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Daniel H Murgida

Publications and source records attributed to Daniel H Murgida.

15 recordsLinked to original sources
PubMed2007

A density functional theory study of the electronic properties of Os(II) and Os(III) complexes immobilized on Au(111).

We present a density functional theory (DFT) study of an osmium polypyridyl complex adsorbed on Au(111). The osmium polypyridyl complex [Os(bpy)2(P0P)Cl]n+ [bpy is 2,2'-bipyridine, P0P is 4,4'-bipyridine, n = 1 for osmium(II), and n = 2 for osmium(III)] is bound to the surface through the free nitrogen of the P0P ligand. The calculations illuminate electronic properties relevant to recent comprehensive characterization of this class of osmium complexes by electrochemistry and electrochemical scanning tunneling microscopy. The optimized structures for the compounds are in close agreement with crystallographic structures reported in the literature. Oxidation of the complex has little effect on these structural features, but there is a substantial reordering of the electronic energy levels with corresponding changes in the electron density. Significantly, the highest occupied molecular orbital shifts from the metal center to the P0P ligand. The surface is modeled by a cluster of 28 gold atoms and gives a good description of the effect of immobilization on the electronic properties of the complexes. The results show that the coupling between the immobilized complex and the gold surface involves electronic polarization at the adsorbate/substrate interface rather than the formation of a covalent bond. However, the cluster is too small to fully represent bulk gold with the result that, contrary to what is experimentally observed, the DFT calculation predicts that the gold surface is more easily oxidized than the osmium(II) complex.

Algorithms↗
PubMed2006

Highly conserved residues Asp-197 and His-250 in Agp1 phytochrome control the proton affinity of the chromophore and Pfr formation.

The mutants H250A and D197A of Agp1 phytochrome from Agrobacterium tumefaciens were prepared and investigated by different spectroscopic and biochemical methods. Asp-197 and His-250 are highly conserved amino acids and are part of the hydrogen-bonding network that involves the chromophore. Both substitutions cause a destabilization of the protonated chromophore in the Pr state as revealed by resonance Raman and UV-visible absorption spectroscopy. Titration experiments demonstrate a lowering of the pK(a) from 11.1 (wild type) to 8.8 in H250A and 7.2 in D197A. Photoconversion of the mutants does not lead to the Pfr state. H250A is arrested in a meta-Rc-like state in which the chromophore is deprotonated. For H250A and the wild-type protein, deprotonation of the chromophore in meta-Rc is coupled to the release of a proton to the external medium, whereas the subsequent proton re-uptake, linked to the formation of the Pfr state in the wild-type protein, is not observed for H250A. No transient proton exchange with the external medium occurs in D197A, suggesting that Asp-197 may be the proton release group. Both mutants do not undergo the photo-induced protein structural changes that in the wild-type protein are detectable by size exclusion chromatography. These conformational changes are, therefore, attributed to the meta-Rc --> Pfr transition and most likely coupled to the transient proton re-uptake. The present results demonstrate that Asp-197 and His-250 are essential for stabilizing the protonated chromophore structure in the parent Pr state, which is required for the primary photochemical process, and for the complete photo-induced conversion to the Pfr state.

Agrobacterium tumefaciens↗
PubMed2006

Time-resolved methods in Biophysics. 1. A novel pump and probe surface-enhanced resonance Raman approach for studying biological photoreceptors.

This article describes a method, based on surface-enhanced resonance Raman (SERR) spectroscopy, for studying the reaction dynamics of photoreceptors immobilized on metal electrodes. Time resolution and fresh sample conditions are achieved by synchronizing the rotational and translational motion of a novel kinematic electrode with the duration and time delay between the pump and probe events. The power and sensitivity of the method is illustrated by studying the photocycle of the sensory photoreceptor NpSRII and its sensitivity to the applied electric field. The results are compared with time-resolved resonance Raman measurements in solution.

Biophysics↗
PubMed2006

Photoisomerization of azobenzenes and spirocompounds in nematic and in twisted nematic liquid crystals.

Samples of a nematic mixture of ZLI1132 and of a twisted nematic mixture composed of ZLI1132 and chiral inductor S811, including 1%-10% (w/w) 4-N,N-dimethylaminoazobenzene (DAB), (4'-nitro)-4-N,N-dimethylaminoazobenzene (NDAB), spiropyran (SP), or spirooxazine (SO) were irradiated to produce the photochromic transformation of the dopant. The changes in the system were monitored by time-resolved transmission spectroscopy, time-resolved birefringence, or polarized Raman scattering. The medium sensitivity of the kinetics and spectroscopy of some of the probes was used to derive information on polarity of the medium. In the systems studied, apart from the changes in absorption spectrum, great changes in birefringence can be photoinduced and the order of the nematic phase can be changed in either direction, depending on the dopant. The open form of SP can discriminate orientation polarity. Although the polarity parallel to the mesogenic director is similar to that for acetone, the perpendicular orientation has a polarity similar to acetonitrile. In agreement with this observation, the kinetics of the Z --> E isomerization of NDAB, oriented parallel to the mesogenic director, also experiences a polarity similar to that for acetone. The decay rate constant of the open form of SP displays a linear relationship between its Arrhenius parameters, which is universal in a great variety of homogeneous solvents, solvent mixtures, and liquid crystals, therefore validating the hypothesis that the same type of transformation is observed in all these cases, namely, the decay of the open form monomer. The dopants used have been proven to be adequate probes of bulklike properties in locally heterogeneous systems as liquid crystals.

Azo Compounds↗
PubMed2006

Redox processes of cytochrome c immobilized on solid supported polyelectrolyte multilayers.

The heme protein cytochrome c (Cyt-c), immobilized on polyelectrolyte multilayers on a silver electrode, was studied by stationary and time-resolved surface-enhanced resonance Raman (SERR) spectroscopy to probe the redox site structure and the mechanism and dynamics of the potential-dependent interfacial processes. The layers were built up by sequential adsorption of polycations (poly[ethylene imine] (PEI); polyallylamine hydrochloride (PAH)) and polyanions (poly[styrene sulfonate] (PSS)). All multilayers terminated by PSS electrostatically bind Cyt-c. On PEI/PSS coatings, Cyt-c is peripherally bound and fully redox-active. Due to the interfacial potential drop, the apparent redox potential is lowered by 40 mV compared to that in solution. The rate constant for the heterogeneous electron transfer (ET) of ca. 0.1 s(-1) is consistent with electron tunneling through largely ordered PEI/PSS layers. ET is coupled to a reversible conformational transition of Cyt-c that involves a change of the coordination pattern of the heme. Additional (PAH/PSS) double layers cause a broadening of the redox transition and a drastic negative shift of the redox potential, which is attributed to the formation of PSS/Cyt-c complexes. It is concluded that Cyt-c can effectively compete with PAH for binding of PSS, resulting in a rearrangement of the layered structure and a penetration of the PSS-bound Cyt-c into the PAH/PSS double layers. This conclusion is consistent with SERR intensity and quartz microbalance measurements. ET was found to be overpotential-independent and faster than that for PEI/PSS coatings, which is interpreted in terms of specific PSS/Cyt-c complexes serving as gates for the heterogeneous ET.

Cytochromes c↗
PubMed2005

Long distance electron transfer in cytochrome c oxidase immobilised on electrodes. A surface enhanced resonance Raman spectroscopic study.

Cytochrome c oxidase was tethered to a functionalised Ag electrode via a histidine-tag on the C-terminus of subunit I or II and embedded in a phospholipid bilayer. The uniformly oriented membrane-bound proteins were studied by surface enhanced resonance Raman spectroscopy (SERRS) that reveals preservation of the native structures of the heme a and heme a(3) sites. On the basis of time-dependent SERRS measurements, the rate constant for the heterogeneous electron transfer to heme a was determined to be 0.002 s(-1) independent of the enzyme orientation and the overpotential. Taking into account that the electrode-to-heme a distance is larger than 50 A, these findings suggest an electron hopping mechanism in which the Cu(A) center is not involved. Electrochemical reduction is restricted to heme a whereas electron transfer from heme a to heme a(3), which in solution occurs on the nanosecond time scale, is drastically slowed down. It may be that the network of cooperativities that links intramolecular electron transfer and proton translocation is perturbed in the immobilised enzyme, possibly due to the effect of the interfacial electric field.

Chemical Phenomena↗
PubMed2005

Conformational transitions and redox potential shifts of cytochrome P450 induced by immobilization.

Cytochrome P450 (P450) from Pseudomonas putida was immobilized on Ag electrodes coated with self-assembled monolayers (SAMs) via electrostatic and hydrophobic interactions as well as by covalent cross-linking. The redox and conformational equilibria of the immobilized protein were studied by potential-dependent surface-enhanced resonance Raman spectroscopy. All immobilization conditions lead to the formation of the cytochrome P420 (P420) form of the enzyme. The redox potential of the electrostatically adsorbed P420 is significantly more positive than in solution and shows a steady downshift upon shortening of the length of the carboxyl-terminated SAMs, i.e., upon increasing the strength of the local electric field. Thus, two opposing effects modulate the redox potential of the adsorbed enzyme. First, the increased hydrophobicity of the heme environment brought about by immobilization on the SAM tends to upshift the redox potential by stabilizing the formally neutral ferrous form. Second, increasing electric fields tend to stabilize the positively charged ferric form, producing the opposite effect. The results provide insight into the parameters that control the structure and redox properties of heme proteins and contribute to the understanding of the apparently anomalous behavior of P450 enzymes in bioelectronic devices.

Biosensing Techniques↗
PubMed2005

Midpoint potentials of hemes a and a3 in the quinol oxidase from Acidianus ambivalens are inverted.

The aa3 type B oxygen reductase from the thermophilic archaeon Acidianus ambivalens (QO) was immobilized on silver electrodes and studied by potential-dependent surface-enhanced resonance Raman (SERR) spectroscopy. The immobilized enzyme retains the native structure at the level of the heme pockets and exhibits reversible electrochemistry. From the potential dependence of specific spectral marker bands, the midpoint potentials of hemes a and a3 were unambiguously determined for the first time, being 320 +/- 20 mV for the former and 390 +/- 20 mV for the latter. Both hemes could be treated as independent one-electron Nernstian redox couples, indicating that the interaction potential is smaller than 50 mV. The reversed order of the midpoint potentials compared to those of type A (mitochondrial-like) oxidases, as well as the lack of substantial Coulombic interactions, suggests a different mechanism of electroprotonic energy transduction. In contrast to type A enzymes, a-a3 intraprotein electron transfer in QO is already guaranteed by the order of the midpoint potentials at the onset of enzyme reduction and, therefore, does not require a complex network of cooperativities to ensure exergonicity. In the immobilized state, conformational transitions of the QO a3-CuB active site, which are believed to be essential for proton translocation, are drastically slowed compared to those in solution. We ascribe this finding to the effect of the interfacial electric field, which is of the same order of magnitude as in biological membranes. These results suggest that the membrane potential may play an active role in the regulation of the enzymatic activity of QO.

Archaea↗
PubMed2005

Redox and redox-coupled processes of heme proteins and enzymes at electrochemical interfaces.

Modern bioelectrochemical methods rely upon the immobilisation of redox proteins and enzymes on electrodes coated with biocompatible materials to prevent denaturation. However, even when protein denaturation is effectively avoided, heterogeneous protein electron transfer is often coupled to non-Faradaic processes like reorientation, conformational transitions or acid-base equilibria. Disentangling these processes requires methods capable of probing simultaneously the structure and reaction dynamics of the adsorbed species. Here we provide an overview of the recent developments in Raman and infrared surface-enhanced spectroelectrochemical techniques applied to the study of soluble and membrane bound redox heme proteins and enzymes. Possible biological implications of the findings are critically discussed.

Biosensing Techniques↗
PubMed2005

Light-induced proton release of phytochrome is coupled to the transient deprotonation of the tetrapyrrole chromophore.

The Pr --> Pfr phototransformation of the bacteriophytochrome Agp1 from Agrobacterium tumefaciens and the structures of the biliverdin chromophore in the parent states and the cryogenically trapped intermediate Meta-R(C) were investigated with resonance Raman spectroscopy and flash photolysis. Strong similarities with the resonance Raman spectra of plant phytochrome A indicate that in Agp1 the methine bridge isomerization state of the chromophore is ZZZasa in Pr and ZZEssa in Pfr, with all pyrrole nitrogens being protonated. Photoexcitation of Pr is followed by (at least) three thermal relaxation components in the formation of Pfr with time constants of 230 micros and 3.1 and 260 ms. H2O/D2O exchange reveals kinetic isotope effects of 1.9, 2.6, and 1.3 for the respective transitions that are accompanied by changes of the amplitudes. The second and the third relaxation correspond to the formation and decay of Meta-R(C), respectively. Resonance Raman measurements of Meta-R(C) indicate that the chromophore adopts a deprotonated ZZE configuration. Measurements with a pH indicator dye show that formation and decay of Meta-R(C) are associated with proton release and uptake, respectively. The stoichiometry of the proton release corresponds to one proton per photoconverted molecule. The coupling of transient chromophore deprotonation and proton release, which is likely to be an essential element in the Pr --> Pfr photocon-version mechanism of phytochromes in general, may play a crucial role for the structural changes in the final step of the Pfr formation that switch between the active and the inactive state of the photoreceptor.

Agrobacterium tumefaciens↗
PubMed2005

Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies.

The tetraheme protein cytochrome c(3) (Cyt-c(3)) from Desulfovibrio gigas, immobilized on a self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid, is studied by theoretical and spectroscopic methods. Molecular dynamics simulations indicate that the protein docks to the negatively charged SAM via its lysine-rich domain around the exposed heme IV. Complex formation is associated with only little protein structural perturbations. This finding is in line with the resonance Raman and surface-enhanced resonance Raman (SERR) spectroscopic results that indicate essentially the same heme pocket structures for the protein in solution and adsorbed on SAM-coated Ag electrodes. Electron- and proton-binding equilibrium calculations reveal substantial negative shifts of the redox potentials compared to the protein in solution. The magnitude of these shifts decreases in the order heme IV (-161 mV) > heme III (-73 mV) > heme II (-57 mV) > heme I (-26 mV), resulting in a change of the order of reduction. These shifts originate from the distance-dependent electrostatic interactions between the SAM headgroups and the individual hemes, leading to a stabilization of the oxidized forms. The results of the potential-dependent SERR spectroscopic analyses are consistent with the theoretical predictions and afford redox potential shifts of -160 mV (heme IV), -90 mV (heme III), -70 mV (heme II), and +20 mV (heme I) relative to the experimental redox potentials for Cyt-c(3) in solution. SERR spectroscopic experiments reveal electric-field-induced changes of the redox potentials also for the structurally very similar Cyt-c(3) from Desulfovibrio vulgaris, although the shifts are somewhat smaller compared to Cyt-c(3) from D. gigas. This study suggests that electric-field-induced redox potential shifts may also occur upon binding to biomembranes or partner proteins and thus may affect biological electron transfer processes.

Biophysical Phenomena↗
PubMed2004

Determination of the chromophore structures in the photoinduced reaction cycle of phytochrome.

The chromophore structures in the parent states Pr and Pfr as well as in the photocycle intermediate Lumi-R of oat phytochrome phyA are determined by comparison of the experimental resonance Raman spectra with calculated Raman spectra that have been obtained by density functional theory calculations (B3LYP) using scaled force fields. The spectra were calculated for various tetrapyrrole geometries including more than twenty different methine bridge isomers. For the parent states Pr and Pfr the best agreement in terms of vibrational frequencies, isotopic shifts, and Raman intensities was achieved with the ZZZasa and ZZEssa geometry, respectively. For the first intermediate Lumi-R, the chromophore geometry is concluded to be the ZZEasa configuration. These finding imply that the primary step of the photoactivation of phytochrome is the Z/E isomerization of the C-D methine bridge double bond, whereas the single bond remains in the anti conformation. The subsequent transition to the physiologically active state Pfr includes a (partial) single bond rotation of the A-B methine bridge.

Biliverdine↗
PubMed2004

Electron-transfer processes of cytochrome C at interfaces. New insights by surface-enhanced resonance Raman spectroscopy.

The heme protein cytochrome c acts as an electron carrier at the mitochondrial-membrane interface and thus exerts its function under the influence of strong electric fields. To assess possible consequences of electric fields on the redox processes of cytochrome c, the protein can be immobilized to self-assembled monolayers on electrodes and studied by surface-enhanced resonance Raman spectroscopy. Such model systems may mimic some essential features of biological interfaces including local electric field strengths. It is shown that physiologically relevant electric field strengths can effectively modulate the electron-transfer dynamics and induce conformational transitions.

Cytochromes c↗
PubMed2002

Active site structure and dynamics of cytochrome c3 from Desulfovibrio gigas immobilized on electrodes.

Cytochrome c3 from Desulfovibrio gigas is electrostatically adsorbed on Ag electrodes coated with self-assembled monolayers (SAMs) of 11-mercaptoundecanoic acid. The redox equilibria and electron transfer dynamics of the adsorbed four-heme protein are studied by surface enhanced resonance Raman spectroscopy. Immobilization on the coated electrodes does not cause any structural changes in the redox sites. The potential-dependent stationary experiments distinguish the redox potential of heme IV (-0.19 V versus normal hydrogen electrode) from those of the other hemes for which an average value of -0.3 V is determined. Taking into account the interfacial potential drops, these values are in good agreement with the redox potentials of the protein in solution. The heterogenous electron transfer between the electrode and heme IV of the adsorbed cytochrome c3 is analyzed on the basis of time-resolved experiments, leading to a formal electron transfer rate constant of 15 s(-1), which is a factor of 3 smaller than that of the monoheme protein cytochrome c.

Binding Sites↗