mitochondrial electron-transfer reactions. Hyperfine sublevel correlation spectroscopy (HYSCORE) was used to study the ligand sphere of iron-sulfur clusters in complex I of the mitochondrial respiratory chain and substrate binding to the molybdenum enzyme polysulfide reductase. These examples demonstrate the potential of the two techniques; however, they also highlight the difficulties of data interpretation when several paramagnetic species with overlapping spectra are present in the protein. In such cases, further approaches and data are very useful to enhance the information content. Relaxation filtered hyperfine spectroscopy (REFINE) can be used to separate the individual components of overlapping paramagnetic species on the basis of differences in their longitudinal relaxation rates; it is applicable to any kind of pulsed hyperfine or dipolar spectroscopy. Here, we show that the spectra of the iron-sulfur clusters in complex I can be separated by this method, allowing us to obtain hyperfine (and dipolar) information from the individual species. Furthermore, performing pulsed EPR experiments at different magnetic fields is another important tool to disentangle the spectral components in such complex systems. Despite the fact that high magnetic fields do not usually lead to better spectral separation for metal centers, they provide additional information about the relative orientation of different paramagnetic centers. Our high-field EPR studies on cytochrome c oxidase reveal essential information regarding the structural arrangement of the binuclear Cu(A) center with respect to both the manganese ion within the enzyme and the cytochrome in the protein-protein complex with cytochrome c.

EPR evidence of cyanide binding to the Mn(Mg) center of cytochrome c oxidase: support for Cu(A)-Mg involvement in proton pumping

We examined the anion binding behavior of the Mg(Mn) site in cytochrome c oxidase to test a possible role of this center in proton pumping. Rhodobacter sphaeroides grown in a Mn(II)-rich medium replaces the intrinsic Mg(II) ion with an EPR-detectable Mn(II) ion without change in activity. Due to its close proximity and a shared ligand, oxidized Cu(A) is spin-coupled to the Mn(II) ion, affecting the EPR spectrum. An examination of both bovine and R.s. oxidase crystal structures reveals a hydrogen-bonding pattern in the vicinity of the Mg(II) site that is consistent with three water ligands of the Mg(Mn) center when Cu(A) is oxidized. In the reduced structure, one water molecule in the vicinity of the Cu(A) ligand, E198, moves closer, appearing to be converted into an ionically bonded hydronium ion, while a second water molecule bonded to Mg(Mn) shows evidence of conversion to a hydroxide. The implied proton movement is proposed to be part of a redox-linked export of a pumped proton from the binuclear center into the exit pathway. To test the model, cyanide and azide were added to the oxidized and reduced forms of the enzyme, and Mn(II) CW-EPR and ESEEM spectra were recorded. Addition of azide broadened the CW-EPR spectra for both oxidized and reduced enzyme. Cyanide addition affected the Mn(II) CW-EPR spectrum of reduced cytochrome c oxidase by increasing Mn(II) zero field splitting and broadening the spectral line shapes but had no effect on oxidized enzyme. ESEEM measurements support a differential ability of Mn(II) to bind cyanide in the reduced state of cytochrome c oxidase. This new observation of anion binding at the Mg/Mn site is of interest in terms of accessibility of the buried site and its potential role in redox-dependent proton pumping.

Kinetic Resolution of a Tryptophan-radical Intermediate in the Reaction Cycle of Paracoccus denitrificans Cytochrome c Oxidase

The catalytic mechanism, electron transfer coupled to proton pumping, of heme-copper oxidases is not yet fully understood. Microsecond freeze-hyperquenching single turnover experiments were carried out with fully reduced cytochrome aa(3) reacting with O(2) between 83 micros and 6 ms. Trapped intermediates were analyzed by low temperature UV-visible, X-band, and Q-band EPR spectroscopy, enabling determination of the oxidation-reduction kinetics of Cu(A), heme a, heme a(3), and of a recently detected tryptophan radical (Wiertz, F. G. M., Richter, O. M. H., Cherepanov, A. V., MacMillan, F., Ludwig, B., and de Vries, S. (2004) FEBS Lett. 575, 127-130). Cu(B) and heme a(3) were EPR silent during all stages of the reaction. Cu(A) and heme a are in electronic equilibrium acting as a redox pair. The reduction potential of Cu(A) is 4.5 mV lower than that of heme a. Both redox groups are oxidized in two phases with apparent half-lives of 57 micros and 1.2 ms together donating a single electron to the binuclear center in each phase. The formation of the heme a(3) oxoferryl species P(R) (maxima at 430 nm and 606 nm) was completed in approximately 130 micros, similar to the first oxidation phase of Cu(A) and heme a. The intermediate F (absorbance maximum at 571 nm) is formed from P(R) and decays to a hitherto undetected intermediate named F(W)(*). F(W)(*) harbors a tryptophan radical, identified by Q-band EPR spectroscopy as the tryptophan neutral radical of the strictly conserved Trp-272 (Trp-272(*)). The Trp-272(*) populates to 4-5% due to its relatively low rate of formation (t((1/2)) = 1.2 ms) and rapid rate of breakdown (t((1/2)) = 60 micros), which represents electron transfer from Cu(A)/heme a to Trp-272(*). The formation of the Trp-272(*) constitutes the major rate-determining step of the catalytic cycle. Our findings show that Trp-272 is a redox-active residue and is in this respect on an equal par to the metallocenters of the cytochrome c oxidase. Trp-272 is the direct reductant either to the heme a(3) oxoferryl species or to Cu (2+)(B). The potential role of Trp-272 in proton pumping is discussed.

Long-range distance determinations in biomacromolecules by EPR spectroscopy

Electron paramagnetic resonance (EPR) spectroscopy provides a variety of tools to study structures and structural changes of large biomolecules or complexes thereof. In order to unravel secondary structure elements, domain arrangements or complex formation, continuous wave and pulsed EPR methods capable of measuring the magnetic dipole coupling between two unpaired electrons can be used to obtain long-range distance constraints on the nanometer scale. Such methods yield reliably and precisely distances of up to 80 A, can be applied to biomolecules in aqueous buffer solutions or membranes, and are not size limited. They can be applied either at cryogenic or physiological temperatures and down to amounts of a few nanomoles. Spin centers may be metal ions, metal clusters, cofactor radicals, amino acid radicals, or spin labels. In this review, we discuss the advantages and limitations of the different EPR spectroscopic methods, briefly describe their theoretical background, and summarize important biological applications. The main focus of this article will be on pulsed EPR methods like pulsed electron-electron double resonance (PELDOR) and their applications to spin-labeled biosystems.

Origin of the zero-field splitting in mononuclear octahedral dihalide MnII complexes: an investigation by multifrequency high-field electron paramagnetic resonance and density functional theory

The synthesis, structural characterization, and electronic properties of a new series of high-spin six-coordinate dihalide mononuclear MnII complexes [Mn(tpa)X2] (tpa=tris-2-picolylamine; X=I (1), Br (2), and Cl (3)) are reported. The analysis of the crystallographic data shows that in all investigated complexes the manganese ion lies in the center of a distorted octahedron with a cis configuration of the halides imposed by the tpa ligand. By a multifrequency high-field electron paramagnetic resonance investigation (95-285 GHz), the electronic properties of 1-3 were determined (DI=-0.600, DBr=-0.360, DCl=+0.115 cm-1), revealing the important effect of (i) the nature of the halide and (ii) the configuration (cis/trans) of the two halides on the magnitude of D. The spin Hamiltonian parameters obtained by density functional theory calculations initiated from the crystal structure of 1-3 are in reasonable agreement with the experimental values. The absolute value of D is consistently overestimated, but the sign and the trend over the chemical series is well reproduced. Theoretical models (cis- and trans-[Mn(NH3)4X2], X=I, Br, Cl and F) have been used to investigate the different contributions to D and also to understand the origin of the experimentally observed changes in D within the series reported here. This study reveals that the spin-spin coupling contributions to the D tensor are non-negligible for the lighter halides (F, Cl) but become insignificant for the heavier halides (I, Br). The four different types of excitations involved in the spin-orbit coupling (SOC) part of the D tensor contribute with comparable magnitudes and opposing signs. The general trend observed for halide MnII complexes (DI>DBr>DCl) can be explained by the fact that the halide SOC dominates the D value in these systems with a major contribution arising from interference between metal- and halide-SOC contributions, which are proportional to the product of the SOC constants of Mn and X.

Transient radical pairs studied by time-resolved EPR

Photogenerated short-lived radical pairs (RP) are common in biological photoprocesses such as photosynthesis and enzymatic DNA repair. They can be favorably probed by time-resolved electron paramagnetic resonance (EPR) methods with adequate time resolution. Two EPR techniques have proven to be particularly useful to extract information on the working states of photoinduced biological processes that is only difficult or sometimes even impossible to obtain by other types of spectroscopy. Firstly, transient EPR yields crucial information on the chemical nature and the geometry of the individual RP halves in a doublet-spin pair generated by a short laser pulse. This time-resolved method is applicable in all magnetic field/microwave frequency regimes that are used for continuous-wave EPR, and is nowadays routinely utilized with a time resolution reaching about 10 ns. Secondly, a pulsed EPR method named out-of-phase electron spin echo envelope modulation (OOP-ESEEM) is increasingly becoming popular. By this pulsed technique, the mutual spin-spin interaction between the RP halves in a doublet-spin pair manifests itself as an echo modulation detected as a function of the microwave-pulse spacing of a two-pulse echo sequence subsequent to a laser pulse. From the dipolar coupling, the distance between the radicals is readily derived. Since the spin-spin interaction parameters are typically not observable by transient EPR, the two techniques complement each other favorably. Both EPR methods have recently been applied to a variety of light-induced RPs in photobiology. This review summarizes the results obtained from such studies in the fields of plant and bacterial photosynthesis and DNA repair mediated by the enzyme DNA photolyase.

Structural Characterization and Electronic Properties Determination by High-Field and High-Frequency EPR of a Series of Five-Coordinated Mn(II) Complexes

The isolation, structural characterization, and electronic properties of a series of high-spin mononuclear five-coordinated Mn(II) complexes, [Mn(terpy)(X)(2)] (terpy = 2, 2':6',2' '-terpyridine; X = I(-) (1), Br(-) (2), Cl(-) (3), or SCN(-) (4)), are reported. The X-ray structures of the complexes reveal that the manganese ion lies in the center of a distorted trigonal bipyramid for complexes 1, 2, and 4, while complex 3 is better described as a distorted square pyramid. The electronic properties of 1-4 were investigated by high-field and high-frequency EPR spectroscopy (HF-EPR) performed between 5 and 30 K. The powder HF-EPR spectra have been recorded in high-field-limit conditions (95-285 GHz) (D << gbetaB). The spectra are thus simplified, allowing an easy interpretation of the experimental data and an accurate determination of the spin Hamiltonian parameters. The magnitude of D varies between 0.26 and 1.00 cm(-)(1) with the nature of the anionic ligand. Thanks to low-temperature EPR experiments, the sign of D was unambiguously determined. D is positive for the iodo and bromo complexes and negative for the chloro and thiocyano ones. A structural correlation is proposed. Each complex is characterized by a significant rhombicity with E/D values between 0.17 and 0.29, reflecting the distorted geometry observed around the manganese. Finally, we compared the spin Hamiltonian parameters of our five-coordinated complexes and those previously reported for other analogous series of dihalo four- and six-coordinated complexes. The effect of the coordination number and of the geometry of the Mn(II) complexes on the spin Hamiltonian parameters is discussed.

Manganese(II) zero-field interaction in cambialistic and manganese superoxide dismutases and its relationship to the structure of the metal binding site

The Mn(II) high-magnetic-field electron paramagnetic resonance (HFEPR) spectra of five different superoxide dismutases (SODs) were measured at 190 and 285 GHz. The native E. coli manganese SOD was found to be distinct from the other SODs by virtue of its large zero-field E-value. The two wild-type cambialistic proteins from Porphyromonas gingivalis and Rhodobacter capsulatus were also distinct. However, the Gly155Thr mutant of the P. gingivalis SOD changed the Mn(II) spectrum so that it closely resembled the spectrum of manganese reconstituted E. coli iron SOD. This observation paralleled enzyme activity measurements that show that this mutation causes the loss of activity with manganese and enhanced activity with iron indicating a conversion from a cambialistic to an iron-specific protein. The Mn(II) magnetic parameters were determined by simultaneously fitting the multifrequency data. Simulations were carried out by numerically diagonalizing the spin Hamiltonian and explicitly calculating all possible transition probabilities. The relationship between the Mn(II) zero-field interaction and structure of the metal binding site is also discussed.

Cytochrome c oxidase--structure, function, and physiology of a redox-driven molecular machine

Cytochome c oxidase is the terminal member of the electron transport chains of mitochondria and many bacteria. Providing an efficient mechanism for dioxygen reduction on the one hand, it also acts as a redox-linked proton pump, coupling the free energy of water formation to the generation of a transmembrane electrochemical gradient to eventually drive ATP synthesis. The overall complexity of the mitochondrial enzyme is also reflected by its subunit structure and assembly pathway, whereas the diversity of the bacterial enzymes has fostered the notion of a large family of heme-copper terminal oxidases. Moreover, the successful elucidation of 3-D structures for both the mitochondrial and several bacterial oxidases has greatly helped in designing mutagenesis approaches to study functional aspects in these enzymes.

Dynamics in the Mn2+ binding site in single crystals of concanavalin A revealed by high-field EPR spectroscopy

EPR spectroscopy at 95 GHz was used to characterize the dynamics at the Mn(2+) binding site in single crystals of the saccharide-binding protein concanavalin A. The zero-field splitting (ZFS) tensor of the Mn(2+) was determined from rotation patterns in the a-c and a-b crystallographic planes, acquired at room temperature and 4.5 K. The analysis of the rotation patterns showed that while at room temperature there is only one type of Mn(2+) site, at low temperatures two types of Mn(2+) sites, not related by any symmetry, are distinguished. The sites differ in the ZFS parameters D and E and in the orientation of the ZFS tensor with respect to the crystallographic axes. Temperature-dependent EPR measurements on a crystal oriented with its crystallographic a axis parallel to the magnetic field showed that as the temperature increases, the two well-resolved Mn(2+) sextets gradually coalesce into a single sextet at room temperature. The line shape changes are characteristic of a two-site exchange. This was confirmed by simulations which gave rates in the range of 10(7)-10(8) s(-1) for the temperature range of 200-266 K and an activation energy of 23.8 kJ/mol. This dynamic process was attributed to a conformational equilibrium within the Mn(2+) binding site which freezes into two conformations at low temperatures.

Examples of high-frequency EPR studies in bioinorganic chemistry

Low-temperature EPR spectroscopy with frequencies between 95 and 345 GHz and magnetic fields up to 12 T has been used to study metal sites in proteins or inorganic complexes and free radicals. The high-field EPR method was used to resolve g-value anisotropy by separating it from overlapping hyperfine couplings. The presence of hydrogen bonding interactions to the tyrosyl radical oxygens in ribonucleotide reductases were detected. At 285 GHz the g-value anisotropy from the rhombic type 2 Cu(II) signal in the enzyme laccase has its g-value anisotropy clearly resolved from slightly different overlapping axial species. Simple metal site systems with S>1/2 undergo a zero-field splitting, which can be described by the spin Hamiltonian. From high-frequency EPR, the D values that are small compared to the frequency (high-field limit) can be determined directly by measuring the distance of the outermost signal to the center of the spectrum, which corresponds to (2 S-1)* mid R: Dmid R: For example, D values of 0.8 and 0.3 cm(-1) are observed for S=5/2 Fe(III)-EDTA and transferrin, respectively. When D values are larger compared to the frequency and in the case of half-integer spin systems, they can be obtained from the frequency dependence of the shifts of g(eff), as observed for myoglobin in the presence ( D=5 cm(-1)) or absence ( D=9.5 cm(-1)) of fluoride. The 285 and 345 GHz spectra of the Fe(II)-NO-EDTA complex show that it is best described as a S=3/2 system with D=11.5 cm(-1), E=0.1 cm(-1), and g(x)= g(y)= g(z)=2.0. Finally, the effects of HF-EPR on X-band EPR silent states and weak magnetic interactions are demonstrated.

Paramagnetic resonance of biological metal centers

The review deals with recent advances in magnetic resonance spectroscopy (hf EPR and NMR) of paramagnetic metal centers in biological macromolecules. In the first half of our chapter, we present an overview of recent technical developments in the NMR of paramagnetic bio-macromolecules. These are illustrated by a variety of examples deriving mainly from the spectroscopy of metalloproteins and their complexes. The second half focuses on recent developments in high-frequency EPR spectroscopy and the application of the technique to copper, iron, and manganese proteins. Special attention is given to the work on single crystals of copper proteins.

Pulsed EPR spectroscopy: biological applications

Pulsed electron paramagnetic resonance (EPR) methods such as ESEEM, PELDOR, relaxation time measurements, transient EPR, high-field/high-frequency EPR, and pulsed ENDOR, have been used successfully to investigate the local structure and dynamics of paramagnetic centers in biological samples. These methods allow different contributions to the EPR spectra to be distinguished and can help unravel complicated EPR spectra consisting of overlapping resonance lines, as are often found in disordered protein samples. The basic principles, specific potentials, technical requirements, and limitations of these advanced EPR techniques will be reviewed together with recent applications to metal centers, organic radicals, and spin labels in proteins.