Biomedical subjects

I Bertini

Publications and source records attributed to I Bertini.

At least 145 records · Page 8Linked to original sources

PubMed1993

One- and two-dimensional NMR characterization of oxidized and reduced cytochrome c' from Rhodocyclus gelatinosus.

1D and 2D NMR spectra of both the reduced and oxidized forms of cytochrome c' from Rhodocyclus gelatinosus have been recorded. The analysis of the pH dependence of the 1H NMR spectrum of the ferric form has been performed, and two main ionizing groups have been identified. By comparison of the pH dependence of the available spectra of cytochromes c', an ambiguity remaining from previous studies on related cytochromes c' has been solved. By means of 2D spectra, an assignment of all the paramagnetically shifted signals is proposed both for the ferrous and for the ferric forms.

Bacteria↗

PubMed1993

A two-dimensional NMR study of Co(II)7 rabbit liver metallothionein.

The 600-MHz 1H-NMR NOESY spectra on Co(II)7-reconstituted metallothionein (Co7MT), exhibiting hyperfine signals in the range 350 ppm to -50 ppm, with nuclear relaxation times of the order of a few milliseconds, have been measured and several interproton connectivities have been detected. To our knowledge, this is the largest spectral window ever reported for a two-dimensional 1H-NMR spectrum in the case of a paramagnetic metalloprotein. No scalar connectivities could be detected. The hyperfine-shifted signals belong to the cysteine-ligand protons of the Co4S11 cluster of Co7MT. Together with results from one-dimensional NOE experiments, the two-dimensional experiments allowed us to proceed with the pairwise assignment of the isotropically shifted signals of the C beta H2 groups of the metal-coordinated cysteines. With the aid of computer-graphics inspection of the four-metal-cluster domain, based on the NMR solution structure of Cd7MT, it is possible to purpose sequence-specific assignments of a few hyperfine-shifted 1H-NMR signals. In particular, a tentative assignment is given for the six signals whose shifts exhibit an antiCurie temperature dependence. The assignment relies on the theoretical model that qualitatively rationalizes the isotropic-shift pattern and its temperature dependence. Inferences on the solution structure of the Co4S11 cluster are drawn.

Animals↗

PubMed1993

Spectroscopic characterization of a newly isolated cytochrome P450 from Rhodococcus rhodochrous.

Cytochrome P450 (P450) from Rhodococcus rhodochrous have been characterized through circular dichroism and nuclear magnetic resonance (NMR) spectroscopy, both in the substrate-free and substrate-bound forms. The data are compared with those of P450cam and indicate a close similarity of the structure of the active site in the two proteins. The substrate-free species contains low-spin iron(III), while the 2-ethoxyphenol bound species contains high-spin iron(III). The substrate is in slow exchange on the NMR time scale. The binding of CN- has been investigated and the final adduct characterized through NMR spectra. Nuclear relaxation times of the isotropically shifted signals turn out to be shorter than in other heme proteins, both in the high- and in the low-spin species. This is the result of longer electron relaxation times in P450s than in peroxidases and metmyoglobin. This property, as well as the electron paramagnetic resonance (EPR) spectrum of the substrate-free form, are discussed in terms of the presence of the cysteine as the fifth ligand of the iron ion instead of a histidine as it occurs in peroxidases and myoglobin.

Circular Dichroism↗

PubMed1992

1H NMR investigation of manganese peroxidase from Phanerochaete chrysosporium. A comparison with other peroxidases.

1H NMR spectra at 200- and 600-MHz of manganese peroxidase from Phanerochaete chrysosporium and of its cyanide derivative are reported. The spectrum of the native protein is very similar to that of other peroxidases. The assignment of the spectrum of the cyanide derivative has been performed through 1D NOE, 2D NOESY, and COSY experiments. This protein is very similar to lignin peroxidase, the only meaningful difference being the shift of H delta 2 of the proximal histidine. The spectra of the cyanide derivative of these two proteins are compared with those of horseradish peroxidase and cytochrome c peroxidase. The shift pattern of the protons of the proximal histidine is discussed relative to the structural properties which affect the Fe3+/Fe2+ redox potential.

Chemical Phenomena↗

PubMed1992

The interaction of acetate and formate with cobalt carbonic anhydrase. An NMR study.

The interaction of formate and acetate ions with cobalt-substituted carbonic anhydrase (CA) has been investigated through 13C-NMR and one-dimensional and two-dimensional 1H-NMR spectroscopy. 13C data on formate are consistent with a regularly coordinated ligand, as previously proposed for the acetate anion [Bertini, I., Luchinat, C. & Scozzafava, A. (1977) J. Chem. Soc. Dalton Trans., 1962-1965]. 1H-NOE experiments on both anions give evidence of through-space interactions between ligand protons and protein protons. The latter are assigned to specific residues in the active cavity through nuclear Overhauser effect spectroscopy (NOESY) experiments. The 13C-derived and 1H-derived constrains allow reliable docking of these ligands in the active-site cavity. The resulting geometries are similar to one another and consistent with five-coordinated structures around the metal ion, as previously proposed from electronic spectroscopy [Bertini, I., Canti, G., Luchinat, C. & Scozzafava, A. (1978) J. Am. Chem. Soc. 100, 4873-4877]. The results are discussed in light of the current debate on anion binding to metal ions in carbonic anhydrase [Lindahl, M., Svensson, A. & Liljas, A. (1992) Proteins, in the press]; Bertini, I., Luchinat, C., Pierattelli, R. & Vila, A. J. (1992) Inorg. Chem., in the press; Banci, L. & Merz, K. (1992) unpublished results] and, in particular, of the proposed long Zn-O distance found in the recent X-ray results on the formate adduct [Hakanson, K., Carlsson, M., Svensson, A. & Liljas, A. (1992) J. Mol. Biol., in the press].

Acetates↗

PubMed1992

pH-dependent properties of cobalt(II) carboxypeptidase A-inhibitor complexes.

1H NMR spectroscopy of the isotropically shifted signals in cobalt carboxypeptidase, CoCPD, permits a direct and selective detection of protons belonging to the residues liganded to the metal. The chemical shift of these protons in the free enzyme and enzyme-inhibitor complexes with changing pH monitors the state of ionization of the ligands directly and of other residues in the active center indirectly. The 1H NMR spectrum of CoCPD at pH 6 shows three well-resolved isotropically shifted signals in the downfield region at 62 (a), 52 (c), and 45 (d) ppm which have been assigned to the NH proton of His-69 and to the C-4 H's of His-69 and His-196, respectively. Titration of signal a with pH is characterized by a pKa of 8.8 which is identical to that seen in prior electronic absorption and kinetic studies. The fact that the signal reflecting the NH of His-69 is still observed at pH 10 and no major shifts occur for the signals reflecting the C-4 H's indicates the alkaline pKa in carboxypeptidase A catalysis, pKEH, cannot be ascribed to ionization of the histidyl NH of either His-69 or His-196. Binding of L-Phe shifts this pKa to 7.7 while not greatly perturbing the downfield 1H NMR signals that reflect the ligation shell of the cobalt coordination sphere. These results indicate the pKa of 8.8 in CoCPD and the pKa of 7.7 in the CoCPD.L-Phe adduct reflect ionization of the same group.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1992

1H-NMR studies on partially and fully reduced 2(4Fe-4S) ferredoxin from Clostridium pasteurianum.

The ferredoxin from Clostridium pasteurianum, containing two Fe4S4 clusters, has been investigated through 1H-NMR spectroscopy in the reduced and partially oxidized states. The 1H-NMR spectrum of fully reduced ferredoxin, obtained by addition of stoichiometric amounts of dithionite, has been characterized. One- and two-dimensional NMR saturation transfer experiments on partially reduced samples have allowed the isotropically shifted signals of the reduced form to be correlated to those of the oxidized form, for which the complete assignment of the beta-CH2 cysteinyl residues is available. In addition, observation of the 1H-NMR signals of the intermediate species with characteristic chemical shift values for each cluster allowed us to assign all the Cys beta-CH2 signals to cluster I or cluster II and to calculate the difference in redox potential between them. Starting from these results, reanalysis of the 1H-NMR features of the two clusters in the oxidized form showed that they are strikingly similar, supporting the idea of a high degree of internal symmetry between them, in agreement with crystallographic results on an homologous ferredoxin. On the other hand, the 1H-NMR properties of the two clusters in the reduced form deviate considerably from each other, suggesting that reduction of the clusters brings about different structural changes and loss of internal symmetry. A theoretical approach is reported to account for the isotropic shifts and the temperature dependence of the NMR signals of the reduced protein.

Clostridium↗

PubMed1992

NOE and two-dimensional correlated 1H-NMR spectroscopy of cytochrome c' from Chromatium vinosum.

1H two-dimensional (nuclear Overhauser effect spectroscopy (NOESY) and two-dimensional correlated spectroscopy (COSY) spectra of cytochrome c' from Chromatium vinosum have been obtained. The protein is of medium size (Mr 28,000), essentially high spin (S = 5/2) although some quantum mechanical spin admixing with S = 3 2 may be present. Under these circumstances NOESY cross peaks have been revealed between geminal protons (alpha-CH2 propionate and beta-CH2 protons of the bound histidine) and between alpha-CH2 propionate protons and the heme methyl groups. COSY maps have confirmed the geminal nature of the proton pairs, even with a linewidth as large as 900 Hz; the J value is about 12 Hz. This assignment has rationalized on a sound basis the biochemical behavior of this protein with pH and has showed the utility of this kind of spectroscopy for the other cytochromes c' structures and analogous systems.

Chemical Phenomena↗

PubMed1991

2D 1H NMR studies of oxidized 2(Fe4S4) ferredoxin from Clostridium pasteurianum.

Oxidized ferredoxin from Clostridium pasteurianum, containing two Fe4S4 clusters, has been investigated using 2D 1H NMR spectroscopy at 600 MHz. 2D NMR experiments allowed complete assignment of the sixteen isotropically shifted signals corresponding to the beta-CH2 protons of the eight metal coordinated cysteines. Geminal connectivities of Cys beta-CH2 protons were identified through magnitude COSY experiments and confirmed through 2D NOESY experiments. A few additional signals could be assigned to the corresponding alpha-CH protons. The importance of 2D experiments to achieve firm assignments of isotropically shifted signals in paramagnetic metalloproteins is stressed.

Clostridium↗

PubMed1991

Proton NMR investigation into the basis for the relatively high redox potential of lignin peroxidase.

Lignin peroxidase shares several structural features with the well-studied horseradish peroxidase and cytochrome c peroxidase but carries a higher redox potential. Here the heme domain of lignin peroxidase and the lignin peroxidase cyanide adduct was examined by 1HNMR spectroscopy, including nuclear Overhauser effect and two-dimensional measurements, and the findings were compared with those for horseradish peroxidase and cytochrome c peroxidase. Structural information was obtained on the orientation of the heme vinyl and propionate groups and the proximal and distal histidines. The shifts of the epsilon1 proton of the proximal histidine were found to be empirically related to the Fe3+/Fe2+ redox potentials.

Journal Article↗

PubMed1991

Assignment of active-site protons in the 1H-NMR spectrum of reduced human Cu/Zn superoxide dismutase.

600-MHz 1H-NMR and nuclear Overhauser enhancement spectroscopy (NOESY) spectra in 2H2O and H2O, as well as truncated driven NOE difference spectra in H2O of reduced human Cu(II)2Zn(II)2 superoxide dismutase (Cu/Zn SOD) have been recorded and used to assign the active-site proton signals. A derivative with histidines selectively deuteriated in the C2 position has been used for the detection of the HC2 histidine protons, 16 out of 17 observed signals of the 18 active-site histidine ring protons have been assigned. The results are compared with previous proposals based on more limited data sets. The numerous cross peaks confirm that the structure in solution is essentially similar to the crystallographic data obtained on the oxidized form. Probably this holds also for His63 which in the reduced form is not bridging any more the two metal ions. The effects of azide binding on the exchangeable 1H-NMR signals of the reduced protein are also reported.

Binding Sites↗

PubMed1991

A characterization of copper/zinc superoxide dismutase mutants at position 124. Zinc-deficient proteins.

Substitution of the completely conserved aspartic acid residue at position 124 of Cu,Zn superoxide dismutase with asparagine and glycine has been performed through site-directed mutagenesis on the human enzyme. Asp124 is H-bonded to the NH of two histidines, one of which is bound to copper and the other to zinc. The mutant proteins, as expressed in Escherichia coli, result in an essential zinc-free enzyme which is similar to that obtained from the wild-type derivative through chemical manipulation. Only by extensive dialysis against 0.5 M ZnCl2 or CoCl2 at pH 5.4 was it possible to reconstitute approximately 50% of the molecules in the Cu2Zn2 or Cu2Co2 form. The new derivatives have been characterized through EPR, CD and nuclear magnetic relaxation dispersion techniques. The Cu2Cox derivatives (x approximately 1) were used to monitor, through electronic and 1H-NMR spectroscopies, the metal sites which are found to be similar to those of the wild type. In addition, a double substitution with asparagine has been made, replacing the invariant aspartate at position 124 and the highly conserved aspartate at position 125. The behavior is similar to that of the other mutants in most respects. The Cu2E2 (E = empty) derivatives of the mutants are stable, even in the pH range 8-10, whereas in the case of the Cu2E2 derivative of the wild type, copper migration occurs at high pH, producing both Cu2Cu2 and apo derivatives. The activity measurements indicate that the various Cu2E2 derivatives have the same activity at low pH and similar to that of the holoenzyme. A full profile up to pH 10.5 was obtained for the mutants.

Cobalt↗

PubMed1991

An investigation of Cu2Zn2 superoxide dismutase and its Ile-137 mutant at high pH.

The activity profile of the Cu2Zn2HSOD Ile-137 mutant has a pKa of 9.6, i.e. one unit lower than the wild type (WT). This property has allowed us to investigate the inactive high pH form of the enzyme before denaturation occurs. The electronic and EPR spectra do not change with the above pKa. The 1H NMR spectrum of the Cu2Co2-analog reveals slight decreases in the hyperfine shifts of the protons of His-48 at high pH, which are consistent with a water molecule becoming closer to the copper ion, as detected through water 1H T-1(1) NMR measurements. The affinity of azide at high pH is lower than at low pH, though still sizeable. The WT follows the same pattern up to pH congruent to pKa. It appears that the drop in activity is not related to any major change involving the metal coordination sphere, but is related to changes in the electrostatic potential due to the deprotonation process.

Azides↗

PubMed1991

1H NMR investigation of reduced copper-cobalt superoxide dismutase.

Human copper-cobalt superoxide dismutase in the reduced form has been investigated through 1H NMR techniques. The aim is to monitor the structural properties of this derivative and to compare them with those of reduced and oxidized native superoxide dismutases. The observed signals of the cobalt ligands have been assigned as well as the signals of the histidines bound to copper(I). The latter signals experience little pseudocontact shifts which allow a rough orientation of the magnetic susceptibility tensor in the molecular frame. The connectivities indicate that, although the histidine bridge is broken in the reduced form, the interproton distances between ligands of both ions are essentially the same.

Amino Acid Sequence↗

PubMed1991

Advances in the understanding of the structure-function relationship in Cu,Zn superoxide dismutase.

The structure-function relationship in Cu,Zn superoxide dismutase has been partially elucidated by the combined use of many spectroscopic techniques (electronic spectroscopy, circular dichroism, EPR and NMR) and site-directed mutagenesis techniques. The comparison of the spectroscopic and catalytic properties of various mutants, in which some active site residues have been substituted through site-directed mutagenesis, allowed us to establish that the activity is in general more sensitive to electrostatic effects rather than to steric effects or changes in the copper hydration or coordination geometry.

Animals↗

PubMed1990

Transient versus steady state NOE in paramagnetic molecules Cu2Co2SOD as an example.

Truncated, steady state and transient NOE experiments have been performed on bovine Cu2Co2 superoxide dismutase. The effectiveness of the different NOE experiments in the general case of paramagnetic macromolecules is discussed. It is concluded that steady state NOEs give superior results. The validity of the two spins approximation is discussed, and NOE values for a fully coupled set of nuclei have been calculated. Transient NOE experiments, when properly performed, confirm the previous assignment of the hyperfine shifted signals in Cu2Co2SOD based on steady state NOE measurements [(1989) Inorg. Chem. 28, 4650] and eliminate any further reason for controversy on an important issue as the assignment of the 1H NMR signals of protons of metal-coordinated imidazoles.

Animals↗

PubMed1990

Identification of localized redox states in plant-type two-iron ferredoxins using the nuclear Overhauser effect.

The homonuclear Overhauser effect (NOE), in conjunction with nonselective spin-lattice relaxation measurements, has been employed to assign the contact-shifted resonances for the reduced form of two typical plant-type two-iron ferredoxins from the algae Spirulina platensis and Porphyra umbilicalis. These results demonstrate that the NOE should have broad general applicability for the assignments and electronic structural elucidation of diverse subclasses of paramagnetic iron-sulfur cluster proteins. NOE connectivities were detected only among sets of resonance exhibiting characteristically different deviations from Curie behavior, providing strong support for the applicability of the spin Hamiltonian formulation for the NMR properties of the antiferromagnetically coupled iron clusters [Dunham, W. R., Palmer, G., Sands, R. H., & Bearden, A. J. (1971) Biochim. Biophys. Acta 253, 373-384; Banci, L., Bertini, I., & Luchinat, C. (1989) Struct. Bonding (in press)]. The geminal beta-methylene protons for the two cysteines bound to the iron(II) center were clearly identified, as well as the C alpha H and one C beta H for each of the cysteines bound to the iron(III). The identification of the iron bound to cysteines 41 and 46 as the iron(II) in the reduced protein was effected on the basis of dipolar contacts between the bound cysteines, as predicted by crystal coordinates of S. platensis Fd [Tsukihara, T., Fukuyama, K., Nakamura, M., Katsube, Y., Tanaka, N., Kakudo, M., Wada, K., Hase, T., & Matsubara, H. (1981) J. Biochem. (Tokyo) 90, 1763-1773].(ABSTRACT TRUNCATED AT 250 WORDS)

Cyanobacteria↗

PubMed1990

1H NMR studies of Chromatium vinosum cytochrome c'.

The cytochrome c' from Chromatium vinosum has been studied through 1H NMR in the pH range 4-11 in both the oxidized and the reduced forms. The 1H NMR spectra are similar to those of the other cytochrome c' systems. Three pKa values of 5.1, 7.0, and 9.2 have been observed for the oxidized species and tentatively assigned to the two carboxylate propionic residues of the heme moiety and to the iron-coordinated histidine 125, respectively. The spectra are consistent with an essentially S = 5/2 state in all the pH ranges investigated. Some evidence is provided for conformational flexibilities. Among the oxidized cytochromes c' the present one is capable of binding cyanide, giving rise to a low spin state. The reduced species is a typical high spin iron(II) system.

Chromatium↗