Biomedical subjects

M Brunori

Publications and source records attributed to M Brunori.

At least 127 records · Page 7Linked to original sources

PubMed1993

Ligand binding and slow structural changes in chlorocruorin from Spirographis spallanzanii.

Chlorocruorin is a cooperative respiratory pigment found in the blood of polychaete worms; its prosthetic group is a derivative of the iron protoporphyrin IX, in which the vinyl group at position 2 is substituted by a formyl group. The quaternary structure of chlorocruorins is complex: myoglobin-like subunits are grouped in tetramers and tetramers in dodecamers; 12 dodecamers are assembled in the 3500-kDa particle. Chlorocruorin from Spirographis spallanzanii displays the following overall functional properties: (i) the oxygen affinity is lower than in human hemoglobin, while that of CO is similar if not higher; (ii) the rates of combination with oxygen and carbon monoxide are low; and (iii) the off rate of oxygen is comparable to that of human hemoglobin, while the off rate of CO is 10 times smaller. When CO is partially photolyzed with a long and powerful light flash (70 microseconds), rebinding is biphasic as in mammalian hemoglobins; however, the slowest rate is faster than that observed by stopped flow, suggesting that the unliganded protein decays from the liganded high affinity state (R) to an intermediate state before reaching the low affinity (T) state. Oxygen binding was followed by stopped-flow and flash photolysis. While partial photolysis yields a fast, second-order time course, stopped-flow experiments yield slow, biphasic, and non-second-order time courses. This pattern of reactivity was attributed to a slow conformational transition(s) which is (are) rare limiting with oxygen, but not with CO.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1993

Proton pumping by cytochrome oxidase as studied by time-resolved stopped-flow spectrophotometry.

The H+/e- stoichiometry for the proton pump of cytochrome c oxidase reportedly varies between 0 and 1, depending on experimental conditions. In this paper, we report the results obtained by a combination of transient optical spectroscopy with a time resolution of 10 ms and a singular value decomposition analysis to follow the kinetics, separate the observed spectral components, and quantitate the stoichiometry of the pump. By using cytochrome oxidase reconstituted into small unilamellar vesicles, we show that the time courses of ferrocytochrome c oxidation and phenol red acidification or alkalinization fit a simple kinetic scheme. The fitting procedure leads to unbiased and objective determination of the H+/e- ratio under various experimental conditions. The proton-pumping stoichiometry was found to be 1.01 +/- 0.10, independent of the number of turnovers, proton back-leak rate, or type of experiment (oxidant or reductant pulse).

Animals↗

PubMed1993

Solution nuclear magnetic resonance determination of active site structure for a paramagnetic protein: cyanomet Aplysia myoglobin.

The active site structure of a paramagnetic protein, cyanomet myoglobin (Mb) from Aplysia limacina, has been determined in solution by NMR in order to investigate the mechanism of ligand stabilization in this protein, which lacks the usual distal His residue. The structure determination relies on using the experimental dipolar shifts from two-dimensional NMR assignments, NOEs and paramagnetic-induced relaxations as the constraints with a combination of the magnetic susceptibility tensor. The magnetic susceptibility tensor was obtained by using the high resolution crystal co-ordinates of other derivatives of Aplysia Mb (notably metMb, metMbF and metMbN3) for the part of the molecule which is unperturbed by the different ligands, together with the observed dipolar shifts of Aplysia metMbCN, to search for the Euler rotation that correctly converts the crystal co-ordinates to the magnetic axes. The magnetic anisotropies, as well as the orientation of the magnetic axes, are well defined by using the various input data sets based on the conserved structural portions of three sets of crystal co-ordinates. An excellent fit between the calculated versus the observed shifts was obtained for both backbone portions (E, F, G helical segments and FG corner) and the proximal side-chains, which demonstrates that the solution structure of the backbone portions and the proximal side for Aplysia metMbCN is identical to those for three other derivatives investigated by crystallography. On the other hand, the distal side was shown to present minor but important structural changes relative to Aplysia metMbF, which reflect the binding of a diatomic ligand (CN-) rather than a monoatomic one. In particular, the guanidinium group of Arg E10(66) is repositioned and further away from the iron at a distance consistent with H-bonding to the bound cyanide. The bound cyanide is tilted approximately 8 degrees (as detected by the major magnetic axis) away from the heme normal approximately towards the gamma-meso-H. This tilt appears to be due to the attractive hydrogen-bonding with Arg E10(66) and the steric repulsion from Ile E11(67). The results strongly support the role of Arg E10 in stabilizing the anionic ligands by hydrogen bonding as proposed before and demonstrate the validity of the dipolar shifts as a unique and sensitive constraint in determining the active site structure of paramagnetic proteins in the low-spin ferric state.

Animals↗

PubMed1993

Structural and functional characterization of sperm whale myoglobin mutants: role of arginine (E10) in ligand stabilization.

1H NMR and ligand-binding data were used to assess the role of residue Arg(E10) in ligand stabilization of several site-directed mutants, all carrying the His(E7) to Val substitution, obtained using a synthetic sperm whale myoglobin gene. Arg(E10) was previously found to form a hydrogen bond with the ligand in fluoro-, azido- and cyanomet derivatives of Aplysia limacina myoglobin, which lacks the distal His(E7) [Qin, J., La Mar, G. N., Ascoli, F., Bolognesi, M., & Brunori, M. (1992) J. Mol. Biol. 224, 891-897]. NMR analysis of the paramagnetically induced relaxation, hyperfine shift patterns, and dipolar connectivities shows that Arg(E10) also falls into the distal pocket in the engineered sperm whale myoglobin mutants and resides at an H-bonding distance from the Fe(3+)-bound cyanide. The rate constant for cyanide dissociation from the ferrous derivative was determined by stopped-flow experiments; the ligand stabilization achieved by Arg(E10) is similar to that exerted by His(E7) in wild-type sperm whale myoglobin, and both are very different from the His(E7)Val single mutant. Contrary to that for the wild-type, the cyanide dissociation rate constant for the mutant containing Arg(E10) is essentially independent of pH (from 6 to 9), as expected on the basis of the guanidinium group of Arg having a pK > 10. This finding is consistent with the NMR data in which the chemical shift of the Arg(E10) N epsilon H is insensitive to pH (6-9), as is also observed in Aphysia limacina cyanometmyoglobin.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1993

Site-directed mutagenesis in hemoglobin. Effect of some mutations at protein interfaces.

The role of selected amino acid residues in the monomer-monomer contacts of Hb A has been studied by site-directed mutagenesis of the alpha chain bearing substitutions in the subunit surfaces. Mutation alpha 38Thr-->Trp induced a stabilization of tetrameric Hb-CO with a decrease of the Kd for the equilibrium alpha 2 beta 2<==>2 alpha beta, but had not effect on ligand binding. Mutation alpha 40Thr-->Arg resulted in a complete loss of cooperativity in ligand binding. Mutation alpha 103His-->Val had no noticeable effect. We also studied the behaviour of isolated, mutated alpha chains with respect to self association: compared to wt alpha chains, mutant alpha 38Thr-->Trp showed stabilization of the dimeric state and (at high protein concentration) a detectable amount of tetramers. Mutant alpha 103His-->Val showed only a minor stabilization of the alpha 2 dimer.

Allosteric Regulation↗

PubMed1993

Crystal structure of a distal site double mutant of sperm whale myoglobin at 1.6 A resolution.

The three-dimensional structure of sperm whale myoglobin His64(E7)-->Val,Thr67(E10)-->Arg double mutant has been studied by X-ray crystallography at 1.6 A resolution, and refined to a crystallographic R-factor of 0.197. The Arg67(E10) side chain is extended in the direction of the ligand binding site, and its NH1 atom is at a distance of 3.11 A from the NH1 atom of Arg45(CD3), which is also pointing towards the distal site. Both are kept in this position by hydrogen bonding and electrostatic interactions with a solvent sulfate ion, located amongst the two, on the protein surface. No liganded water molecule is present at the sixth coordination position of the Fe(III) heme.

Animals↗

PubMed1993

Hydration and allosteric transitions in hemoglobin.

Sucrose and other neutral solutes reduce the oxygen affinity of human hemoglobin. This effect was attributed by Colombo et al. (Colombo, M.F., Rau, D.C., and Parsegian, V.A. (1992) Science 256, 655-659) to a stabilization of the deoxy-T quaternary state of hemoglobin A, via a reduction of the activity coefficient of water. This was correlated to crystallographic results which showed that a significant surface area at the alpha 1 beta 2 interface, which is exposed to the solvent in the oxy-R state, is buried in the deoxy-T state. We show that sucrose has no effect on the oxygen affinity of trout hemoglobin I, which is cooperative in oxygen binding but lacks heterotropic effects, and that in spite of the large buried surface exposed to solvent upon dissociation of human hemoglobin into alpha beta dimers, sucrose leads either to an increased dissociation of hemoglobin A-CO into dimers or to no effect at all (in the presence of inositol hexakisphosphate). These results may demand a reconsideration of the hypothesis extensively discussed by Colombo et al.

Allosteric Regulation↗

PubMed1993

Protein dynamics in minimyoglobin: is the central core of myoglobin the conformational domain?

The kinetics of CO binding to the horse myoglobin fragment Mb-(32-139), the so-called "mini-Mb," were investigated by laser flash photolysis in 0.1 M phosphate buffer and in buffer with 75% (vol/vol) glycerol. The reaction displays complex time courses that can be approximated satisfactorily only with a sum of five exponentials. The features of the kinetic components and a comparison of the deoxy-minus-carbonyl difference spectra of mini-Mb and horse Mb obtained under equilibrium conditions, with the kinetic difference spectra resulting from the global analysis of the traces recorded between 400 and 450 nm, show that CO binding to mini-Mb is accompanied by large structural changes. In view of the fact that mini-Mb is an approximation of the Mb-(31-105) fragment encoded by the central exon of the Mb gene, this finding is particularly relevant. On the basis of our data and previous reports [De Sanctis, G., Falcioni, G., Giardina, B., Ascoli, F. & Brunori, M. (1988) J. Mol. Biol. 200, 725-733; De Sanctis, G., Falcioni, G., Grelloni, F., Desideri, A., Polizo, F., Giardina, B., Ascoli, F. & Brunori, M. (1992) J. Mol. Biol. 222, 637-643], we propose that the protein fragment encoded by the central exon of the Mb gene is the domain responsible for ligand-linked conformational transitions, while the two terminal fragments dampen the amplitude of the structural changes that accompany ligand binding, thus rendering the protein stable and kinetically more efficient in its physiological function.

Animals↗

PubMed1993

Solution 1H nuclear magnetic resonance determination of the distal pocket structure of cyanomet complexes of genetically engineered sperm whale myoglobin His64 (E7)-->Val, Thr67 (E10)-->Arg. The role of distal hydrogen bonding by Arg67 (E10) in modulating ligand tilt.

Sequence-specific 2D methodology has been used to assign the 1H NMR signals for all active site residues in the paramagnetic cyano-met complexes of sperm whale synthetic double mutant His64[E7]-->Val/Thr67[E10]-->Arg (VR-met-MbCN) and triple mutant His64[E7]-->Val/Thr67[E10]-->Arg/Arg45[CD3]-->Asn (VRN-metMbCN). The resulting dipolar shifts for noncoordinated proximal side residues were used to quantitatively determine the orientation of the paramagnetic susceptibility tensor in the molecular framework for the two mutants, which were found indistinguishable but distinct from those of both wild-type and the His64[E7]-->Val single point mutant (V-metMbCN). The observed dipolar shifts for the E helix backbone protons and Phe43[CD1], together with steady-state nuclear Overhauser effect between the E helix and the heme, were analyzed to show that both the E helix and Phe43[CD1] move slightly closer to the iron to minimize the vacancy resulting from the His64[E7]-->Val substitution, as found in V-metMbCN (Rajarathnam, K., J. Qin, G.N. LaMar, M. L. Chiu, and S. G. Sligar. 1993. Biochemistry. 32:5670-5680). The dipolar shifts of the mutated Val64[E7] and Arg67[E10] allow the determination of their orientations relative to the heme, and the latter residue is shown to insert into the pocket and provide a hydrogen bond to the coordinated ligand, as found in the naturally occurring ValE7/ArgE10 genetic variant, Aplysia limacina Mb. The oxy-complex of both A. limacina Mb and VR-Mb, VRN-Mb have been proposed to be stabilized by this hydrogen bonding interaction (Travaglini Allocatelli, C. et al. 1993. Biochemistry. 32:6041-6049). The magnitude of the tilt of the major magnetic axes from the heme normal in VR-metMbCN and VRN-metMbCN, which is related to the tilt of the ligand, is the same as in wild-type or V-metMbCN, but the direction of tilt is altered from that in V-metMbCN. It is concluded that the change in the direction of the ligand tilt in both the double and triple mutants, as compared to WT metMbCN and V-metMbCN single mutant, is due to the attractive hydrogen-bonding between ArgE10 and the bound cyanide.

Amino Acid Sequence↗

PubMed1993

Time-resolved optical spectroscopy on intact myocytes.

Myocytes prepared from perfused rat heart were studied spectroscopically using a photodiode array spectrophotometer adapted to a rapid mixing stopped-flow apparatus. The isolated cells were found to be viable for 3 to 4 hours, i.e. over the total time of the experiments. Sodium ascorbate and tetramethyl-para-phenylenediamine were used as exogenous reductants. Cytoplasmic and mitochondrial membranes were found to be freely permeable to tetramethyl-para-phenylenediamine. The use of singular value decomposition proved to be powerful in resolving the spectral contributions of the chromophoric components within the overall absorption spectrum. Spectral resolution was improved by adding carbon monoxide at a concentration that kept myoglobin fully saturated without affecting the activity of cytochrome c oxidase. The redox state of cytochrome c and cytochrome a was observed during the steady-state consumption of oxygen and during the reduction following the exhaustion of oxygen. The redox state of the two chromophores was found to be approximately equal and close to 25-30% oxidized during steady-state respiration; during the final reduction they changed simultaneously. These experiments suggest that in living cells, as in the purified enzyme, the rate limiting step of the turnover of cytochrome oxidase is the internal transfer of electrons from cytochrome a to cytochrome a3.

Animals↗

PubMed1993

Release of cytochromes from hypoxic and reoxygenated guinea pig heart.

Isolated, perfused hearts from guinea pigs were subjected to hypoxia for 30 minutes followed by reoxygenation for 30 minutes. Cellular damage was assessed by measuring the release of the cytoplasmic enzyme lactate dehydrogenase and the mitochondrial markers cytochrome c and cytochrome oxidase. The release of the enzymes was correlated with electron microscopy. Hypoxia induced an increase in the release of lactate dehydrogenase and cytochrome c. During reoxygenation, the release of lactate dehydrogenase was exacerbated while that of cytochrome c decreased, suggesting a partial recovery of the mitochondria. Cytochrome oxidase was not detectable in the extracellular space during hypoxia or reoxygenation. It is suggested that cytochrome c is a specific marker for damage to mitochondria caused by hypoxia and its loss may affect respiratory chain function.

Animals↗

PubMed1992

The oxygen reactive species of cytochrome-c-oxidase: an alternative view.

In a recent review article Babcok and Wikström (Nature, 1992, 356, 301-309) proposed that the species of cytochrome-c-oxidase which binds molecular oxygen during turnover is the so-called mixed valence enzyme, in which the binuclear center cytochrome a3-CuB is reduced, while the cytochrome a/CuA sites are oxidized. This proposal is based on earlier work (Morgan and Wikström, Biochemistry 1991, 30, 948-958) in which it was found that the steady-state reduction levels of cytochrome c and cytochrome a in respiring rat liver mitochondria (sustained by ascorbate and TMPD) are quite different, the latter being much more oxidized than the former; evaluation of the steady-state reduction levels demanded a large correction due to the optical contribution of oxidized TMPD+ which overlaps with the cytochromes. We report below that application of transient spectroscopy and SVD analysis to respiring rat heart myocytes, under conditions in which the contribution of TMPD+ is very small or absent, allows to show that the steady-state reduction levels of cytochrome c and cytochrome a are comparable at all times accessible to measurement in the rapid-scanning stopped-flow spectrophotometer. Our conclusion, in agreement with previous results, is that mixed valence cytochrome-c-oxidase as defined above is not the prevailing oxygen binding species of cytochrome-c-oxidase, unless electron donation to cytochrome c becomes rate limiting.

Animals↗

PubMed1992

Spectral analysis of cytochromes in rat heart myocytes: transient and steady-state photodiode array spectrophotometry measurements.

Myocytes prepared from rat heart have been studied by optical spectroscopy using a photodiode array spectrophotometer adapted to a stopped flow apparatus (PASF). The isolated cells were viable for 3-4 h (i.e., over the total time of the experiments), as tested employing morphological parameters of cell damage, reactivity toward trypan blue, and the ability to use succinate in the absence and presence of digitonin. Respiration was activated by addition of sodium ascorbate and tetramethyl-para-phenylenediamine (TMPD) as exogenous reductants, in order to single out the contributions of cytochrome c and cytochrome c oxidase among the complexes of the mitochondrial respiratory chain. TMPD was shown to be freely permeable across cytoplasmic and mitochondrial membranes, with a measured KD = 0.9 mM. The use of singular value decomposition analysis coupled to PASF acquisition proved very powerful in resolving statically and kinetically, in the millisecond time region, the spectral contributions of the cytochromes. Spectral analysis was improved by adding carbon monoxide at concentrations which did not affect cytochrome c oxidase activity, but kept myoglobin fully saturated (and thus uninfluential to absorbance changes).

Animals↗

PubMed1992

Investigation of the electron-transfer properties of cytochrome c oxidase covalently cross-linked to Fe- or Zn-containing cytochrome c.

Complexes of cytochrome c oxidase and cytochrome c (Fe- or Zn-containing) have been prepared by 1-ethyl-3-[3-(dimethylamino)propyl]carbodi-imide (EDC) cross-linking. The site to which the cytochrome c covalently binds has been identified as being the same, or close to, the site occupied by cytochrome c in the electrostatic complex which may be formed between the proteins. Stopped-flow experiments, monitored either at a single wavelength or through a rapid wavelength-scan facility, showed that covalently bound Fe-containing cytochrome c cannot donate electrons to cytochrome a. Free Fe-containing cytochrome c was, however, able to transfer electrons to cytochrome a in covalent complexes containing either Fe- or Zn-containing cytochrome c. Turnover experiments showed that the complexed enzyme remains catalytically competent but with decreased (40-80%) activity. The steady-state levels of reduction of both free cytochrome c and cytochrome a in the covalent complex were higher than found in the control (uncomplexed) enzyme. These results are discussed with reference to the structure of the covalent complex and lead us to conclude that cytochrome a may accept electrons directly from free cytochrome c and that cross-linking impairs the redox properties of the CuA site.

Animals↗

PubMed1992

Hemoglobin Dallas (alpha 97(G4)Asn-->Lys): functional characterization of a high oxygen affinity natural mutant.

Hemoglobin Dallas, an alpha-chain variant with a substitution of lysine for asparagine at position 97(G4), was found to have increased oxygen affinity (p1/2 = 1 mmHg at pH 7.3 and 20 degrees C), diminished cooperativity (n, the Hill coefficient = 1.7) and reduced Bohr effect (about 50%). Addition of allosteric effectors (such as 2,3-diphosphoglycerate, inositol hexakisphosphate and bezafibrate) led to a decrease in oxygen affinity and increase in cooperative energy. Kinetic studies at pH 7.0 and 20 degrees C revealed that (i), the overall rate of oxygen dissociation is 1.4-fold slower than that for HbA and (ii), the carbon monoxide dissociation rate is unaffected. The abnormal properties of this hemoglobin variant can be attributed to a more 'relaxed' T-state.

Allosteric Regulation↗

PubMed1992

Expression of Pseudomonas aeruginosa nitrite reductase in Pseudomonas putida and characterization of the recombinant protein.

Nitrite reductase from Pseudomonas aeruginosa has been successfully expressed in Pseudomonas putida. The purified recombinant enzyme contains haem c but no haem d1. Nonetheless, like the holoenzyme from Ps. aeruginosa, it is a stable dimer (molecular mass 120 kDa), and electron transfer to oxidized azurin is biphasic and follows bimolecular kinetics (k1 = 1.5 x 10(5) and k2 = 2.2 x 10(4) M-1.s-1). Unlike the chemically produced apoenzyme, recombinant nitrite reductase containing only haem c is water-soluble, stable at neutral pH and can be quantitatively reconstituted with haem d1, yielding a holoenzyme with the same properties as that expressed by Ps. aeruginosa (namely optical and c.d. spectra, molecular mass, cytochrome c551 oxidase activity and CO-binding kinetics).

Azurin↗

PubMed1992

Antarctic fishes survive exposure to carbon monoxide.

The extensive in vivo conversion of haemoglobin to the carbon monoxide derivative has no discernible effect on the survival of the red-blooded Antarctic fish Pagothenia bernacchii. Analysis of caudally sampled blood of cannulated specimens revealed that reconversion of carbon-monoxy haemoglobin to oxyhaemoglobin was complete within 48 hours. Thus, under stress-free conditions, haemoglobin is not necessary for survival of P. bernacchii. Red-blooded Antarctic fishes can carry oxygen necessary for routine delivery dissolved in plasma, in a similar way to the haemoglobinless Channichthyidae, although they lack the morphological and physiological adaptations which allow the latter to prosper without any haemoglobin.

Animals↗

PubMed1992

Respiratory control in cytochrome oxidase vesicles is correlated with the rate of internal electron transfer.

Cytochrome c oxidase, after reconstitution into phospholipid vesicles, displays respiratory control. This appears as an inhibition of substrate oxidation (cytochrome c) or reduction (O2) rates which, in the first few turnovers, can be largely removed upon addition of valinomycin, a specific K+ carrier. We report experiments designed to measure directly the internal electron transfer leading to the reduction of cytochrome a3/CuB, in the presence and the absence of a membrane potential. The results suggest that, after the complete oxidation and partial re-reduction of the protein, electron transfer to the binuclear site is valinomycin-sensitive, i.e. is inhibited by the membrane potential. The first-order rate constants calculated in the absence and presence of valinomycin were 0.5-0.6 and 5-6 s-1 respectively. Kinetic analysis of the reduction process is consistent with the conclusion that the membrane potential is below the critical threshold until the first electron is transferred to the cytochrome a3/CuB site. Furthermore, the respiratory control ratio obtained from the dependence of the internal electron transfer rate constant on valinomycin is always higher (by factor of 2) than that measured under turnover conditions either polarographically or spectrophotometrically. Two possible interpretations of this discrepancy are discussed.

Animals↗