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PubMed2002

Interprotein electron transfer in a confined space: uncoupling protein dynamics from electron transfer by sol-gel encapsulation.

In this paper, we describe the first observations of photoinitiated interprotein electron transfer (ET) within sol-gels. We have encapsulated three protein-protein complexes, specifically selected because they represent a full range of affinities, are sensitive to different types of dynamic processes, and thus are expected to respond differently to sol-gel encapsulation. The three systems are (i) the [Zn, Fe(3+)L] mixed-metal hemoglobin hybrids, where the alpha(1)-Zn and beta(2)-Fe subunits correspond to a "predocked" protein-protein complex with a crystallographically defined interface (Natan, M. J.; Baxter, W. W.; Kuila, D.; Gingrich, D. J.; Martin, G. S.; Hoffman, B. M. Adv. Chem. Ser. 1991, 228 (Electron-Transfer Inorg., Org., Biol. Syst.), 201-213), (ii) the Zn-cytochrome c peroxidase complex with cytochrome c, [ZnCcP, Fe(3+)Cc], having an intermediate affinity between its partners (Nocek, J. M.; Zhou, J. S.; De Forest, S.; Priyadarshy, S.; Beratan, D. N.; Onuchic, J. N.; Hoffman, B. M. Chem. Rev. 1996, 96, 2459-2489), and (iii) the [Zn-deuteromyoglobin, ferricytochrome b(5)] complex, [ZnDMb, Fe(3+)b(5)], which is loosely bound and highly dynamic (Liang, Z.-X.; Nocek, J.; Huang, K.; Hayes, R. T.; Kurnikov, I. V.; Beratan, D. N.; Hoffman, B. M. J. Am. Chem. Soc. 2002, 124, 6849-6859. Intersubunit ET within the hybrid does not involve second-order processes or subunit rearrangements, and thus is influenced only by perturbations of high-frequency motions coupled to ET. For the latter two complexes, sol-gel encapsulation eliminates second-order processes: protein partners encapsulated as a complex must stay together throughout a photoinitiated ET cycle, while proteins encapsulated alone cannot acquire a partner. It further modulates intracomplex motions of the two partners.

Crystallography↗
PubMed2002

Pulsed electron-electron double resonance on multinuclear metal clusters: assignment of spin projection factors based on the dipolar interaction.

The interaction between two paramagnetic metal centers, a [3Fe-4S](+) cluster and a [NiFe] center, is investigated in the hydrogenase from Desulfovibrio vulgaris Miyazaki F by pulsed ELDOR (electron-electron double resonance). The distance between the metal centers is known from X-ray crystallography. The experimental dipolar spin-spin interaction deviates from the value expected for two point-dipoles located at the centers of the metal clusters. An extended spin-coupling model accounting for the spin coupling in the [3Fe-4S](+) cluster yields the observed interaction under the assumption of a particular magnetic coupling scheme for the three Fe ions. These results demonstrate that pulsed ELDOR can be used to gain insight into the inner structure of a multinuclear metal cluster.

Computer Simulation↗
PubMed2004

Hydrogen bond geometries from electron paramagnetic resonance and electron-nuclear double resonance parameters: density functional study of quinone radical anion-solvent interactions.

Density functional theory was used to study the impact of hydrogen bonding on the p-benzosemiquinone radical anion BQ(*-) in coordination with water or alcohol molecules. After complete geometry optimizations, (1)H, (13)C, and (17)O hyperfine as well as (2)H nuclear quadrupole coupling constants and the g-tensor were computed. The suitability of different model systems with one, two, four, and 20 water molecules was tested; best agreement between theory and experiment could be obtained for the largest model system. Q-band pulse (2)H electron-nuclear double resonance (ENDOR) experiments were performed on BQ(*-) in D(2)O. They compare very well with the spectra simulated by use of the theoretical values from density functional theory. For BQ(*-) in coordination with four water or alcohol molecules, rather similar hydrogen-bond lengths between 1.75 and 1.78 A were calculated. Thus, the computed electron paramagnetic resonance (EPR) parameters are hardly distinguishable for the different solvents, in agreement with experimental findings. Furthermore, the distance dependence of the EPR parameters on the hydrogen-bond length was studied. The nuclear quadrupole and the dipolar hyperfine coupling constants of the bridging hydrogens show the expected dependencies on the H-bond length R(O.H). A correlation was obtained for the g-tensor. It is shown that the point-dipole model is suitable for the estimation of hydrogen-bond lengths from anisotropic hyperfine coupling constants of the bridging (1)H nuclei for H-bond lengths larger than approximately 1.7 A. Furthermore, the estimation of H-bond lengths from (2)H nuclear quadrupole coupling constants of bridging deuterium nuclei by empirical relations is discussed.

Alcohols↗
PubMed2004

Long-range electron transfer across Peptide bridges: the transition from electron superexchange to hopping.

Long-range electron transfer rate constants for complexes of the type [(bpy)2RuIIL-Pron-apyRuIII)(NH3)5]5++ proline residues (n) varying from 0 to 9 were determined by complementary electron pulse radiolysis and flash photolysis techniques from the picosecond to the millisecond time scales. The activationless kmax values from both techniques coalesce into one data set. The distance dependence of the reactions is consistent with a smooth transition from a superexchange mechanism with attenuation constant beta = 1.4 A-1 to a hopping mechanism with attenuation constant beta = 0.17 A-1. The transition occurs between n = 3 and 4 prolines, and the virtual hopping rate constant at the shortest distance is about 1 x 106 times slower than that observed for the superexchange value.

2,2'-Dipyridyl↗
PubMed2005

Charge transfer excited-state dynamics in DNA duplexes substituted with an ethynylpyrenyldeoxyuridine electron source and a fluorodeoxyuridine electron trap.

Studies of six 5-(pyren-1-yl-ethynyl)-2'-deoxyuridine (U(PY))-substituted DNA duplexes in this work test and support the conclusions reported by Gaballah et al. (J. Phys. Chem. B 2005, 109, 5927-5934) based on investigations of 5-(2-pyren-1-yl-ethylenyl)-2'-deoxyuridine (U(PE))-substituted DNA hairpins. As expected because of the rigid ethynyl linker in U(PY) (compared to the flexible ethylenyl linker in U(PE)), U(PY)-substituted duplexes do not show enhanced charge transfer (CT) emission quantum yields for duplexes with 5-fluorodeoxyuridine (U(F)) electron traps near U(PY) compared to duplexes without traps. Furthermore, the average CT lifetime and emission quantum yield of U(PY)-substituted duplexes is independent of the U(F) trap location. These new results strongly suggest that the excess electron in the PY*+/dU*- CT state of U(PY) is restrained from hopping to nearby U(F) traps due to attraction to PY*+.

Base Sequence↗
PubMed2005

Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-condon theory for the energy gap dependence of electron transfer rate.

Developing the quantum transition rate theory of Prezhdo and Rossky (J. Chem. Phys. 1997, 107, 5863), we produced a new non-Condon theory of the rate of electron transfer (ET) which happens through a protein medium with conformational fluctuation. The new theory is expressed by a convolution form of the power spectrum for the autocorrelation function of the electronic tunneling matrix element T(DA)(t) with quantum correction and the ordinary Franck-Condon factor. The new theory satisfies the detailed balance condition for the forward and backward ET rates. The ET rate formula is divided into two terms of elastic and inelastic tunneling mechanisms on the mathematical basis. The present theory is applied to the ET from Bph(-) to Q(A) in the reaction center of Rhodobacter sphaeroides. Numerical calculations of T(DA)(t) were made by a combined method of molecular dynamics simulations and quantum chemistry calculations. We showed that the normalized autocorrelation function of T(DA)(t) is almost expressed by exponential forms. The calculated energy gap law of the ET rate is nearly Marcus' parabola in most of the normal region and around the maximum region, but it does not decay substantially in the inverted region, which is called the anomalous inverted region. We also showed that the energy gap law at the high uphill energy gap in the normal region is elevated considerably from the Marcus' parabola, which is called the anomalous normal region. Those anomalous energy gap laws are due to the inelastic tunneling mechanism which works actively at the energy gap far from zero. We presented an empirical formula for easily calculating the non-Condon ET rate, which is usable by many researchers. We provided experimental evidence for the anomalous inverted region which was basically reproduced by the present theory. The present theory was extensively compared with the previous non-Condon theories.

Bacterial Proteins↗
PubMed2006

Voltammetric monitoring of gold nanoparticle formation facilitated by glycyl-L-tyrosine: relation to electronic spectra and transmission electron microscopy images.

Voltammetric techniques have been introduced to monitor the formation of gold nanoparticles produced via the reaction of the amino acid glycyl-L-tyrosine with Au(III) (bromoaurate) in 0.05 M KOH conditions. The alkaline conditions facilitate amino acid binding to Au(III), inhibit the rate of reduction to Au(0), and provide an excellent supporting electrolyte for voltammetric studies. Data obtained revealed that a range of time-dependent gold solution species are involved in gold nanoparticle formation and that the order in which reagents are mixed is critical to the outcome. Concomitantly with voltammetric measurements, the properties of gold nanoparticles formed are probed by examination of electronic spectra in order to understand how the solution environment present during nanoparticle growth affects the final distribution of the nanoparticles. Images obtained by the ex situ transmission electron microscopy (TEM) technique enable the physical properties of the nanoparticles isolated in the solid state to be assessed. Use of this combination of in situ and ex situ techniques provides a versatile framework for elucidating the details of nanoparticle formation.

Dipeptides↗
PubMed2006

Collective fluctuations in ordered fluids investigated by two-dimensional electron-electron double resonance spectroscopy.

Two-dimensional electron-electron double resonance (2D-ELDOR) is a technique that is sensitive to the dynamical processes affecting spin labels in complex fluid environments. In ordered fluids, such as membrane vesicles, the 2D-ELDOR experiment is affected by the molecular tumbling in the locally ordered environment. This motion occurs on two different time scales, the faster molecular motion relative to the local director, and the slower collective fluctuations of the director field. In the experimental study of Patyal, Crepeau, and Freed (Biophys. J. 1997, 73, 2201), it was found that the widths of the autopeaks of the 2D-ELDOR spectrum increased as a function of the mixing time. In the present work, a theory is developed for the effects of director fluctuations on the autopeaks in the 2D-ELDOR experiment by employing an analytical solution of the stochastic Liouville equation for which the director field is treated as a multidimensional Gaussian process, as previously developed by Frezzato, Kothe, and Moro (J. Phys. Chem. B 2001, 105, 1281 and J. Phys. Chem. B 2004, 108, 9505). Good agreement is found between theory and experiment, notably the only adjustable parameter is k, the bending elastic modulus of the membrane. The values of k = 11 x 10(-20) J for 1,2-dipalmitoyl-sn-glycero-phosphatidylcholine (DPPC) vesicles and k = 15 x 10(-20) J for DPPC/gramicidin A (5:1) vesicles, both at 45 degrees C, were found from the analysis and agree well with previous related measurements by other physical techniques. This establishes 2D-ELDOR as a useful technique to study the elastic properties of biological membranes.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2006

Photoinduced electron transfer from N,N-dimethylaniline to 7-amino coumarins in protein-surfactant complex: slowing down of electron transfer dynamics compared to micelles.

Photoinduced electron transfer from N,N-dimethylaniline to different Coumarin dyes has been investigated in dodecyl trimethyl ammonium bromide (DTAB) micelles and in Bovine serum albumin (BSA)-DTAB protein-surfactant complex using steady-state and picosecond time-resolved fluorescence spectroscopy. We observed a slower fluorescence quenching rate in the DTAB micelles and in the protein-surfactant complex as compared to that in pure acetonitrile solution. Moreover, the observed fluorescence quenching in BSA-DTAB complex was found to be slower than that in DTAB micelles. In the correlation of free-energy change with the fluorescence quenching constant we observed a deviation in the fluorescence quenching electron transfer rate for Coumarin 151 (C-151) from the normal Marcus curve. This observation is ascribed to the stronger interaction of C-151 with the surfactant molecules present in the micelles. This is evident from the slower translation diffusion (D(L)) of Coumarin 151 compared to other probe molecules.

Aniline Compounds↗
PubMed2005

Protein dynamics and electron transfer: electronic decoherence and non-Condon effects.

We compute the autocorrelation function of the donor-acceptor tunneling matrix element for six Ru-azurin derivatives. Comparison of this decay time to the decay time of the time-dependent Franck-Condon factor {computed by Rossky and coworkers [Lockwood, D. M., Cheng, Y.-K. & Rossky, P. J. (2001) Chem. Phys. Lett. 345, 159-165]} reveals the extent to which non-Condon effects influence the electron-transfer rate. is studied as a function of donor-acceptor distance, tunneling pathway structure, tunneling energy, and temperature to explore the structural and dynamical origins of non-Condon effects. For azurin, the correlation function is remarkably insensitive to tunneling pathway structure. The decay time is only slightly shorter than it is for solvent-mediated electron transfer in small organic molecules and originates, largely, from fluctuations of valence angles rather than bond lengths.

Azurin↗
PubMed1972

Electron transfer to ferricytochrome c: reaction with hydrated electrons and conformational transitions involved.

The reaction of horse-heart cytochrome c with hydrated electrons has been studied by the pulseradiolysis technique. In neutral solution, the ferriheme group was reduced in a bimolecular reaction that takes place at a rate equal to that of the decay of the e(-) (aq), and approaches the diffusion-controlled limit. This reduction is assigned mainly to a direct reaction, proceeding via the exposed edge of the porphyrin projecting into the cytochrome c crevice. The reaction absorption spectrum observed 20 musec after an electron pulse was very similar, yet blue-shifted relative to, the difference spectrum between the reduced and oxidized forms of cytochrome c. However, this shift vanishes in a slow monomolecular reaction, which seems to reflect the conformational relaxation of the protein to the final equilibrium state of its reduced form. In alkaline solutions, the transition of cytochrome c molecules into an irreducible conformation causes a proportionate decrease in the amount of ferricytochrome c reduced in the direct reaction. The rate of conformational transition of the protein into the reactive form is now the limiting step for a substantial part of the reduction that takes place via this slow monomolecular reaction. Pseudomonas cytochrome c 551 which, in contrast to horse-heart cytochrome c, is a negatively charged protein at neutral pH reacts with e(-) (aq) at a rate lower than does the horse-heart protein. The reduction of the heme group follows that of the e(-) (aq) decay with a small, yet significant, delay.

Animals↗
PubMed1994

Characterization of calcium-binding sites in the kidney stone inhibitor glycoprotein nephrocalcin with vanadyl ions: electron paramagnetic resonance and electron nuclear double resonance spectroscopy.

Nephrocalcin (NC) is a calcium-binding glycoprotein of 14,000 molecular weight. It inhibits the growth of calcium oxalate monohydrate crystals in renal tubules. The NC used in this study was isolated from bovine kidney tissue and purified with the use of DEAE-cellulose chromatography into four isoforms, designated as fractions A-D. They differ primarily according to the content of phosphate and gamma-carboxy-glutamic acid. Fractions A and B are strong inhibitors of the growth of calcium oxalate monohydrate crystal, whereas fractions C and D inhibit crystal growth weakly. Fraction A, with the highest Ca(2+)-binding affinity, was characterized with respect to its metal-binding sites by using the vanadyl ion (VO2+) as a paramagnetic probe in electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopic studies. By EPR spectrometric titration, it was shown that fraction A of NC bound VO2+ with a stoichiometry of metal:protein binding of 4:1. Also, the binding of VO2+ to NC was shown to be competitive with Ca2+. Only protein residues were detected by proton ENDOR as ligands, and these ligands bound with complete exclusion of solvent from the inner coordination sphere of the metal ion. This type of metal-binding environment, as derived from VO(2+)-reconstituted NC, differs significantly from the binding sites in other Ca(2+)-binding proteins.

Animals↗
PubMed1995

EPR, electron spin echo envelope modulation, and electron nuclear double resonance studies of the 2Fe2S centers of the 2-halobenzoate 1,2-dioxygenase from Burkholderia (Pseudomonas) cepacia 2CBS.

The 2-halobenzoate 1,2-dioxygenase from Burkholderia (Pseudomonas) cepacia 2CBS (Fetzner, S., Müller, R., and Lingens, F. (1992) J. Bacteriol. 174, 279-290) contains both a ferredoxin-type and a Rieske-type 2Fe2S center. These two significantly different 2Fe2S clusters were characterized with respect to their EPR spectra, electrochemical properties (Rieske-type cluster with gz = 2.025, gy = 1.91, gx = 1.79, gav = 1.91, Em = -125 +/- 10 mV; ferredoxin-type center with gz = 2.05, gy = 1.96, gx = 1.89, gav = 1.97, Em = -200 +/- 10 mV) and pH dependence thereof. X band electron spin echo envelope modulation and electron nuclear double resonance spectroscopy was applied to study the interaction of the Rieske-type center of the 2-halobenzoate 1,2-dioxygenase with 14N and 1H nuclei in the vicinity of the 2Fe2S cluster. The results are compared to those obtained on the Rieske protein of the cytochrome b6f complex (Em = +320 mV) and the water-soluble ferredoxin (Em = -430 mV) of spinach chloroplasts, as typical representatives of the gav = 1.91 and gav = 1.96 class of 2Fe2S centers. Properties common to all Rieske-type clusters and those restricted to the respective centers in bacterial oxygenases are discussed.

Burkholderia cepacia↗
PubMed2004

Direct probing of copper active site and free radical formed during bicarbonate-dependent peroxidase activity of bovine and human copper, zinc-superoxide dismutases. Low-temperature electron paramagnetic resonance and electron nuclear double resonance studies.

Using X-band electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopy at liquid helium temperatures, the Cu(II) coordination geometry at the active site of bovine and human copper,zinc-superoxide dismutases (bSOD1 and hSOD1) treated with H(2)O(2) and bicarbonate (HCO(3)(-)) was examined. The time course EPR of wild type human SOD1 (WT hSOD1), W32F hSOD1 mutant (tryptophan 32 substituted with phenylalanine), and bSOD1 treated with H(2)O(2) and HCO(3)(-) shows an initial reduction of active site Cu(II) to Cu(I) followed by its oxidation back to Cu(II) in the presence of H(2)O(2). However, HCO(3)(-) induced a Trp-32-derived radical from WT hSOD1 but not from bSOD1. The mutation of Trp-32 by phenylalanine totally eliminated the Trp-32 radical signal generated from W32F hSOD1 treated with HCO(3)(-) and H(2)O(2). Further characterization of the free radical was performed by UV irradiation of WT hSOD1 and bSOD1 that generated tryptophanyl and tyrosyl radicals. Both proton ((1)H) and nitrogen ((14)N) ENDOR studies of bSOD1 and hSOD1 in the presence of H(2)O(2) revealed a change in the geometry of His-46 (or His-44) and His-48 (or His-46) coordinated to Cu(II) at the active site of WT hSOD1 and bSOD1, respectively. However, in the presence of HCO(3)(-) and H(2)O(2), both (1)H and (14)N ENDOR spectra were almost identical to those derived from native bSOD1. We conclude that HCO(3)(-)-derived oxidant does not alter significantly the Cu(II) active site geometry and histidine coordination to Cu(II) in SOD1 as does H(2)O(2) alone; however, the oxidant derived from HCO(3)(-) (i.e. carbonate anion radical) reacts with surface-associated Trp-32 in hSOD1 to form the corresponding radical.

Animals↗
PubMed2005

Musculoskeletal responses of 2-year-old Thoroughbred horses to early training. 8. Quantitative back-scattered electron scanning electron microscopy and confocal fluorescence microscopy of the epiphysis of the third metacarpal bone.

AIM: To characterise and explain the increase in density evident by computerised tomography (CT) and radiography in companion studies as a response to training, in bone in the palmar and dorsal regions of the condyles of the third metacarpal bone (Mc3) of 2-year-old Thoroughbred horses. METHODS: Compositional back-scattered electron (BSE) imaging in scanning electron microscopy (SEM) and confocal scanning laser microscopy (CSLM) were conducted on polymethyl methacrylate (PMMA)-embedded mediolateral slices of the right distal Mc3 from seven 2-year-old Thoroughbred horses trained on a racetrack and seven untrained horses kept at pasture. One left Mc3 from each group was studied in transverse section planes. This study focussed on regions of Mc3 found to differ in density between the trained and untrained horses in companion studies using CT and radiography. RESULTS: The increase of bone density in the condyles of Mc3 in trained horses compared with untrained horses occurred, without prior osteoclastic resorption, via the deposition of new bone on pre-existing internal surfaces. Within prior marrow spaces of cancellous bone, there was also rapid formation of immature strands and fronds of bone which were more cellular and mineralised, and more lamellar bone tissue was deposited on these new scaffolding elements in the trained horses. Both resulted in increased bone volume fraction (BVF). The microscopic mineralisation density of the bulk of the new tissue was lower than in pre-existing bone, and CT and radiography underestimated the increase in BVF. The new tissue was thus probably less stiff at the microscopic scale than pre-existing bone, though its addition would stiffen the global structure. CONCLUSIONS: In Mc3 of all the trained horses, there were obvious differences in microscopic structure compared with those from the untrained horses. Moderate, industry-standard levels of exercise used to prepare young horses for racing induced the formation of new bone in non-bone spaces in bone tissue, such that the bone organ should better withstand later increased levels of exercise.

Animals↗