NMR assignment of Rhodobacter capsulatus ferricytochrome c', a 28 kDa paramagnetic heme protein

Construction of a Biosensor Based on a Combination of Cytochrome c, Graphene, and Gold Nanoparticles

A biosensor based on a combination of cytochrome c (Cyt c), electrochemical reduced graphene oxides (ERGO), and gold nanoparticles (AuNPs) on a glassy carbon electrode (GCE) was fabricated. The proposed biosensor electrode was denoted as GCE/ERGO-Nafion/AuNPs/Cyt c/Nafion, where ERGO-Nafion was deposited by dropping graphene oxides-Nafion mixed droplet first and following electrochemical reduction, AuNPs were directly deposited on the surface of the ERGO-Nafion modified electrode by electrochemical reduction, and other components were deposited by the dropping-dry method. The effect of the deposition amount of AuNPs on direct electrochemistry of Cyt c in the proposed electrode was investigated. The hydrogen peroxide was taken to evaluate the performance of the proposed biosensor. The results showed that the biosensor has great analytical performance, including a high sensitivity, a wide linear range, a low detection limit, and good stability, reproducibility, and reliability.

Reduced dimensionality 3D HNCAN for unambiguous HN, CA and N assignment in proteins

We present here an improvisation of HNN (Panchal, Bhavesh et al., 2001) called RD 3D HNCAN for backbone (HN, CA and (15)N) assignment in both folded and unfolded proteins. This is a reduced dimensionality experiment which employs CA chemical shifts to improve dispersion. Distinct positive and negative peak patterns of various triplet segments along the polypeptide chain observed in HNN are retained and these provide start and check points for the sequential walk. Because of co-incrementing of CA and (15)N, peaks along one of the dimensions appear at sums and differences of the CA and (15)N chemical shifts. This changes the backbone assignment protocol slightly and we present this in explicit detail. The performance of the experiment has been demonstrated using Ubiquitin and Plasmodium falciparum P2 proteins. The experiment is particularly valuable when two neighboring amino acid residues have nearly identical backbone (15)N chemical shifts.

Solution NMR characterization of the electronic structure and magnetic properties of high-spin ferrous heme in deoxy myoglobin from Aplysia limacina

Solution (1)H NMR has been used to elucidate the magnetic properties and electronic structure of the prosthetic group in high-spin, ferrous deoxy myoglobin from the sea hare Aplysia limacina. A sufficient number of dipolar shifted residue signals were assigned to allow the robust determination of the orientation and anisotropy of the paramagnetic susceptibility tensor, chi. The resulting quantitative description of dipolar shifts allows a determination of the contact shifts for the heme. Chi was found to be axial, with Deltachi(ax) = -2.07 x 10(-8) m(3)/mol, with the major axis tilted (approximately 76 degrees) almost into the heme plane and in the general direction of the orientation of the axial HisF8 imidazole plane which coincides approximately with the beta-,delta-meso axis. The factored contact shifts for the heme are shown to be consistent with the transfer of positive pi spin density into one of the two components of the highest filled pi molecular orbital, 3e(pi), and the transfer of negative pi-spin density, via spin-spin correlation, into the orthogonal excited-state component of the 3e(pi) molecular orbital. The thermal population of the excited state leads to strong deviation from the Curie law for the heme substituents experiencing primarily the negative pi-spin density. The much larger transfer of negative spin density via the spin-paired dpi orbital into the excited state 3e(pi) in high-spin iron(II) than in low-spin iron(III) hemoproteins is attributed to the much stronger correlation exerted by the four unpaired spin on the iron in the former, as compared to the single unpaired spins on iron in the latter.

Models for cytochromes c': spin states of mono(imidazole)-ligated (meso-tetramesitylporphyrinato)iron(III) complexes as studied by UV-Vis, 13C NMR, 1H NMR, and EPR spectroscopy

A number of mono(imidazole)-ligated complexes of perchloro(meso-tetramesitylporphyrinato)iron(III), [Fe(TMP)L]ClO(4), have been prepared, and their spin states have been examined by (1)H NMR, (13)C NMR, and EPR spectroscopy as well as solution magnetic moments. All the complexes examined have shown a quantum mechanical spin admixed state of high and intermediate-spin (S = 5/2 and 3/2) states though the contribution of the S = 3/2 state varies depending on the nature of axial ligands. While the complex with extremely bulky 2-tert-butylimidazole (2-(t)()BuIm) has exhibited an essentially pure S = 5/2 state, the complex with electron-deficient 4,5-dichloroimidazole (4,5-Cl(2)Im) adopts an S = 3/2 state with 30% of the S = 5/2 spin admixture. On the basis of the (1)H and (13)C NMR results, we have concluded that the S = 3/2 contribution at ambient temperature increases according to the following order: 2-(t)BuIm < 2-(1-EtPr)Im < 2-MeIm <or= 2-EtIm <or= 2-(i)PrIm < 4,5-Cl(2)Im. The effective magnetic moments determined by the Evans method in CH(2)Cl(2) solution are 5.9 and 5.0 mu(B) at 25 degrees C for [Fe(TMP)(2-(t)BuIm)]ClO(4) and [Fe(TMP)(2-MeIm)]ClO(4), respectively, which further verify the order given above. Comparison of the NMR and EPR data has revealed that the S = 3/2 contribution changes sensitively by the temperature; the S = 3/2 contribution decreases as the temperature is lowered for all the mono(imidazole) complexes examined in this study. The solvent polarity also affects the spin state; polar solvents such as methanol and acetonitrile increase the S = 3/2 contribution while nonpolar solvents such as benzene decrease it. These results are explained in terms of the structurally flexible nature of the mono(imidazole) complexes; structural parameters such as the Fe(III)-N(axial) bond length, displacement of the iron from the N4 core, tilting of the Fe(III)-N(axial) bond to the heme normal, orientation of the coordinated imidazole ligand, etc., could be altered by the nature of the axial ligands as well as by the solvent polarity and temperature. Some mysteries on the spin states of cytochromes c' isolated from various bacterial sources are possibly explained in terms of the flexible nature of the mono(imidazole)-ligated structure.

Intraresidue HNCA and COHNCA experiments for protein backbone resonance assignment

Two novel experiments, intra-HNCA and intra-COHNCA, are presented for sequential backbone resonance assignment of (13)C, (15)N labeled proteins. The advantage with respect to conventional pulse schemes is the suppression of the sequential (15)N-->(13)C(alpha) coherence transfer pathway, which can be separately obtained from a HNCOCA correlation experiment. This results in a two-fold reduction of the number of detected correlation peaks. Spectral simplification is especially important for efficient automated assignment protocols as required in the context of high-throughput protein studies by NMR. The performance of the new experiments is demonstrated on an 18-kDa protein fragment of the E. coli sulfite reductase and compared to conventional techniques in terms of sensitivity and resolution.

Solution structure of the functional domain of Paracoccus denitrificans cytochrome c552 in the reduced state

In order to determine the solution structure of Paracoccus denitrificans cytochrome c552 by NMR, we cloned and isotopically labeled a 10.5-kDa soluble fragment (100 residues) containing the functional domain of the 18.2-kDa membrane-bound protein. Using uniformly 15N-enriched samples of cytochrome c552 in the reduced state, a variety of two-dimensional and three-dimensional heteronuclear double-resonance NMR experiments was employed to achieve complete 1H and 15N assignments. A total of 1893 distance restraints was derived from homonuclear 2D-NOESY and heteronuclear 3D-NOESY spectra; 1486 meaningful restraints were used in the structure calculations. After restrained energy minimization a family of 20 structures was obtained with rmsd values of 0.56 +/- 0. 10 A and 1.09 +/- 0.09 A for the backbone and heavy atoms, respectively. The overall topology is similar to that seen in previously reported models of this class of proteins. The global fold consists of two long helices at the N-terminus and C-terminus and three shorter helices surrounding the heme moiety; the helices are connected by well-defined loops. Comparison with the X-ray structure shows some minor differences in the positions of the Trp57 and Phe65 side-chain rings as well as the heme propionate groups.

De novo determination of protein structure by NMR using orientational and long-range order restraints

Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.

Mapping the cytochrome c553 interacting site using 1H and 15N NMR

Cytochrome c553 is the electron transfer partner of formate dehydrogenase and of [Fel-hydrogenase, two metalloenzymes essential in the metabolism of sulfate reducing bacteria. These two enzymes contain a 'ferredoxin-like' domain which presents 30% identity with Desulfovibrio desulfuricans Norway ferredoxin 1. This was chosen as a model for the 'ferredoxin-like' domain involved in the electron transfer reaction with cytochrome c553. ID NMR titration of complex formation gave us the stoichiometry (1:1) and the dissociation constant of the complex (Kd approximately 3x10(-6) M). 2D heteronuclear NMR experiments were performed to analyze the 1H and 15N chemical shift variations that are induced by the protein-protein recognition. This is the first mapping of the interaction site on a c-type cytochrome, using heteronuclear NMR.

Cellular applications of a sensitive and selective fiber-optic nitric oxide biosensor based on a dye-labeled heme domain of soluble guanylate cyclase

Nitric oxide-selective sensors have been prepared with the heme domain of soluble guanylate cyclase (sGC), the only known receptor for signal transduction involving nitric oxide. Expressed in and purified from E. coli, the heme domain contains a stoichiometric amount of heme that has electronic and resonance Raman spectra almost identical to those of heterodimeric (native) sGC purified from bovine lung. The small size of the heme domain, its inability to bind oxygen, and its high affinity for nitric oxide make it well-suited for sensor applications. The heme domain has been labeled with a fluorescent reporter dye and changes in this dye's intensity are observed based on the sGC heme domain's characteristic binding of nitric oxide. The current sensors are prepared with 100-microns optical fiber but could also be prepared using submicrometer fiber tips. These sensors have fast, linear, and reversible responses to nitric oxide and are unaffected by numerous common interferents, such as oxygen, nitrite and nitrate. The sensor limit of detection is 1 microM nitric oxide. Glutathione has been shown to decrease the sensitivity of the sensor; however, the sensor response remains linear and can be calibrated on the basis of the glutathione concentration present in the biological environment of interest. The sensors have been used to measure extracellular nitric oxide production by BALB/c mouse macrophages. Minimal nitric oxide was produced by untreated cells, while high levels of nitric oxide were released from activated cells, e.g., 111 +/- 2 microM in a given cell culture.

Ratiometric and fluorescence-lifetime-based biosensors incorporating cytochrome c' and the detection of extra- and intracellular macrophage nitric oxide

Ratiometric and lifetime-based sensors have been designed for cellular detection of nitric oxide. These sensors incorporate cytochrome c', a hemoprotein known to bind nitric oxide selectively. The cytochrome c' is labeled with a fluorescent reporter dye, and changes in this dye's intensity or fluorescence lifetime are observed as the protein binds nitric oxide. The ratiometric sensors are composed of dye-labeled cytochrome c' attached to the optical fiber via colloidal gold, along with fluorescent microspheres as intensity standards. These ratiometric sensors exhibit linear response, have fast response times (< or = 0.25 s), and are completely reversible. The sensors are selective over numerous common interferents such as nitrite, nitrate, and oxygen species, and the limit of detection is 8 microM nitric oxide. The lifetime-based measurements are made using free, dye-labeled cytochrome c' in solution and have a limit of detection of 30 microM nitric oxide. The use of these two techniques has allowed measurement of intra- and extracellular macrophage nitric oxide. Employing the ratiometric fiber sensors gave a multicell culture average extracellular nitric oxide concentration of 210 +/- 90 microM for activated macrophages, while an average intracellular concentration of 160 +/- 10 microM was determined from the lifetime-based measurements of dye-labeled cytochrome c' in the macrophage cytosol. Microscopic adaptation of the lifetime-based methods described here would allow direct correlation of intracellular nitric oxide levels with specific cellular activities, such as phagocytosis.

15N-labelling and preliminary heteronuclear NMR study of Desulfovibrio vulgaris Hildenborough cytochrome c553

When using heteronuclear NMR, 15N-labelling is necessary for structural analysis, dynamic studies and determination of complex formation. The problems that arise with isotopic labelling of metalloproteins are due to their complex maturation process, which involves a large number of factors. Cytochromes c are poorly expressed in Escherichia coli and the overexpression that is necessary for 15N-labelling, requires an investigation of the expression host and special attention to growth conditions. We have succeeded in the heterologous expression and the complete and uniform isotopic 15N-labelling of the cytochrome c553 from Desulfovibrio vulgaris Hildenborough, in a sulphate-reducing bacterium, D. desulfuricans G200, by using a growth medium combining 15N-ammonium chloride and 15N-Celtone. These conditions allowed us to obtain approximately 0.8 mg x L-1 of pure labelled cytochrome c553. 1H and 15N-assignments for both the oxidized and the reduced states of cytochrome c553 were obtained from two-dimensional heteronuclear experiments. Pseudocontact effects due to the haem Fe3+ have been analysed for the first time through 15N and 1H chemical shifts in a c-type cytochrome.

Fiber-optic nitric oxide-selective biosensors and nanosensors

Fiber-optic biosensors that are selective for nitric oxide and do not respond to most potential interferents have been prepared with cytochromes c'. Both micro- and nanosensors have been prepared, and their response is fast (< 1 s), reversible, and linear up to 1 mM nitric oxide. The detection limit is 20 microM, making the sensor useful for some biological samples, such as the macrophages studied here. While sensors have been prepared based on the fluorescence of the cytochromes c', optodes with greatly enhanced signal-to-noise ratios have been made by labeling the cytochrome c' with a fluorescent dye. Comparisons of cytochromes c' from three species of bacteria as well as of two matrixes were performed and the optimum sensor configuration is described.

Differential levels of specific cytochrome c biogenesis proteins in response to oxygen: analysis of the ccl operon in Rhodobacter capsulatus

The photosynthetic bacterium Rhodobacter capsulatus synthesizes c-type cytochromes under a variety of growth conditions. For example, under aerobic growth, c-type cytochromes are synthesized as part of an electron transport pathway, using oxygen as the terminal electron acceptor. Anaerobically in the light, R. capsulatus requires cytochrome bc1 and other c-type cytochromes for the photosynthetic electron transport pathway. It is shown here that the ccl1 and ccl2 genes of R. capsulatus are required for the synthesis of all c-type cytochromes, including the cytochrome c' protein of unknown function but of structural similarity to cytochrome b562. Polar and nonpolar mutations constructed in each gene demonstrated that the ccl12 genes form an operon. Expression of the ccl12 genes was examined by using lacZ and phoA fusions as translational reporters. Primer extension analysis was used to determine transcriptional control and the start site of the ccl12 promoter. Finally, antiserum to the Ccl2 protein was used to quantitate levels of Ccl2 under six different growth conditions. The Ccl2 protein is present at 20-fold-higher levels under conditions where oxygen is present. In contrast, other cytochromes c biogenesis proteins, HelA and HelX, previously shown to be part of an helABCDX operon, are at relatively similar levels under these six growth conditions. This discovery is discussed in terms of the physiology and evolution of cytochromes c biogenesis, with particular attention to oxidative environments.

Molecular and immunological analysis of an ABC transporter complex required for cytochrome c biogenesis

The helABC genes are predicted to encode an ATP-binding cassette (ABC) transporter necessary for heme export for ligation in bacterial cytochrome c biogenesis. The recent discoveries of homologs of the helB and helC genes in plant mitochondrial genomes suggest this is a highly conserved transporter in prokaryotes and some eukaryotes with the HelB and HelC proteins comprising the transmembrane components. Molecular genetic analysis in the Gram-negative bacterium Rhodobacter capsulatus was used to show that the helABC and helDX genes are part of an operon linked to the secDF genes. To facilitate analysis of this transporter, strains with non-polar deletions in each gene, epitope and reporter-tagged HelABCD proteins, and antisera specific to the HelA and HelX proteins were generated. We directly demonstrate that this transporter is present in the cytoplasmic membrane as an HelABCD complex. The HelB and HelC but not HelD proteins are necessary for the binding and stability of the HelA protein, the cytoplasmic subunit containing the ATP-binding region. In addition we show that the HelA protein co-immunoprecipitates with either the HelC or HelD proteins. Thus, the HelABCD heme export complex is distinguished by the presence of four membrane-associated subunits and represents a unique subfamily of ABC transporters.

Concerted movement of side chains in the haem vicinity observed on ligand binding in cytochrome c' from rhodobacter capsulatus

We have determined the structure of n-butylisocyanide-bound Rhodobacter capsulatus cytochrome c'. This is the first example of a ligand-bound structure of a class IIa cytochrome c. Compared with the structure of native cytochrome c', there are significant conformational changes of amino acid residues in the haem vicinity, accompanied by a rearrangement of the hydrogen bonding pattern. The results suggest that rearrangements resulting from ligand binding could drive dimer dissociation in some species and also that the haem propionate may participate in proton transfer.

Characterization of the dynamic properties of Rhodobacter capsulatus ferricytochrome c'--a 28 kDa paramagnetic heme protein

The cytochrome c' are paramagnetic heme proteins generally consisting of two identical 14 kDa subunits. The recent assignment of the 1H and 15N resonances of the Rhodobacter capsulatus ferricytochrome c' has allowed characterization of the dynamic properties by measurement of the heteronuclear NOE for each resolved amide group. The relative importance of fast local motion and paramagnetic effect on nuclear relaxation were distinguished by comparison of the measured heteronuclear NOE with that of the overall experimental average. We show that the average experimental value of -0.16 corresponds to the rigid body motion expected for a spherical complex of 28 kDa. Residues 3-5, 50-55 and 69-70 exhibit decreased heteronuclear NOE due to local motions on a fast time scale with respect to molecular tumbling. Based on the X-ray crystal structure of the homologous cytochrome c' from Chromatium vinosum, the mobile regions correspond to the N-terminus of helix-1 and 2 regions of nonregular secondary structure located between helices-2 and -3.