Dynamics of carbon monoxide recombination to fully reduced cytochrome c oxidase in plant mitochondria after low-temperature flash photolysis.

Rebinding of CO to reduced cytochrome c oxidase in plant mitochondria has been monitored optically at 590-630 nm after flash photolysis at low temperature from 160 to 200 K. (1) Under 100%-CO saturation, CO rebinding exhibits a four-step mechanism. The thermodynamic parameters of the first phase have been determined; its activation energy, Ea1, is 38.9 kJ.mol-1 and its enthalpy, delta H+/-1, and entropy, delta S+/-1, of activation are respectively 37.5 kJ.mol-1 and -75.8J.mol-1.K-1. (2) When the CO concentration is decreased to 0.2%, rebinding still occurs according to a four-step mechanism. The rate constant of the first phase is CO-concentration-independent. Under non-saturating conditions there is only one CO molecule per occupied site. The rebinding mechanism does not require additional CO molecules to be present in the haem pocket. (3) Dual-wavelength scanning experiments failed to detect optical forms correlated with the resolved phases. (4) Results are discussed with respect to previous work related to CO rebinding to mammalian cytochrome c oxidase and myoglobin.     

Photolysis method for determination of the tetramer-dimer dissociation constant of deoxyhemoglobin

A new method for determination of the tetramer-dimer dissociation constant Ku4.2 of deoxyhemoglobin is described. The method involves photolysis of hemoglobin solutions containing a few percent of bound CO (e.g. less than 3%). Under these conditions the nature of the observed CO rebinding is primarily determined by the properties of the dominant species, deoxyhemoglobin. The method makes use of the 30-fold difference in the rate constant describing CO binding to hemoglobin dimers and deoxyhemoglobin tetramers. Because of this large difference in rate constants CO rebinding is made significantly more rapid by the presence of even small concentrations of dimers. Treating this reaction as CO binding to a mixture of hemoglobin dimers and tetramers allows the determination of Ku4.2. Data is presented showing application of the method to human deoxyhemoglobin in the range from pH 9.5 to 11.2.     

A flash photolysis method to characterize hexacoordinate hemoglobin kinetics

A flash photolysis method is described for analyzing ligand binding to the new and growing group of hemoglobins which are hexacoordinate in the unligated, ferrous state. Simple analysis of a two exponential fit to time courses for CO rebinding at varying CO concentrations yields rate constants for formation and dissociation of the hexacoordinate complex, and the bimolecular rate constant for CO binding. This method was tested with a nonsymbiotic plant hemoglobin from rice for which these values had not previously been determined. For this protein, dissociation and rebinding of the hexacoordinating amino acid side chain, His(73), is rapid and similar to the rate of CO binding at high CO concentrations. These results indicate that hexacoordination must be taken into account when evaluating the affinity of hexacoordinate hemoglobins for ligands.     

Time-resolved absorption and magnetic circular dichroism spectroscopy of cytochrome c3 from Desulfovibrio.

The UV-visible absorption and magnetic circular dichroism (MCD) spectra of the ferric, ferrous, CO-ligated forms and kinetic photolysis intermediates of the tetraheme electron-transfer protein cytochrome c3 (Cc3) are reported. Consistent with bis-histidinyl axial coordination of the hemes in this Class III c-type cytochrome, the Soret and visible region MCD spectra of ferric and ferrous Cc3 are very similar to those of other bis-histidine axially coordinated hemeproteins such as cytochrome b5. The MCD spectra indicate low spin state for both the ferric (S = 1/2) and ferrous (S = 0) oxidation states. CO replaces histidine as the axial sixth ligand at each heme site, forming a low-spin complex with an MCD spectrum similar to that of myoglobin-CO. Photodissociation of Cc3-CO (observed photolysis yield = 30%) produces a transient five-coordinate, high-spin (S = 2) species with an MCD spectrum similar to deoxymyoglobin. The recombination kinetics of CO with heme Fe are complex and appear to involve at least five first-order or pseudo first-order rate processes, corresponding to time constants of 5.7 microseconds, 62 microseconds, 425 microseconds, 2.9 ms, and a time constant greater than 1 s. The observed rate constants were insensitive to variation of the actinic photon flux, suggesting noncooperative heme-CO rebinding. The growing in of an MCD signal characteristic of bis-histidine axial ligation within tens of microseconds after photodissociation shows that, although heme-CO binding is thermodynamically favored at 1 atm CO, binding of histidine to the sixth axial site competes kinetically with CO rebinding.     

Electron paramagnetic resonance- (EPR-) resolved kinetics of cryogenic nitric oxide recombination to cytochrome c oxidase and myoglobin.

By the electron paramagnetic resonance (EPR) technique, recovery kinetics for nitric oxide (NO) to heme following cryogenic photolysis were studied for the nitrosylferrocytochrome a3 center in cytochrome c oxidase and for myoglobin. The recovery was nonexponential, as has been observed in previous cryogenic CO and O2 rebinding to heme systems. NO rebinding to heme a3 started near a temperature of 50 K and was related to a distribution of thermal activation energies. At the peak of the distribution the activation energy was 3.1 kcal/mol, and the preexponential in the recovery rate was 10(9.9) s-1. For recovery of NO back to the a3 heme, the activation energy was threefold less than that for CO where CO binds to nearby Cua3 following photolysis from heme a3, but was larger than the activation energy for CO, O2, and probably NO rebinding to myoglobin. NO ligand rebinding to myoglobin occurred at a temperature as low as 15 K and in a temperature regime where tunneling could occur. However, the rate of NO rebinding to myoglobin did increase with temperature in the 15-25 K range.     

Flash-photolysis of fully reduced and mixed-valence CO-bound Rhodobacter sphaeroides cytochrome c oxidase: heme spectral shifts

Conformational changes, internal electron transfer, and CO rebinding processes in cytochrome c oxidase from Rhodobacter sphaeroides reduced to different degrees were investigated. The reactions were followed using a gated optical spectrometric multichannel analyzer. Light-induced difference spectra, recorded in the 350-700 nm region over the 100 ns to 1 s time interval, were analyzed by singular value decomposition and global exponential fitting. The photolyzed fully reduced enzyme showed two relaxations, approximately 1 and 190 mus, prior to the 20 ms CO rebinding process. Intramolecular electron transfer was monitored following photolysis of the mixed-valence CO-bound enzyme. The analysis revealed 1.1 micros, 2.4 micros, 31 micros, 68 ms, and 240 ms apparent lifetimes, the first three of which are attributed to electron transfer from heme a3 to heme a with contribution from a relaxation process at the heme a3 site. Spectral changes associated with the microsecond processes are consistent with 75% electron transfer from heme a3 to heme a. A comparison of the experimental spectra and model difference spectra for the intramolecular electron transfer indicated approximately 3 nm blue shift in the absolute spectra of both the oxidized heme a3 and reduced heme a generated in the process. The 68 and 240 ms lifetimes are due to CO recombination to heme a3 and are attributed to the presence of two conformers, the slower rate corresponding to the conformer in higher abundance. The dependency of the apparent rate of CO rebinding on the intensity of the probe beam in single-wavelength experiments is explained.     

Analysis of the kinetic barriers for ligand binding to sperm whale myoglobin using site-directed mutagenesis and laser photolysis techniques

Time courses for NO, O2, CO, methyl and ethyl isocyanide rebinding to native and mutant sperm whale myoglobins were measured at 20 degrees C following 17-ns and 35-ps laser excitation pulses. His64 (E7) was replaced with Gly, Val, Leu, Phe, and Gln, and Val68 (E11) was replaced with Ala, Ile, and Phe. For both NO and O2, the effective picosecond quantum yield of unliganded geminate intermediates was roughly 0.2 and independent of the amino acids at positions 64 and 68. Geminate recombination of NO was very rapid; 90% rebinding occurred within 0.5-1.0 ns for all of the myoglobins examined; and except for the Gly64 and Ile68 mutants, the fitted recombination rate parameters were little influenced by the size and polarity of the amino acid at position 64 and the size of the residue at position 68. The rates of NO recombination and ligand movement away from the iron atom in the Gly64 mutant increased 3-4-fold relative to native myoglobin. For Ile68 myoglobin, the first geminate rate constant for NO rebinding decreased approximately 6-fold, from 2.3 x 10(10) s-1 for native myoglobin to 3.8 x 10(9) s-1 for the mutant. No picosecond rebinding processes were observed for O2, CO, and isocyanide rebinding to native and mutant myoglobins; all of the observed geminate rate constants were less than or equal to 3 x 10(8) s-1. The rebinding time courses for these ligands were analyzed in terms of a two-step consecutive reaction scheme, with an outer kinetic barrier representing ligand movement into and out of the protein and an inner barrier representing binding to the heme iron atom by ligand occupying the distal portion of the heme pocket. Substitution of apolar amino acids for His64 decreased the absolute free energies of the outer and inner kinetic barriers and the well for non-covalently bound O2 and CO by 1 to 1.5 kcal/mol, regardless of size. In contrast, the His64 to Gln mutation caused little change in the barrier heights for all ligands, showing that the polar nature of His64 inhibits both the bimolecular rate of ligand entry into myoglobin and the unimolecular rate of binding to the iron atom from within the protein. Increasing the size of the position 68(E11) residue in the series Ala to Val (native) to Ile caused little change in the rate of O2 migration into myoglobin or the equilibrium constant for noncovalent binding but did decrease the unimolecular rate for iron-O2 bond formation.(ABSTRACT TRUNCATED AT 400 WORDS)     

A re-evaluation of the low-temperature kinetics of the reaction of fully reduced mitochondrial cytochrome oxidase with carbon monoxide and the spectral characterization of species Ic in the Soret and visible regions

The kinetics of the reaction of fully reduced membrane bound cytochrome oxidase with CO following photolysis of the fully reduced cytochrome oxidase-CO complex habe been re-examined by re-analysing the data of Clore and Chance (1978) Biochem. J. 175, 709-725) at six temperatures in the 178-203 K range simultaneously at only a single wavelength pair, 444-463 nm. The choice of the 444-463 nm wavelength pair was based on the fact that the absorbance change produced at 444-463 nm on photolysis of the CO complex is sufficiently large and the separation between monitoring and reference wavelengths sufficiently small to render the effects of any possible time dependent scattering changes insignificant. On the basis of our analysis only a two step mechanism (Model 1 of Clore and Chance (1978) Biochem. J. 175, 709-725) satisfies the triple requirement of a S.D. within the standard error of the data, a random distribution of residuals and good determination of the optimized parameters. The single step mechanism of De Fonseka and Chance (1978) Biochem. J. 175, 1137-1138) fails to satisfy all three requirements. The pure difference spectra of species Ic minus E, E minus IIc and Ic minus IIc are calculated from the computed kinetics of the individual species and repetitive slow wavelength scanning difference spectra (reaction sample minus the CO complex) taken during the course of the reaction of fully reduced cytochrome oxidase with CO at 176 K.     

Analysis of the kinetics of CO binding to neuronal nitric oxide synthase by flash photolysis: dual effects of substrates, inhibitors, and tetrahydrobiopterin

The effects of substrates, inhibitors and tetrahydrobiopterin (H4B) on CO rebinding to the isolated heme-bound oxygenase domain (nNOSox) of neuronal nitric oxide synthase were examined by laser flash photolysis. The rate constant of CO recombination with substrate and inhibitor-free nNOSox in the absence of H4B was 1.0 x 10(6) M(-1) s(-1). The addition of H4B led to a marked decrease in the rate to 0.59 x 10(6) M(-1) s(-1). Interestingly, the substrates, L-Arg and N-hydroxy-L-Arg (NHA), altered CO binding behavior in that the binding rate was modified to CO concentration-independent, both with and without H4B. In the absence of H4B, agmatine, NG-monomethyl-L-Arg (NMMA) and NG-nitro-L-Arg methyl ester (NAME) decreased the CO concentration-dependent rate constants of rebinding by half (0.43 x 10(6) M(-1) s(-1) for the NMMA-bound complex), whereas N6-(l-iminoethyl)-L-Lys (NIL) and 7-nitro-1H-indazole (7-NI) increased the rate constants by more than 70% (up to 2.1 x 10(6) M(-1) s(-1) for the NIL-bound complex). In the presence of H4B, the binding rate was independent of CO concentration for the agmatine-bound complex. The differential effects of the inhibitors on the CO concentration-dependent rate constants were significantly diminished for the H4B-bound system. Interestingly, these variable effects of inhibitors on the CO binding rate were more pronounced in the absence of H4B. Accordingly, we suggest that H4B significantly influences CO binding by altering the CO access channel, and further reduces the divergent effects of different inhibitors.     

Volume and enthalpy profiles of CO rebinding to horse heart myoglobin

Carbon monoxide binding to myoglobin was characterized using the photothermal beam deflection method. The volume and enthalpy changes coupled to CO dissociation were found to be 9.3+/-0.8 mL x mol(-1) and 7.4+/-2.8 kcal x mol(-1), respectively. The corresponding values observed for CO rebinding have the same magnitude but opposite sign: Delta V=-8.6+/-0.9 mL x mol(-1) and Delta H=-5.8+/-2.9 kcal x mol(-1). Ligand rebinding occurs as a single conformational step with a rate constant of 5 x 10(5) M(-1) s(-1) and with activation enthalpy of 7.1+/-0.8 kcal x mol(-1) and activation entropy of -22.4+/-2.8 cal x mol(-1) K(-1). Activation parameters for the ligand binding correspond to the activation parameters previously obtained using the transient absorption methods. Hence, at room temperature the CO binding to Mb can be described as a two-state model and the observed volume contraction occurs during CO-Fe bond formation. Comparing these results with CO dissociation reactions, for which two discrete intermediates were characterized, indicates differences in mechanism by which the protein modulates ligand association and dissociation.     

In vivo binding of carbon monoxide to cytochrome c oxidase in rat brain

The possibility of binding of CO to cytochrome c oxidase (cytochrome a,a3) in brain cortex has been examined in vivo by reflectance spectrophotometry. During ventilation with CO-containing gases, cytochrome a,a3 absorption at 605 nm increased in the parietal cortex of anesthetized rats during carboxyhemoglobin (HbCO) formation. HbCO levels, measured by changes in absorption at 569-586 nm in vivo, correlated positively with arterial HbCO by CO oximetry. Arterial blood pressure and calculated O2 content varied inversely with HbCO. During CO exposure, decreases in blood pressure, O2 content, and cytochrome a,a3 oxidation level could be reversed partly at constant HbCO by compression to 3 atmospheres absolute (ATA). After removing CO from inspired gas at 3 ATA, optical and physiological parameters recovered completely to control values except for minor persistent elevations of HbCO. Difference spectra from parallel experiments at constant HbCO revealed absorption minima at 588-592 nm and 600-605 nm as a result of hyperbaric exposure. Spectral analysis of these components was consistent with partial dissociation of a cytochrome a3-CO complex and cytochrome a reoxidation with increasing dissolved O2 in hyperbaric conditions.     

The effect of water on the rate of conformational change in protein allostery

The influence of solvation on the rate of quaternary structural change is investigated in human hemoglobin, an allosteric protein in which reduced water activity destabilizes the R state relative to T. Nanosecond absorption spectroscopy of the heme Soret band was used to monitor protein relaxation after photodissociation of aqueous HbCO complex under osmotic stress induced by the nonbinding cosolute poly(ethylene glycol) (PEG). Photolysis data were analyzed globally for six exponential time constants and amplitudes as a function of osmotic stress and viscosity. Increases in time constants associated with geminate rebinding, tertiary relaxation, and quaternary relaxation were observed in the presence of PEG, along with a decrease in the fraction of hemes rebinding CO with the slow rate constant characteristic of the T state. An analysis of these results along with those obtained by others for small cosolutes showed that both osmotic stress and solvent viscosity are important determinants of the microscopic R --> T rate constant. The size and direction of the osmotic stress effect suggests that at least nine additional water molecules are required to solvate the allosteric transition state relative to the R-state hydration, implying that the transition state has a greater solvent-exposed area than either end state.     

Spectroscopic and photothermal study of myoglobin conformational changes in the presence of sodium dodecyl sulfate

Interactions between sodium dodecyl sulfate (SDS) and horse heart myoglobin (Mb) at surfactant concentrations below the critical micelle concentration have been studied using steady-state and transient absorption spectroscopies and photoacoustic calorimetry. SDS binding to Mb induces a heme transition from high-spin five-coordinate to low-spin six-coordinate in met- and deoxyMb, with the distal His residue likely to be the sixth ligand. The transition is complete at an SDS concentration of approximately 350 microM and approximately 700 microM for met- and deoxyMb, respectively. DeltaG(H(2)O) and m values determined from equilibrium SDS-induced unfolding curves indicate similar stability of met- and deoxyMb toward unfolding; however, the larger m value for the deoxyMb equilibrium intermediate indicates that its structure differs from that of metMb. Results from transient absorption spectroscopy show that CO rebinding to Fe(2+)-Mb in the presence of SDS is a biphasic process with the rate constant of the first process approximately 5.5 x 10(3) s(-1), whereas the second process displays a rate similar to that for CO rebinding to native Mb (k(obs) = 7.14 x 10(2) s(-1)) at 1 mM CO. Results of photoacoustic calorimetry show that CO dissociation from deoxyMb occurs more than 10 times faster in the presence of SDS than in native Mb. These data suggest that the heme binding pocket is more solvent-exposed in the SDS-induced equilibrium intermediate relative to native Mb, which is likely due to the electrostatic and hydrophobic interactions between surfactant molecules and the protein matrix.     

Role of an isoform-specific substrate access channel residue in CO ligand accessibilities of neuronal and inducible nitric oxide synthase isoforms

The rates of the bimolecular CO rebinding to the oxygenase domains of inducible and neuronal NOS proteins (iNOSoxy and nNOSoxy, respectively) after photolytic dissociation have been determined by laser flash photolysis. The following mutants at the isoform-specific sites (murine iNOSoxy N115L and rat nNOSoxy L337N, L337F) have been constructed to investigate role of the residues in the CO ligand accessibilities of the NOS isoforms. These residues are in the NOS distal substrate access channel. The effect of the (6R)-5,6,7,8-tetrahydrobiopterin (H(4)B) cofactor and l-arginine (Arg) substrate on the rates of CO rebinding have also been assessed. Addition of l-Arg to the iNOSoxy N115L mutant results in much faster CO rebinding rates, compared to the wild type. The results indicate that modifications to the iNOS channel in which the hydrophilic residue N115 is replaced by leucine (to resemble its nNOS cognate) open the channel somewhat, thereby improving access to the axial heme ligand binding position. On the other hand, introduction of a hydrophilic residue (L337N) or a bulky rigid aromatic residue (L337F) in the nNOS isoform does not significantly affect the kinetics profile, suggesting that the geometry of the substrate access pocket is not greatly altered. The bimolecular CO rebinding rate data indicate that the opening of the substrate access channel in the iNOS N115L mutant may be due to more widespread structural alterations induced by the mutation.     

Purification and properties of a peroxidase from Halobacterium halobium L-33

A peroxidase was purified from Halobacterium halobium L-33 to an electrophoretically homogeneous state and some of its properties were studied. The enzyme showed an absorption peak at 406 nm in the oxidized form and peaks at 440, 558, and 591 nm in the reduced form. The difference spectrum, reduced + CO minus reduced, of the enzyme showed peaks at 425, 538, and 577 nm and troughs at 444, 562, and 596 nm. These spectral properties were apparently similar to those of "cytochrome a1" except for the occurrence of the peak at 558 nm in the reduced form. The molecular weight of the enzyme was 110,000 and the enzyme possessed one unit of protoheme in the molecule. The activity to oxidize guaiacol in the presence of H2O2 of the peroxidase was about one-twentieth of that of horseradish peroxidase. The enzyme also showed a catalase-activity one-fourth as active as that of liver catalase. The reactions catalyzed by the enzyme were strongly inhibited by KCN.     

Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca

CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to ～100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of ～2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at ～100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from ～3 to ～100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb.     

Carbon monoxide-binding cytochromes in the respiratory chain of the thermophilic bacterium PS3 grown with sufficient or limited aeration

The effects of aeration on the growth and cytochrome patterns of thermophilic bacterium PS3 were studied; bacteria grown with strong aeration synthesized cytochromes c, b, and aa3, while those grown with low aeration, showing non-exponential growth, synthesized higher amounts of cytochromes c and b including o, and a lower amount of cytochrome a (a3). The CO-difference spectra indicated that the terminal oxidase was cytochrome aa3 for high aeration conditions and the cytochrome o for low aeration conditions. Cytochrome o can be solubilized by Triton X-100 from the membrane fraction of bacteria grown under oxygen-limited conditions. The carbon monoxide complex of cytochrome o, obtained by exposing this extract to CO, was photolyzed and the subsequent rebinding of CO was analyzed; it followed first order kinetics with a rate constant of around 8 s-1 at 25 degrees C. At liquid nitrogen temperature, CO-rebinding did not occur. The CO-difference spectrum of purified cytochrome oxidase sample from the bacteria grown with strong aeration (Sone, N., et al. (1979) FEBS Lett. 106, 39-42) revealed the presence of a small amount of a cytochrome o-like pigment besides cytochrome aa3. Analysis of the CO complexes of these chromophores showed rate constants of 29-30 s-1 for cytochrome aa3 and 35-42 s-1 for the o-like pigment, indicating that the cytochrome o-like pigment contaminating the purified cytochrome oxidase preparation was not typical cytochrome o.     

Proximal and distal influences on ligand binding kinetics in microperoxidase and heme model compounds

We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound heme complexes to study proximal and distal influences on ligand rebinding kinetics. We report kinetics of CO rebinding to microperoxidase (MP) and 2-methylimidazole ligated Fe protoporphyrin IX in the 10 ns to 10 ms time window. We also report CO rebinding kinetics of MP in the 150 fs to 140 ps time window. For dilute, micelle-encapsulated (monodisperse) samples of MP, we do not observe the large amplitude geminate decay at approximately 100 ps previously reported in time-resolved IR measurements on highly concentrated samples [Lim, M., Jackson, T. A., and Anfinrud, P. A. (1997) J. Biol. Inorg. Chem. 2, 531-536]. However, for high concentration aggregated samples, we do observe the large amplitude picosecond CO geminate rebinding and find that it is correlated with the absence of the iron-histidine vibrational mode in the time-resolved Raman spectrum. On the basis of these results, the energetic significance of a putative distal pocket CO docking site proposed by Lim et al. may need to be reconsidered. Finally, when high concentration samples of native myoglobin (Mb) were studied as a control, an analogous increase in the geminate rebinding kinetics was not observed. This verifies that studies of Mb under dilute conditions are applicable to the more concentrated regime found in the cellular milieu.     

Internal electron transfer in cytochrome c oxidase: evidence for a rapid equilibrium between cytochrome a and the bimetallic site.

Internal electron-transfer reactions in cytochrome oxidase following flash photolysis of the CO compounds of the enzyme reduced to different degrees (2-4 electron equiv) have been followed at 445, 605, and 830 nm. Apart from CO dissociation and recombination, two kinetic phases are seen both at 445 and at 605 nm with rate constants of 2 x 10(5) and 1.3 x 10(4) s-1, respectively; at 605 nm, an additional phase with a rate constant of 400 s-1 is resolved. At 830 nm, only the second reaction phase (rate constant of 1.3 x 10(4) s-1) is observed. The amplitude of the first phase is largest with the two-electron-reduced enzyme, whereas that of the second phase is maximal at the three-electron-reduction level. Neither phase shows any marked pH dependence. The reaction in the first phase has a free energy of activation of 41 kJ mol-1 and an entropy of activation of -14 JK-1 mol-1. Analysis suggests that the two rapid reaction phases represent internal electron redistributions between the bimetallic site and cytochrome a, and between cytochrome a and CuA, respectively. The slow phase (400 s-1) probably involves a structural rearrangement.