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T Yonetani

Publications and source records attributed to T Yonetani.

At least 19 recordsLinked to original sources
PubMed2005

High pressure reveals that the stability of interdimeric contacts in the R- and T-state of HbA is influenced by allosteric effectors: Insights from computational simulations.

The molecular details of the mechanism of action of allosteric effectors on hemoglobin oxygen affinity are not clearly understood. The global allostery model proposed by Yonetani et al. suggests that the binding of allosteric effectors can take place both in the R and T states and that they influence oxygen affinity through inducing global tertiary changes in the subunits. Recently published high pressure studies yielded dissociation constants at atmospheric pressure that showed a stabilizing effect of heterotropic allosteric effectors on the dimer interface in the R state, and a more pronounced destabilizing effect in a T state model. In the present work, we report on computational modeling used to interpret the high pressure experimental data. We show structural changes in the hemoglobin interdimeric interfaces, indicative of a global tertiary structural change induced by the binding of allosteric effectors. We also show that the number of water molecules bound at the interface is significantly influenced by binding effectors in the T state in accordance with the experimental data. Our results suggest that the binding of effectors at definite sites leads to tertiary changes that propagate to the interfaces and results in overall structural re-organizations.

Allosteric Regulation↗
PubMed2001

Unusual spin state equilibrium of azide metmyoglobin induced by ferric corrphycene.

Myoglobin was reconstituted with the ferric complex of corrphycene, a novel porphyrin isomer with a rearranged tetrapyrrole array, to investigate the influence of porphyrin deformation on the equilibrium between high-spin (S = 5/2) and low-spin (S = 1/2) states in the azide derivative. The azide affinity, 2.5 x 10(4) M(-1), was 1 order of magnitude lower than the corresponding values of a reference myoglobin containing an electron-deficient diformylheme similar to the corrphycene. Analysis of the visible absorption spectrum over a range of 0-40 degrees C reveals that the population of high-spin iron is 76-82% at room temperature for azide metmyoglobin complexed with ferric corrphycene. The unusual predominance of the high-spin state was verified from the infrared spectrum of coordinating azide, where the high-spin peak at 2046 cm(-1) is 4-fold larger in intensity than the 2023 cm(-1) low-spin band. Electron paramagnetic resonance at 15 K further indicated that the iron-histidine bond is cleaved to form a five-coordinate derivative in some fraction of the myoglobin. The remarkable high-spin bias of the spin equilibrium at room temperature and cleavage of the iron-histidine bond at 15 K could be explained in terms of the contracted and trapezoidal metallo core that weakens the iron-histidine bond of azide metmyoglobin bearing corrphycene.

Electrochemistry↗
PubMed2001

Oxygenation properties of human erythrocytes containing exclusively alpha-nitrosyl hemoglobin: a promising blood transfusant candidate.

We have prepared human erythrocytes that contain exclusively alpha-nitrosyl hemoglobin (Hb), i.e., alpha(Fe-NO)2beta(Fe-O2)2, by incorporating nitric oxide (NO) into erythrocytes in a well-controlled nitrosylation process. The amount of alpha(Fe-NO) corresponding to 50% of the total heme content of the erythrocytes and exclusive binding of NO to alpha-subunits of intraerythrocytic Hb were confirmed by EPR. Oxygenation experiments on the intraerythrocytic alpha-nitrosyl Hb over a wide range of pH showed that: (1) the oxygen affinity of cell-free and intraerythrocytic alpha-nitrosyl Hbs were much lower than native Hb in their respective environments; (2) the oxygenation characteristics of the intraerythrocytic alpha-nitrosyl Hb in the acidic range was similar to that of the cell-free alpha-nitrosyl Hb in the presence of 2,3-diphosphoglycerate; and (3) the apparent Bohr effect in the intraerythrocytic alpha-nitrosyl Hb was dramatically diminished. This can be due to a restricted variation in intraerythrocytic pH in the alkaline region and the presence and/or production of endogenous 2,3-diphosphoglycerate. By comparing oxygen saturation characteristics, it was found that the intraerythrocytic alpha-nitrosyl Hb, despite its halved oxygen carrying capacity, could deliver more oxygen than DPG-depleted erythrocytes under similar experimental conditions. This makes alpha-nitrosyl Hb-containing erythrocytes a promising candidate for blood transfusant.

Blood Substitutes↗
PubMed2000

Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals.

Oxygen binding by hemoglobin fixed in the T state either by crystallization or by encapsulation in silica gels is apparently noncooperative. However, cooperativity might be masked by different oxygen affinities of alpha and beta subunits. Metal hybrid hemoglobins, where the noniron metal does not bind oxygen, provide the opportunity to determine the oxygen affinities of alpha and beta hemes separately. Previous studies have characterized the oxygen binding by alpha(Ni2+)2beta(Fe2+)2 crystals. Here, we have determined the three-dimensional (3D) structure and oxygen binding of alpha(Fe2+)2beta(Ni2+)2 crystals grown from polyethylene glycol solutions. Polarized absorption spectra were recorded at different oxygen pressures with light polarized parallel either to the b or c crystal axis by single crystal microspectrophotometry. The oxygen pressures at 50% saturation (p50s) are 95 +/- 3 and 87 +/- 4 Torr along the b and c crystal axes, respectively, and the corresponding Hill coefficients are 0.96 +/- 0.06 and 0.90 +/- 0.03. Analysis of the binding curves, taking into account the different projections of the alpha hemes along the optical directions, indicates that the oxygen affinity of alpha1 hemes is 1.3-fold lower than alpha2 hemes. Inspection of the 3D structure suggests that this inequivalence may arise from packing interactions of the Hb tetramer within the monoclinic crystal lattice. A similar inequivalence was found for the beta subunits of alpha(Ni2+)2beta(Fe2+)2 crystals. The average oxygen affinity of the alpha subunits (p50 = 91 Torr) is about 1.2-fold higher than the beta subunits (p50 = 110 Torr). In the absence of cooperativity, this heterogeneity yields an oxygen binding curve of Hb A with a Hill coefficient of 0.999. Since the binding curves of Hb A crystals exhibit a Hill coefficient very close to unity, these findings indicate that oxygen binding by T-state hemoglobin is noncooperative, in keeping with the Monod, Wyman, and Changeux model.

Crystallization↗
PubMed1999

UV resonance Raman studies of alpha-nitrosyl hemoglobin derivatives: relation between the alpha 1-beta 2 subunit interface interactions and the Fe-histidine bonding of alpha heme.

Human alpha-nitrosyl beta-deoxy hemoglobin A, alpha(NO)beta(deoxy), is considered to have a T (tense) structure with the low O(2) affinity extreme and the Fe-histidine (His87) (Fe-His) bond of alpha heme cleaved. The Fe-His bonding of alpha heme and the intersubunit interactions at the alpha 1-beta 2 contact of alpha(NO)-Hbs have been examined under various conditions with EPR and UV resonance Raman (UVRR) spectra excited at 235 nm, respectively. NOHb at pH 6.7 gave the UVRR spectrum of the R structure, but in the presence of inositol-hexakis-phosphate (IHP) for which the Fe-His bond of the alpha heme is broken, UVRR bands of Trp residues behaved half-T-like while Tyr bands remained R-like. The half-ligated nitrosylHb, alpha(NO)beta(deoxy), in the presence of IHP at pH 5.6, gave T-like UVRR spectra for both Tyr and Trp, but binding of CO to its beta heme (alpha(NO)beta(CO)) changed the UVRR spectrum to half-T-like. Binding of NO to its beta heme (NOHb) changed the UVRR spectrum to 70% T-type for Trp but almost R-type for Tyr. When the pH was raised to 8.2 in the presence of IHP, the UVRR spectrum of NOHb was the same as that of COHb. EPR spectra of these Hbs indicated that the Fe-His bond of alpha(NO) heme is partially cleaved. On the other hand, the UVRR spectra of alpha(NO)beta(deoxy) in the absence of IHP at pH 8.8 showed the T-like UVRR spectrum, but the EPR spectrum indicated that 40-50% of the Fe-His bond of alpha hemes was intact. Therefore, it became evident that there is a qualitative correlation between the cleavage of the Fe-His bond of alpha heme and T-like contact of Trp-beta 37. We note that the behaviors of Tyr and Trp residues at the alpha 1-beta 2 interface are not synchronous. It is likely that the behaviors of Tyr residues are controlled by the ligation of beta heme through His-beta 92(F8)-->Val-beta 98(FG5)-->Asp-beta 99(G1 )-->Tyr-alpha 42(C7) or Tyr-beta 145(HC2).

Carboxyhemoglobin↗
PubMed1998

Electron paramagnetic resonance and oxygen binding studies of alpha-Nitrosyl hemoglobin. A novel oxygen carrier having no-assisted allosteric functions.

alpha-Nitrosyl hemoglobin, alpha(Fe-NO)2beta(Fe)2, which is frequently observed upon reaction of deoxy hemoglobin with limited quantities of NO in vitro as well as in vivo, has been synthetically prepared, and its reaction with O2 has been investigation by EPR and thermodynamic equilibrium measurements. alpha-Nitrosyl hemoglobin is relatively stable under aerobic conditions and undergoes reversible O2 binding at the heme sites of its beta-subunits. Its O2 binding is coupled to the structural/functional transition between T- (low affinity extreme) and R- (high affinity) states. This transition is linked to the reversible cleavage of the heme Fe-proximal His bonds in the alpha(Fe-NO) subunits and is sensitive to allosteric effectors, such as protons, 2,3-biphosphoglycerate, and inositol hexaphosphate. In fact, alpha(Fe-NO)2beta(Fe)2 is exceptionally sensitive to protons, as it exhibits a highly enhanced Bohr effect. The total Bohr effect of alpha-nitrosyl hemoglobin is comparable to that of normal hemoglobin, despite the fact that the oxygenation process involves only two ligation steps. All of these structural and functional evidences have been further confirmed by examining the reactivity of the sulfhydryl group of the Cysbeta93 toward 4, 4'-dipyridyl disulfide of several alpha-nitrosyl hemoglobin derivatives over a wide pH range, as a probe for quaternary structure. Despite the halved O2-carrying capacity, alpha-nitrosyl hemoglobin is fully functional (cooperative and allosterically sensitive) and could represent a versatile low affinity O2 carrier with improved features that could deliver O2 to tissues effectively even after NO is sequestered at the heme sites of the alpha-subunits. It is concluded that the NO bound to the heme sites of the alpha-subunits of hemoglobin acts as a negative allosteric effector of Hb and thus might play a role in O2/CO2 transport in the blood under physiological conditions.

2,3-Diphosphoglycerate↗
PubMed1998

[Nitric oxide and hemoglobin].

Nitric oxide (NO) is produced by nitric oxide synthases (cNOS and iNOS) in endothelial cells upon stimulation by various agents like Ca(2+)-calmodulin, cytokines and TNF. It acts as a paracrine on adjacent cells to activate soluble guanylyl cyclase in the production of cGMP, a second messenger in signal transduction cascades, leading to various cellular responses. The circulating blood contains certain steady-state concentrations of NO in the plasma in order to maintain normal vascular tone and other appropriate conditions for the systemic and pulmonary circulation. This homeostasis of NO in the rapidly moving blood must be maintained by a delicate balance between its production by NOSs and its instant scavenging by hemoglobin (Hb) in the erythrocytes. Under physiological conditions ([NO] <<< [Hb]), NO is sequestered by deoxy Hb to form alpha-nitrosyl Hb, alpha (Fe-NO)2 beta (Fe)2, where NO is tightly (KD = 10(-12) M) bound to the alpha-subunits. Upon binding NO to the alpha-subunbits, Hb shifts its conformation to a T-(low-affinity extreme) state and its beta-subunits become an efficient O2 carrier. The same molecular mechanism of NO-induced conformation change operates in both Hb and soluble guanylyl cyclase. This is caused by the NO-induced trans-axial cleavage of the heme Fe-proximal His bonds in these hemoproteins. This bond cleavage mechanism allows Hb to survive as an effective O2 carrier even after sequestration of NO. The NO sequestered in Hb is eventually oxidized aerobically to NO3- in the reaction of Fe-NO + O2-->Fe(+) + NO3. Met Hb (Fe+) so formed is cycled back to deoxy Hb (Fe) by intra-erythrocyte Hb reductase to complete the NO scavenging. Thus, the NO in the blood acts on soluble guanylyl cyclase in vascular smooth muscles to dilate the blood vessels to increase blood delivery, whereas excess NO in the blood, which is sequestered by Hb, could help Hb to deliver O2 more efficiently in peripheral tissues.

Animals↗
PubMed1996

Infrared spectroscopy of the cyanide complex of iron (II) myoglobin and comparison with complexes of microperoxidase and hemoglobin.

The cyanide complex of FeIIMb prepared and maintained at temperatures below 0 degrees C is sufficiently stable to permit spectroscopic characterization and allow comparison with free HCN and other ferric and ferrous CN complexes. The visible absorption spectrum of FeIIMb-CN has a split alpha band maxima at 571 and 563 nm, suggesting distortion in the x-y plane of the porphyrin. FeIIMb-CN, like the CO complex, was found to be optically active by circular dichroism. The C-N stretching frequencies for the CN-ferrous complexes are very sensitive to parameters within the heme pocket. The values are as follows: FEIIMb at pH 8, 2057 cm-1 with a shoulder appearing at 2078 cm-1 at pH 5.6; FeIIMp, 2034 cm-1. In contrast, the frequencies for C-N stretch differ little among ferric heme complexes, ranging from 2123 to 2125 cm-1 for myoglobin, hemoglobin, and microperoxidase. These values compare with free HCN (2094 cm-1) or CN- (2080 cm-1). Quantum chemical modeling of the neutral iron-porphyrin complex with imidazole and cyanide and of its anion was used to explain the effects of the cyanide coordination and of iron reduction on the C-N stretching frequencies. The lower nu C-N for FeIIMb-CN relative to the ferric complex is attributed to the appearance of additional electron density on all the anti-bonding CN orbitals. The extra electron density was also used to explain that the band width of C-N stretching mode was greater in the ferrous complexes than in the ferric complex. Finally, the calculation shows that sigma donation weakens the Fe-C bond, in qualitative agreement with the spontaneous dissociation of CN- from FeIIMb at -5 degrees C. The sensitivity of CN complexes of ferrous heme proteins to the heme pocket environment and the ability to correlate spectroscopic parameters with calculated electron density suggest that infrared spectroscopy of the CN ligand is an appropriate tool to study ferrous heme proteins.

Animals↗
PubMed1996

Heterometallic hybrids of homometallic human hemoglobins.

Hybridization experiments between normal Hb tetramers (Fe2+ Hb) and those with four metal-substituted hemes (i.e., replacement of Fe2+ by Co2+, Mg2+, Mn2+, Mn3+, Ni2+, or Zn2+) have revealed unexpected behavior. These homometallic Hbs have previously served as models that mimic the deoxy or oxy properties of normal Fe2+ Hb. In this study, hybrids were composed of one alpha 1 beta 1 dimer that is metal-substituted at both hemes, in association with a second dimer alpha 2 beta 2 that has normal Fe2+ hemes. Both metal-substituted subunits are unligated, whereas the two Fe2+ subunits either are both unligated or both ligated with O2, CO, or CN. It was found that four of the metal-substituted Hbs (Mg2+ Hb, Mn2+ Hb, Ni2+ Hb, and Zn2+ Hb) did not form detectable amounts of heterometallic hybrids with normal Fe2+ Hb even though (i) their homometallic parents formed tight tetrameric complexes with stabilities similar to that of Fe2+ Hb and (ii) hybrids with metal substitution at both alpha sites or both beta sites are known to form readily. This striking positional effect was independent of whether the normal Fe2+ hemes were ligated and of which ligand was used. These findings indicate that surprisingly large changes in tetramer behavior can arise from small and subtle perturbations at the heme sites. Possible origins of these effects are considered.

Binding Sites↗
PubMed1996

Oxygen binding by single crystals of hemoglobin: the problem of cooperativity and inequivalence of alpha and beta subunits.

Oxygen binding by the human hemoglobin tetramer in the T quaternary structure is apparently noncooperative in the crystalline state (Hill n = 1.0), as predicted by the two-state allosteric model of Monod, Wyman, and Changeux (MWC) (Mozzarelli et al., Nature 351:416-419, 1991; Rivetti et al., Biochemistry 32:2888-2906, 1993). However, cooperativity within the tetramer can be masked by a difference in affinity between the alpha and beta subunits. Indeed, analysis of the binding curves derived from absorption of light polarized along two different crystal directions, for which the projections of the alpha and beta hemes are slightly different, revealed an inequivalence in the intrinsic oxygen affinity of the alpha and beta subunits (p50(alpha) approximately 80 torr, p50(beta) approximately 370 torr at 15 degrees C) that compensates a small amount of cooperativity (Rivetti et al., Biochemistry 32:2888-2906, 1993). To further investigate this problem, we have measured oxygen binding curves of single crystals of hemoglobin (in a different lattice) in which the iron in the alpha subunits has been replaced by the non-oxygen-binding nickel(II). The Hill n is 0.90 +/- 0.06, and the p50 is slightly different for light polarized parallel to different crystal directions, indicating a very small difference in affinity between the two crystallographically inequivalent beta subunits. The average crystal p50 is 110 +/- 20 torr at 15 degrees C, close to the p50 of 80 torr observed in solution, but about threefold less than the p50 calculated by Rivetti et al. (Biochemistry 32:2888-2906, 1993) for the beta subunits of the unsubstituted tetramer. These results suggest that Rivetti et al., if anything, overestimated the alpha/beta inequivalence. They therefore did not underestimate the cooperativity within the T quaternary structure, when they concluded that it represents a small deviation from the perfectly noncooperative binding of an MWC allosteric model. Our conclusion of nearly perfect MWC behavior for binding to the T state of unmodified hemoglobin raises the question of the relevance of the large T-state cooperativity inferred for cyanide binding to partially oxidized hemoglobin (Ackers et al., Science 255:54-63, 1992).

Allosteric Site↗
PubMed1995

Mechanism of ligand binding to Ni(II)-Fe(II) hybrid hemoglobins.

The geminate and bimolecular binding of CO, O2 and NO to [alpha-Ni(II)]2-[beta-Fe(II)]2 and [alpha-Fe(II)]2-[beta-Ni(II)2] hybrid hemoglobins has been studied. Biomolecular reactions: At pH 6.6 and 20 degrees both hybrids bind CO at 0.15 x 10(6) M-1 s-1. Reactions with oxygen: At pH 6.6 the on rates are 4.8 and 7.5 x 10(6) M-1 S-1 for alpha- and beta-hybrids, respectively; the off rate is approximately 2 x 10(3) S-1 for both. At pH 8 the alpha-Fe shows cooperativity whereas the beta-hybrid does not. Nanosecond geminate reactions: Faster bimolecular rates correlate with larger geminate amplitudes; thus alpha-Fe hybrids have larger amplitudes, and O2 geminate amplitudes are larger than those with CO. At pH 8.50% of O2 recombines with the alpha-hybrid. With NO, nanosecond geminate recombination is observable only with the beta-hybrid. Picosecond reactions: alpha-Hybrids show picosecond recombination of O2. With NO, alpha-hybrids recombine at 30 ns-1, beta-hybrids at 0.3 ns-1. The NO picosecond rates correlate with the molecular dynamics which shows ligands leaving the beta-Fe atom early and regularly, but remaining near the alpha-Fe atom. The results may be explained by assuming an interaction between the alpha-subunits giving rise to a high-affinity faster-reacting form, whereas the beta-subunits only become fast-reacting when an R-T conformation change analogous to that of hemoglobin A takes place. A third allosteric state is postulated to explain the results.

Allosteric Regulation↗
PubMed1995

Electron spin echo envelope modulation study of oxygenated iron-cobalt hybrid hemoglobins reveals molecular features analogous to those of the oxy ferrous protein.

Two oxygenated iron-cobalt hybrid hemoglobins (Hbs), (alpha Co-O2 beta Fe-O2)2 and (alpha Fe-O2 beta Co-O2)2, were studied by electron spin echo envelope modulation (ESEEM) spectroscopy in order to measure (i) electron-nuclear hyperfine and nuclear quadrupole coupling to the N epsilon of the proximal histidyl imidazole and (ii) nuclear hyperfine coupling to exchangeable 2H in the oxyCo subunits. 14N couplings were found to be smaller in the oxyCo alpha subunits than in the oxyCo beta subunits, suggesting a more ionic and shorter Co-O2 bond in the alpha subunits [Lee et al. (1994) Biochemistry 33, 7609], which correlates with the higher O2 affinity found for (alpha Co beta Fe-O2)2 Hb than for (alpha Fe-O2 beta Co)2 Hb [Imai et al. (1980) J. Mol. Biol. 138, 635]. A smaller nuclear quadrupole coupling constant found for the proximal histidyl N epsilon in the oxyCo alpha subunits also suggests an increase in the overlap between the N epsilon sp2 hybrid and the Co dz2 orbital, i.e., a shorter Co-N epsilon bond, than in the oxyCo beta subunits. On the other hand, the relative orientation of the g and 14N epsilon nuclear quadrupole tensors, obtained by spectral simulation, suggests that the Co-O-O bond angle is similar in the two types of oxyCo subunits. An X-ray crystallographic study of oxyFe Hb A [Shaanan, B. (1982) Nature 296, 683] has also reported similar Fe-O-O bond angles in both alpha and beta subunits, but with shorter Fe-N epsilon and Fe-O2 bonds in the alpha subunits.(ABSTRACT TRUNCATED AT 250 WORDS)

Cobalt↗
PubMed1995

Modulation of the heme environment of neutrophil cytochrome b558 to a "cytochrome P450-like" structure by pyridine.

The effect of pyridine on the heme environment of cytochrome b558 was studied using ESR and optical absorption spectroscopy in relation to the O2(-)-generating activity in the NADPH oxidase system of stimulated pig neutrophils. As the concentration of pyridine increased, the absorption maxima of the alpha- and gamma-bands of cytochrome b558 shifted which correlated with a concomitant decrease in O2(-)-generating activity. In addition, the g = 3.2 signal of cytochrome b558 decreased with the concomitant appearance of a new ESR spectrum that strikingly resembled that of cytochrome P450. The results suggest that pyridine induces a structural modification in the heme environment of cytochrome b558 by shifting the 5th heme ligand (histidine) to a nearby thiolate group without direct binding of pyridine to the heme. The existence of a reactive thiolate near the heme iron was confirmed by pretreatment of blocked cytochrome b558 with p-chloromercuribenzoate, which completely inhibited the formation of the cytochrome P450-like ESR spectrum. The results provide further evidence that a low-spin heme iron of cytochrome b558 with a g-value of 3.2 is essential to the O2(-)-forming reaction of the NADPH oxidase system. From sequence alignments of cytochrome P450 with those of large and small subunits of cytochrome b558, the heme in cytochrome b558 appears to be specifically associated with the large subunit.

Amino Acid Sequence↗
PubMed1994

Fluorescent derivatives of human hemoglobin. Differences in interaction of the porphyrin with the protein between the alpha and beta subunits.

The fluorescence properties of porphyrin were compared in protoporphyrin-protoheme hybrid hemoglobins (Hb) in which the protohemes (Fe) in either the alpha or beta subunits were substituted with protoporphyrin IX, alpha (P)2 beta (Fe)2-Hb and alpha (Fe)2 beta(P)2-Hb, respectively. The fluorescence lifetimes of the porphyrin in these hybrid derivatives are shorter than for the tetra-substituted protoporphyrin Hb, indicating that there is energy transfer from the porphyrin to the heme. The energy transfer resulted in only approximately 20% diminution of donor fluorescence, thereby allowing for the examination by fluorescence of the interaction of porphyrin with a given subunit peptide chain. Fluorescence line-narrowing spectroscopy, a high resolution fluorescence technique that involves laser excitation, produced vibrationally resolved emission spectra in which the zero phonon lines were separated from a broadened background consisting of phonon wings. Resolved spectra were obtained in the temperature range of 5-50 K; above 70 K the spectra were unresolved. By changing the excitation frequency the mean energy of the 0,0 transition, characterizing the separation in energy between the ground and excited states, can be determined. For both derivatives a bimodal distribution was seen, indicating that more than one conformation of molecules was present. The distribution of 0,0 transition energies of the porphyrin in the beta-chain in alpha(Fe)2 beta(P)2-Hb was shifted to lower energy relative to the alpha chain in alpha(P)2 beta(P)2-Hb, whereas the excited state molecules in the two subunits had very little difference in vibrational energy. These data point to the same configuration of the porphyrins in the two sites, but differences in the electric field for the alpha and beta subunits.

Heme↗
PubMed1994

The crystal structure of the iron-free cytochrome c peroxidase and its implication for the enzymatic mechanism.

We report the refined structure of an iron-free form of cytochrome c peroxidase (CcP) at 2.3 A resolution. The backbone comparison between native CcP and iron-free CcP shows that the two structures have the same protein fold within experimental error. The only difference noted is in the heme pocket where the distance between the proximal histidine and the center of the protoporphyrin has increased. The results show that the iron-free CcP should be a good substitute for native CcP in fluorescence studies and thus also validate previous studies using iron-free CcPs as efficient fluorescent probes in electron transfer studies.

Binding Sites↗
PubMed1994

Role of the proximal ligand in peroxidase catalysis. Crystallographic, kinetic, and spectral studies of cytochrome c peroxidase proximal ligand mutants.

The role of the proximal histidine ligand in peroxidase function was studied by replacing the His side chain in cytochrome c peroxidase with Gln, Glu, or Cys. In addition, a double mutant was prepared where His-175 is converted to Gln and the site of free radical formation in Compound I, Trp-191 (Sivaraja, M., Goodin, D.B., Smith, M., and Hoffman, B. M. (1989) Science 245, 738-740), is converted to Phe. With the exception of the His-175-->Cys mutant, the proximal ligand mutants retain high levels of enzyme activity. Stopped flow studies show that replacing the His ligand with Gln has only a modest effect on the rate of Compound I formation demonstrating that the precise nature of the proximal ligand is not important in achieving a high rate of peroxide O-O bond cleavage. The double mutant, His-175-->Gln/Trp-191-->Phe, also forms Compound I rapidly but the initial product formed is very likely a long-lived porphyrin pi cation radical that slowly converts to a species more closely resembling the heme oxyferryl center of wild type Compound I. The relevance of these studies to the cytochrome c peroxidase-cytochrome c electron transfer system are discussed.

Crystallography, X-Ray↗
PubMed1994

Electric field and conformational effects of cytochrome c and solvent on cytochrome c peroxidase studied by high-resolution fluorescence spectroscopy.

Electronic spectra of mesoporphyrin-substituted yeast cytochrome c peroxidase (MP-CcP) were measured as a function of pH, ionic strength, and binding of cytochrome c (cyt c) by fluorescence line narrowing (FLN) spectroscopy at 5 K. The FLN spectra provided information about the vibrational structure of the first excited singlet state of MP-CcP, the various tautomeric forms of mesoporphyrin, and the positions and widths of their 0,0 bands. The composite 0,0 band of MP-CcP at pH 6 could be resolved into three components with peak positions at 16,046, 16,103, and 16,203 cm-1. MP-CcP at pH 8 could be analyzed using two components with peak positions at 16,048 and 16,193 cm-1. The disappearance of the 16,103-cm-1 component at alkaline pH suggests that it is due to a "chemical substate" arising from protonation of His52 in the distal side of the porphyrin. Computer simulations of the electrostatic field that CcP imposes on its porphyrin show that, in the presence of charged axial histidines His52 and His175, the electrostatic field at porphyrin nitrogens increases, especially along the normal to the heme by about 200 mV/A. Electric field effects may account for pH-dependent spectral shifts of the 0,0 positions of the resolved components, although hydrogen bonding may also affect these positions. On the other hand, the peak position of the components was not affected by ionic strength or binding of cyt c, implying that the electrostatic field of the heme pocket of MP-CcP remains unchanged. Indeed, computed changes in ionic strength of the solvent show no modification of the electrostatic field at the porphyrin. The only detectable effect of ionic strength and binding of cyt c to MP-CcP is on the relative contributions of the components, suggesting some rearrangements in the vicinity of the heme. Finally, shifts in the position of the vibrational lines for MP-CcP components indicate either that the tautomers have different vibrational frequencies due to the nonsymmetry of the porphyrin and/or that tautomers experience various distortions. Comparison of the vibrational spectrum of the first excited singlet state of mesoporphyrin in CcP and horseradish peroxidase also suggests that the heme pocket in the two peroxidases provides different steric restrictions.

Binding Sites↗