Oxygen‐binding Protein Fiber and Microgel: Supramolecular Myoglobin–Poly(acrylate) Conjugates

A supramolecular conjugate of myoglobin (Mb) and water‐soluble poly(acrylate), (PA_5k and PA_25k, where 5k and 25k represent the molecular weight of the polymers, respectively), is constructed on the basis of a noncovalent heme‐heme pocket interaction. The modified heme with an amino group linked to the terminus of one of the heme‐propionates is coupled to the side‐chain carboxyl groups of poly(acrylate) activated by N‐hydroxysuccinimide. The ratios of the heme‐modified monomer unit and the unmodified monomer unit (m:n) in the polymer chains of Heme‐PA_5k and Heme‐PA_25k were determined to be 4.5:95.5 and 3.1:96.9, respectively. Subsequent addition of apoMb to the conjugated polymers provides Mb‐connected fibrous nanostructures confirmed by atomic force microscopy. A mixture of the heme‐modified polymer and dimeric apomyoglobin as a cross‐linker forms a microgel in which the reconstituted myoglobin retains its native exogenous ligand binding activity.     

Distinct reaction pathways followed upon reduction of oxy-heme oxygenase and oxy-myoglobin as characterized by Mössbauer spectroscopy

Activation of O(2) by heme-containing monooxygenases generally commences with the common initial steps of reduction to the ferrous heme and binding of O(2) followed by a one-electron reduction of the O(2)-bound heme. Subsequent steps that generate reactive oxygen intermediates diverge and reflect the effects of protein control on the reaction pathway. In this study, M?ssbauer and EPR spectroscopies were used to characterize the electronic states and reaction pathways of reactive oxygen intermediates generated by 77 K radiolytic cryoreduction and subsequent annealing of oxy-heme oxygenase (HO) and oxy-myoglobin (Mb). The results confirm that one-electron reduction of (Fe(II)-O(2))HO is accompanied by protonation of the bound O(2) to generate a low-spin (Fe(III)-O(2)H(-))HO that undergoes self-hydroxylation to form the alpha-meso-hydroxyhemin-HO product. In contrast, one-electron reduction of (Fe(II)-O(2))Mb yields a low-spin (Fe(III)-O(2)(2-))Mb. Protonation of this intermediate generates (Fe(III)-O(2)H(-))Mb, which then decays to a ferryl complex, (Fe(IV)=O(2-))Mb, that exhibits magnetic properties characteristic of the compound II species generated in the reactions of peroxide with heme peroxidases and with Mb. Generation of reactive high-valent states with ferryl species via hydroperoxo intermediates is believed to be the key oxygen-activation steps involved in the catalytic cycles of P450-type monooxygenases. The M?ssbauer data presented here provide direct spectroscopic evidence supporting the idea that ferric-hydroperoxo hemes are indeed the precursors of the reactive ferryl intermediates. The fact that a ferryl intermediate does not accumulate in HO underscores the determining role played by protein structure in controlling the reactivity of reaction intermediates.     

Ultrathin layered myoglobin-polyion films functional and stable at acidic pH values

Cross-linking of myoglobin (Mb) promoted by 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide within films of polystyrene sulfonate after layer-by-layer self-assembly provided remarkable stabilization. Cross-linking greatly improved adhesion of the films to fused silica slides and allowed extensive optical studies over a wide pH range. Circular dichroism and visible absorbance spectra showed that Mb retained its native conformation when films were placed in solutions of pH as low as 2 and up to pH 11. Linear dichroism revealed an average orientation of the Mb iron heme cofactors of 58 degrees to the film normal. High concentrations of urea did denature the protein in the films, however. At pH 1, Mb in solution is fully unfolded but retained considerable alpha-helical content in the cross-linked films. Both the polyion film environment and cross-linking seem to play roles in stabilizing protein secondary structure and function at low pH. Cross-linked myoglobin-polyion films on pyrolytic graphite electrodes were used in strongly acidic solutions for the electrochemical catalytic reduction of trichloracetic acid, hydrogen peroxide, and oxygen. The pH-dependent catalytic reduction of trichloracetic acid was faster in 0.1 M HCl than in the medium pH range.     

The rhodamine B intercalation of montmorillonite

Using photometric methods the dissociation constants and weight fractions of rhodamine B dimer in water solutions at different concentrations were determined. The montmorillonite (SWy) samples were fully intercalated with rhodamine B (RhB) solutions at various monomer/dimer ratios. The amount of rhodamine B in fully intercalated montmorillonite (RhB-SWy) increases with increasing concentration of dye in water solutions, i.e., with increasing dimer/monomer ratio. The sum of exchangeable guest cations in RhB-SWy is approximately constant (0.900 meq g(-1)) for all samples, because RhB-SWy samples with prevailing dye monomer also contain higher amounts of non-exchanged alkali elements. The experimental data are supported by calculated structure models that illustrate the changes in RhB-SWy structure depending on monomeric and/or dimeric arrangement of guests. The analysis of the calculated structure models confirmed the existence of two phases with different basal spacings, d approximately 1.8 and approximately 2.3 nm, revealed by X-ray diffraction.     

Rate constants for the gas-phase reactions of OH and O3 with β-ocimene, β-myrcene, and α- and β-farnesene as a function of temperature

The rate constants for the gas-phase reactions of hydroxyl radicals and ozone with the biogenic hydrocarbons β-ocimene, β-myrcene, and α- and β-farnesene were measured using the relative rate technique over the temperature ranges 313-423 (for OH) and 298-318 K (for O?) at about 1 atm total pressure. The OH radicals were generated by photolysis of H?O?, and O? was produced from the electrolysis of O?. Helium was used as the diluent gas. The reactants were detected by online mass spectrometry, which resulted in high time resolution, allowing large amounts of data to be collected and used in the determination of the Arrhenius parameters. The following Arrhenius expressions have been determined for these reactions (in units of cm3 molecules?1 s?1): for β-ocimene + OH, k = (4.35(-0.66)(+0.78)) × 10?11 exp[(579 ± 59)/T]; for β-ocimene + O?, k = (3.15(-0.95)(+1.36)) × 10?1? exp[-(626 ± 110)/T]; for β-myrcene + O?, k = (2.21(-0.66)(+0.94)) × 10?1? exp[-(520 ± 109)/T]; for α-farnesene + OH, k(OH) = (2.19 ± 0.11) × 10?1? for 23-413 K; for α-farnesene + O?, k = (3.52(-2.54)(+9.09)) × 10?12 exp[-(2589 ± 393)/T]; for β-farnesene + OH, k(OH) = (2.88 ± 0.15) × 10?1? for 323-423 K; for β-farnesene + O?, k = (1.81(-1.19)(+3.46)) × 10?12 exp[-(2347 ± 329)/T]. The Arrhenius parameters here are the first to be reported. The reactions of α- and β-farnesene with OH showed no significant temperature dependence. Atmospheric residence times due to reactions with OH and O? were also presented.     

Probing the binding kinetics of proinflammatory cytokine-antibody interactions using dual color fluorescence cross correlation spectroscopy

Dual color fluorescence cross correlation spectroscopy (FCCS) was used to investigate quantitatively the binding kinetics of tumor necrosis factor (TNFα) with TNFα antibody (anti-TNFα) following fluorescent labeling. Through the analysis of the auto correlation curves of fluorescence correlation spectroscopy (FCS), diffusion coefficients of 100.06 ± 4.9 μm(2) s(-1) and 48.96 ± 2.52 μm(2) s(-1) for Alexa488-TNFα and Atto647N-anti-TNFα were obtained. In addition, the calculated hydrodynamic diameters of the Alexa488-TNFα and Atto647N-anti-TNFα were approximately 4.89 ± 0.24 nm and 9.99 ± 0.52 nm, respectively, which agrees with the values of 5.20 ± 1.23 nm and 9.28 ± 0.86 nm for the native TNFα and the anti-TNFα as determined from dynamic light scattering measurements. For the binding kinetics, association (k(on)) and dissociation (k(off)) rate constants were (1.13 ± 0.08) × 10(4) M(-1) s(-1) and (1.53 ± 0.19) × 10(-3) s(-1) while the corresponding dissociation constant (K(d)) at 25 °C was (1.36 ± 0.10) × 10(-7) M. We believe this is the first report on the binding kinetics for TNFα-antibody recognition in the homogeneous phase. Using this technology, we have shown that controlled experiments can be performed to gain insight into molecular mechanisms involved in the immune response.     

De novo design, synthesis, and function of semiartificial myoglobin conjugated with coiled-coil two-alpha-helix peptides

The introduction of a flavin chromophore on the myoglobin (Mb) surface and an effective electron-transfer (ET) reaction through the flavin were successfully achieved by utilizing the self-assembly of heterostranded coiled-coil peptides. We have prepared a semiartificial Mb, named Mb-1alphaK, in which an amphiphilic and cationic alpha-helix peptide is conjugated at the heme propionate (Heme-1alphaK). Heme-1alphaK has a covalently bound iron-protoporphyrin IX (heme) at the N terminus of a 1alphaK peptide sequence. This sequence was designed to form a heterostranded coiled-coil in the presence of a counterpart amphiphilic and anionic 1alphaE peptide sequence in a parallel orientation. Two peptides, Fla(1)-1alphaE and Fla(31)-1alphaE, both incorporating a 10-methylisoalloxazine moiety as an artificial flavin molecule, were also prepared (Fla=2-[7-(10-methyl)isoalloxazinyl]-2-oxoethyl). Heme-1alphaK was successfully inserted into apomyoglobin to give Mb-1alphaK. Mb-1alphaK recognized the flavin-modified peptides and a two-alpha-helix structure was formed. In addition, an efficient ET from reduced nicotinamide adenine dinucleotide to the heme center through the flavin unit was observed. The ET rate was faster in the presence of Fla(1)-1alphaE than in the presence of Fla(31)-1alphaE or the equivalent molecule that has no peptide chain. These results demonstrate that the introduction of a functional chromophore on the Mb surface can be achieved by using specific peptide-peptide interactions. Moreover, the dependence of the ET rate on the position of the flavin indicated that the distance between the heme active site and the flavin chromophore was regulated by the three-dimensional structure of the designed polypeptide.     

Electrochemical and electrocatalytic properties of myoglobin and hemoglobin incorporated in carboxymethyl cellulose films

Protein-CMC films were made by casting a solution of myoglobin (Mb) or hemoglobin (Hb) and carboxymethyl cellulose (CMC) on pyrolytic graphite electrodes. In pH 7.0 buffers, Mb and Hb incorporated in CMC films gave a pair of well-defined and quasi-reversible cyclic voltammetric peaks at about -0.34 V vs. SCE, respectively, characteristic of heme Fe(III)/Fe(II) redox couples of the proteins. The electrochemical parameters such as apparent standard heterogeneous electron transfer rate constants (k(s)) and formal potentials (E degrees ') were estimated by square wave voltammetry with nonlinear regression analysis. In aqueous solution, stable CMC films absorbed large amounts of water and formed hydrogel. Scanning electron microscopy of the films showed that interaction between Mb or Hb and CMC would make the morphology of dry protein-CMC films different from the CMC films alone. Positions of Soret absorbance band suggest that Mb and Hb in CMC films retain their secondary structure similar to the native states in the medium pH range. Trichloroacetic acid, nitrite, oxygen, and hydrogen peroxide were catalytically reduced at protein-CMC film electrodes.     

Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes

Horse myoglobin (Mb) provides a convenient "workbench" for probing the effects of electrostatics on binding and reactivity in the dynamic [Mb, cytochrome b(5)] electron-transfer (ET) complex. We have combined mutagenesis and heme neutralization to prepare a suite of six Mb surface-charge variants: the [S92D]Mb and [V67R]Mb mutants introduce additional charges on the "front" face, and incorporation of the heme di-ester into each of these neutralizes the charge on the heme propionates which further increases the positive charge on the "front" face. For this set of mutants, the nominal charge of Mb changes by -1 to +3 units relative to that for native Mb. For each member of this set, we have measured the bimolecular quenching rate constant (k(2)) for the photoinitiated (3)ZnDMb --> Fe(3+)b(5) ET reaction as a function of ionic strength. We find: (i) a dramatic decoupling of binding and reactivity, in which k(2) varies approximately 10(3)-fold within the suite of Mbs without a significant change in binding affinity; (ii) the ET reaction occurs within the "thermodynamic" or "rapid exchange" limit of the "Dynamic Docking" model, in which a large ensemble of weakly bound protein-protein configurations contribute to binding, but only a few are reactive, as shown by the fact that the zero-ionic-strength bimolecular rate constant varies exponentially with the net charge on Mb; (iii) Brownian dynamic docking profiles allow us to visualize the microscopic basis of dynamic docking. To describe these results we present a new theoretical approach which mathematically combines PATHWAY donor/acceptor coupling calculations with Poisson-Boltzmann-based electrostatics estimates of the docking energetics in a Monte Carlo (MC) sampling framework that is thus specially tailored to the intermolecular ET problem. This procedure is extremely efficient because it targets only the functionally active complex geometries by introducing a "reactivity filter" into the computations themselves, rather than as a subsequent step. This efficiency allows us to employ more computationally expensive and accurate methods to describe the relevant intermolecular interaction energies and the protein-mediated donor/acceptor coupling interactions. It is employed here to compute the changes in the bimolecular rate constant for ET between Mb and cyt b(5) upon variations in the myoglobin surface charge, pH, and ionic strength.     

On the dimerization of α-mercaptoacetone: An n.m.r. study

¹H n.m.r. is used to show that α-mercaptoacetone is formed as a mixture of monomer and a dimer. No evidence is found to support the previously claimed isolation of two dimeric species. The dimer dissociates to the monomer on standing as a solution in chloroform, but the monomer is dimerized by grinding. 1-Mercapto-3-phenylpropan-2-one behaves similarly.     

Noncovalent associations of glutathione S-transferase and ligands: A study using electrospray quadrupole/time-of-flight mass spectrometry

Human glutathione S-transferase A1-1 was observed predominantly as dimeric ions (51 kDa) during electrospray mass spectrometric analysis from aqueous solution at pH 7.4, in keeping with the known dimeric structure in solution. When analyses were performed on solutions of the enzyme containing glutathione (GSH), noncovalent adducts of protein dimer and one or two ligand molecules were observed; each mass increment, which exceeded the mass of GSH alone, was provisionally interpreted to indicate concomitant association of two water molecules per bound GSH. Noncovalent adducts of ligand and protein dimer were similarly observed for oxidized glutathione and for two glutathione inhibitors, both incorporating substituted thiol structures. In these instances, the mass increments exactly matched the ligand masses, suggesting that the apparent concomitant binding of water was associated with the presence in the ligand of a free thiol group. Collisionally activated decomposition during tandem mass spectrometry analyses of noncovalent adducts incorporating protein dimer and ligands yielded initially the denuded dimer; at higher collision energies the monomer and a protein fragment were formed.     

A combined experimental and theoretical study of the kinetics and mechanism of the addition of alcohols to electronically stabilized silenes: a new mechanism for the addition of alcohols to the Si=C bond

The stabilized silene 1,1-bis(trimethylsilyl)-2-adamantylidenesilane (4) has been generated by photolysis of a novel trisilacyclobutane derivative in various solvents and studied directly by kinetic UV spectrophotometry. Silene 4 decays with second-order kinetics in degassed hexane solution at 23 degrees C (k/epsilon = 8.6 x 10(-6) cm s(-1)) due to head-to-head dimerization. It reacts rapidly with oxygen [k(25 degrees C) approximately 3 x 10(5) M(-1) s(-1)] but approximately 10 orders of magnitude more slowly with methanol (MeOH) than other silenes that have been studied previously. The data are consistent with a mechanism involving reaction with the hydrogen-bonded dimer of the alcohol, (MeOH)(2) (k = 40 +/- 3 M(-1) s(-1); k(H)/k(D) = 1.7 +/- 0.2). The stable analogue of silene 4, 1-tert-butyldimethylsilyl-1-trimethylsilyl-2-adamantylidenesilane (5), reacts approximately 50 times more slowly, but via the same mechanism. The mechanism for addition of water and methanol (ROH; R = H, Me) to 4, 5, and the model compound 1,1-bis(silyl)-2,2-dimethylsilene (3a) has been studied computationally at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. Hydrogen-bonded complexes with monomeric and dimeric methanol, in which the Si=C bond plays the role of nucleophile, have been located computationally for all three silenes. Reaction pathways have been characterized for reaction of the three silenes with monomeric and dimeric ROH and reveal significantly lower barriers for reaction with the dimeric form of the alcohol in each case. The calculations indicate that 5 should be approximately 40-fold less reactive toward dimeric MeOH than 4, in excellent agreement with the approximately 50-fold difference in the experimental rate constants for reaction in hexane solution.     

Solution behavior of iron(III) and iron(II) porphyrins in DMSO and reaction with superoxide. Effect of neighboring positive charge on thermodynamics, kinetics and nature of iron-(su)peroxo product

The solution behavior of iron(III) and iron(II) complexes of 5(4),10(4),15(4),20(4)-tetra-tert-butyl-5,10,15,20-tetraphenylporphyrin (H(2)tBuTPP) and the reaction with superoxide (KO(2)) in DMSO have been studied in detail. Applying temperature and pressure dependent NMR studies, the thermodynamics of the low-spin/high-spin equilibrium between bis- and mono-DMSO Fe(II) forms have been quantified (K(DMSO) = 0.082 ± 0.002 at 298.2 K, ΔH° = +36 ± 1 kJ mol(-1), ΔS° = +101 ± 4 J K(-1) mol(-1), ΔV° = +16 ± 2 cm(3) mol(-1)). This is a key activation step for substitution and inner-sphere electron transfer. The superoxide binding constant to the iron(II) form of the studied porphyrin complex was found to be (9 ± 0.5) × 10(3) M(-1), and does not change significantly in the presence of the externally added crown ether in DMSO (11 ± 4) × 10(3) M(-1). The rate constants for the superoxide binding (k(on) = (1.30 ± 0.01) × 10(5) M(-1) s(-1)) and release (k(off) = 11.6 ± 0.7 s(-1)) are not affected by the presence of the external crown ether in solution. The resulting iron(II)-superoxide adduct has been characterized (mass spectrometry, EPR, high-pressure UV/Vis spectroscopy) and upon controlled addition of a proton source it regenerates the starting iron(II) complex. Based on DFT calculations, the reaction product without neighboring positive charge has iron(II)-superoxo character in both high-spin side-on and low-spin end-on forms. The results are compared to those obtained for the analogous complex with covalently attached crown ether, and more general conclusions regarding the spin-state equilibrium of iron(II) porphyrins, their reaction with superoxide and the electronic structure of the product species are drawn.     

PEGylation of an artificial O2 and CO receptor: synthesis, characterisation and pharmacokinetic study

A synthetic oxygen (O(2)) and carbon monoxide (CO) receptor (hemoCD) composed of 5,10,15,20-tetrakis(4-sulfonatophenyl)porphinatoiron(ii) and a per-O-methylated β-cyclodextrin dimer with a pyridine linker (Py3CD) was functionalised with poly(ethylene glycol) (PEG) to elongate the circulation time of the receptor in the bloodstream. α-PEG monocarboxylic acid (HOOC(CH(2))(3)(CO)O-PEG(mw)-OCH(3); mw = 750 or 5k) or α,ω-PEG dicarboxylic acid (HOOC(CH(2))(3)(CO)O-PEG(mw)-O(CO)(CH(2))(3)COOH; mw = 10k or 20k) was reacted with the amino group of 5-(4-aminophenyl)-10,15,20-tris(4-sulfonatophenyl)porphyrin to afford a porphyrin monomer having a PEG chain or a porphyrin dimer having a PEG linker, respectively. The ferrous complexes of these PEGylated porphyrins (PEG750-, PEG5k-, PEG10k- and PEG20k-hemoCDs) bound O(2) in aqueous solution, P(1/2) values being 6.5-8.1 Torr at pH 7.0 and 25 °C. Each PEG(mw)-hemoCD was infused into the femoral vein of a Wistar male rat. After 6 h of the infusions, 67, 82, 86 and 42% of PEG750-, PEG5k-, PEG10k- and PEG20k-hemoCD were excreted in the urine. PEG750-hemoCD with a hydrodynamic diameter (D(h)) of 3.4 nm seemed to partly leak from the blood vessels (pore size: 2-6 nm) before renal filtration (pore size: 4-14 nm). PEG5k- (D(h) = 6.2 nm) and PEG10k-hemoCDs (9.0 nm) hardly passed through the blood vessels but were fully filtered by the kidney, resulting in high excretion rates. A considerable amount of PEG20k-hemoCD (D(h) = 12.0 nm) was retained in the blood even at 6 h after administration. The present study demonstrates that the behaviour of hemoCD in blood after administration can be controlled by modification of hemoCD with PEG having an appropriate molecular weight.     

Role of heme types in heme-copper oxidases: effects of replacing a heme b with a heme o mimic in an engineered heme-copper center in myoglobin

To address the role of the secondary hydroxyl group of heme a/o in heme-copper oxidases, we incorporated Fe(III)-2,4 (4,2) hydroxyethyl vinyl deuterioporphyrin IX, as a heme o mimic, into the engineered heme-copper center in myoglobin (sperm whale myoglobin L29H/F43H, called Cu(B)Mb). The only difference between the heme b of myoglobin and the heme o mimic is the substitution of one of the vinyl side chains of the former with a hydroxyethyl group of the latter. This substitution resulted in an approximately 4 nm blue shift in the Soret band and approximately 20 mV decrease in the heme reduction potential. In a control experiment, the heme b in Cu(B)Mb was also replaced with a mesoheme, which resulted in an approximately 13 nm blue shift and approximately 30 mV decrease in the heme reduction potential. Kinetic studies of the heme o mimic-substituted Cu(B)Mb showed significantly different reactivity toward copper-dependent oxygen reduction from that of the b-type Cu(B)Mb. In reaction with O2, Cu(B)Mb with a native heme b showed heme oxygenase activity by generating verdoheme in the presence of Cu(I). This heme degradation reaction was slowed by approximately 19-fold in the heme o mimic-substituted Cu(B)Mb (from 0.028 s(-1) to 0.0015 s(-1)), while the mesoheme-substituted Cu(B)Mb shared a similar heme degradation rate with that of Cu(B)Mb (0.023 s(-1)). No correlation was found between the heme reduction potential and its O2 reactivity. These results strongly suggest the critical role of the hydroxyl group of heme o in modulating heme-copper oxidase activity through participation in an extra hydrogen-bonding network.     

The oxidative degradation of dibenzoazepine derivatives by cerium(IV) complexes in acidic sulfate media

The kinetics of the oxidation of imipramine and desipramine using cerium(IV) complexes were studied in the presence of a large excess of azepine derivative (TCA) in acidic sulfate media using UV-Vis spectroscopy. The reaction proceeds via dibenzoazepine radical formation, identified by EPR measurements. The kinetics of the first degradation step were studied independently of the further slower degradation reactions. Linear dependences, with zero intercept, of the pseudo-first-order rate constants (k(obs)) on [TCA] were established for both dibenzoazepine radical formation processes. Rates of reactions decreased with increasing concentration of the H(+) ion indicating that cerium(IV) as well as both reductants exist in an equilibrium with their protolytic forms. The activation parameters for the degradation of dibenzoazepine derivatives in the first oxidation stage were as follows: ΔH(≠) = 39 ± 2 kJ mol(-1), ΔS(≠) = -28 ± 8 J K(-1) mol(-1) for imipramine and ΔH(≠) = 39 ± 2 kJ mol(-1), ΔS(≠) = -28 ± 6 J K(-1) mol(-1) for desipramine, respectively. Imipramine and desipramine radicals dimerized leading to an intermediate radical dimer, which decayed in a first-order consecutive decay process. These two further reactions proceed with rates which are characterized by non-linear dependences of the pseudo-first-order rate constants (k(obs)) on [TCA]. The degradation reaction of the intermediate radical dimer leads to an uncharged dimer as a final product. Mechanistic consequences of all the results are discussed.     

Vibrational coherence spectroscopy of the heme domain in the CO-sensing transcriptional activator CooA

Femtosecond vibrational coherence spectroscopy was used to investigate the low-frequency vibrational dynamics of the heme in the carbon monoxide oxidation activator protein (CooA) from the thermophilic anaerobic bacterium Carboxydothermus hydrogenoformans (Ch-CooA). Low frequency vibrational modes are important because they are excited by the ambient thermal bath (k(B)T = 200 cm(-1)) and participate in thermally activated barrier crossing events. However, such modes are nearly impossible to detect in the aqueous phase using traditional spectroscopic methods. Here, we present the low frequency coherence spectra of the ferric, ferrous, and CO-bound forms of Ch-CooA in order to compare the protein-induced heme distortions in its active and inactive states. Distortions take place predominantly along the coordinates of low-frequency modes because of their weak force constants, and such distortions are reflected in the intensity of the vibrational coherence signals. A strong mode near ~90 cm(-1) in the ferrous form of Ch-CooA is suggested to contain a large component of heme ruffling, consistent with the imidazole-bound ferrous heme crystal structure, which shows a significant protein-induced heme distortion along this coordinate. A mode observed at ~228 cm(-1) in the six-coordinate ferrous state is proposed to be the ν(Fe-His) stretching vibration. The observation of the Fe-His mode indicates that photolysis of the N-terminal α-amino axial ligand takes place. This is followed by a rapid (~8.5 ps) transient absorption recovery, analogous to methionine rebinding in photolyzed ferrous cytochrome c. We have also studied CO photolysis in CooA, which revealed very strong photoproduct state coherent oscillations. The observation of heme-CO photoproduct oscillations is unusual because most other heme systems have CO rebinding kinetics that are too slow to make the measurement possible. The low frequency coherence spectrum of the CO-bound form of Ch-CooA shows a strong vibration at ~230 cm(-1) that is broadened and up-shifted compared to the ν(Fe-His) of Rr-CooA (216 cm(-1)). We propose that the stronger Fe-His bond is related to the enhanced thermal stability of Ch-CooA and that there is a smaller (time dependent) tilt of the histidine ring with respect to the heme plane in Ch-CooA. The appearance of strong modes at ~48 cm(-1) in both the ferrous and CO-bound forms of Ch-CooA is consistent with coupling of the heme doming distortion to the photolysis reaction in both samples. Upon CO binding and protein activation, a heme mode near 112 ± 5 cm(-1) disappears, probably indicating a decreased heme saddling distortion. This reflects changes in the heme environment and geometry that must be associated with the conformational transition activating the DNA-binding domain. Protein-specific DNA binding to the CO-bound form of Ch-CooA was also investigated, and although the CO rebinding kinetics are significantly perturbed, there are negligible changes in the low-frequency vibrational spectrum of the heme.     

Monomer–Dimer Control and Crystal Engineering in TASPs

We have reported a template assembled synthetic protein (cavitein Q4) as an unexpected dimer in the solid state and as a monomer–dimer equilibrium in solution. We have since reported an ability to bias a cavitein’s monomer–dimer equilibrium in solution by sequence design involving histidine metal chelation or disulfide incorporation. However, little remains known about the forces contributing to dimeric cavitein crystal nucleation and lattice stabilization. We, therefore, designed glutamine variants to probe factors involved in dimeric cavitein crystallization. It was found that a key glutamate hydrogen-bonding interaction between dimers is integral to crystal formation and stabilization. Additionally, we obtained a crystal structure of a cavitein (Q4-E3H) designed to bias the dimeric structure via histidine metal coordination. The resolved structure indicates a histidine cluster interaction that likely accounts for the biased dimeric form observed in solution.     

Double-threaded dimer and supramolecular oligomer formed by stilbene modified cyclodextrin: effect of acyl migration and photostimuli

We observed changing supramolecular structures of stilbene-α-cyclodextrin (StiO-α-CD) by photoirradiation and migration. Stilbene derivatives show photoinduced isomerization under irradiation with λ = 340 nm to give 2-cis-StiO-α-CD and with λ = 254 nm to give 2-trans-StiO-α-CD. Photoisomerization of StiO-α-CD shows the photostationary state during 30 min. 2D NMR and diffusion coefficient studies revealed that 2-trans-StiO-α-CD forms a double-threaded dimer but 2-cis-StiO-α-CD changes to a supramolecular oligomer by photoirradiation. We found that the mutual migration of a stilbene group (StiO) on α-CD occurs under neutral conditions. The StiO group of α-CD (StiO-α-CD) moves between the C2 and C3 positions on the secondary hydroxyl group of StiO-α-CD (the wider rim of α-CD) to give 3-trans-StiO-α-CD. 3-trans-StiO-α-CD forms a supramolecular oligomer, whereas 3-cis-StiO-α-CD changes to a double-threaded dimer, indicating that 3-StiO-α-CDs gives the opposite results in the supramolecular structures of 2-StiO-α-CDs. The thermal isomerization (migration) is very slow. It takes about 300 h to reach the equilibrium state. Moreover, the migration rate constant (k(trans3→2)) of the trans-StiO group from the C3 position to the C2 position of α-CD is faster than k(trans2→3) from the C2 position to the C3 position of α-CD. On the other hand, k(cis2→3) of the cis-StiO group from the C2 position to the C3 position of α-CD is faster than k(cis3→2) from the C3 position to the C2 position, meaning k(cis2→3) > k(cis3→2), which is the opposite result for k(trans3→2) > k(trans2→3). The formation of a stable double-threaded dimer would suppress the migration of the StiO group of StiO-α-CDs in aqueous solutions.     

Mechanism of hydride donor generation using a Ru(II) complex containing an NAD+ model ligand: pulse and steady-state radiolysis studies

The mechanistic pathways of formation of the NADH-like [Ru(bpy) 2(pbnHH)] (2+) species from [Ru(bpy)2(pbn)](2+) were studied in an aqueous medium. Formation of the one-electron-reduced species as a result of reduction by a solvated electron (k=3.0 x 10(10) M(-1) s(-1)) or CO2(*-) (k=4.6 x 10(9) M(-1) s(-1)) or reductive quenching of an MLCT excited state by 1,4-diazabicyclo[2.2.2]octane (k=1.1 x 10(9) M(-1) s(-1)) is followed by protonation of the reduced species (p K a = 11). Dimerization (k7a=2.2 x 10(8) M(-1) s(-1)) of the singly reduced protonated species, [Ru(bpy) 2(pbnH(*))](2+), followed by disproportionation of the dimer as well as the cross reaction between the singly reduced protonated and nonprotonated species (k8= 1.2 x 10(8) M(-1) s(-1)) results in the formation of the final [Ru(bpy)2(pbnHH)](2+) product together with an equal amount of the starting complex, [Ru(bpy)2(pbn)](2+). At 0.2 degrees C, a dimeric intermediate, most likely a pi-stacking dimer, was observed that decomposes thermally to form an equimolar mixture of [Ru(bpy)2(pbnHH)](2+) and [Ru(bpy)2(pbn)](2+) (pH<9). The absence of a significant kinetic isotope effect in the disproportionation reaction of [Ru(bpy)2(pbnH(*))](2+) and its conjugate base (pH>9) indicates that disproportionation occurs by a stepwise pathway of electron transfer followed by proton transfer.