Biomedical subjects

J M Vanderkooi

Publications and source records attributed to J M Vanderkooi.

At least 37 records · Page 2Linked to original sources

PubMed1998

Microperoxidase-11: molecular dynamics and Q-band excited resonance Raman of the oxidized, reduced and carbonyl forms.

Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undecapeptides are consistent with a six-coordinate, low spin iron in both oxidation states. Porphyrin core size correlations yield a porphyrin-centre to pyrrole-nitrogen distance of 2.00 A for MP11, suggestive of a six-coordinate species in a distorted heme environment. Molecular dynamics results show that the non-planarity of the heme of the parent cytochrome is conserved in the microperoxidase and its carbonmonoxy analog.

Carbon Monoxide↗

PubMed1997

Surface of cytochrome c: infrared spectroscopy of carboxyl groups.

The carboxylate groups of organic acids give strong absorption in the infrared between approximately 1550 and 1650 cm-1. For acetate and chloroacetate derivatives, the infrared (IR) frequency of the carboxylate antisymmetric stretching mode (v(a)OCO) is related to the square root of the pK of the acid, with a shift of approximately 20 cm-1 to higher frequency for a pK drop in the range 5-3. It follows that v(a)OCO may respond to conditions on the protein surface. In this paper, the IR amide I' and carboxylate absorptions of cytochrome c from horse, yeast, and tuna are compared with model compounds such as Val-Glu and microperoxidase-11, the 11 amino acid fragment of horse cytochrome c containing the covalently bound heme. For microperoxidase-11, the contribution from all four carboxylates can be accounted for and the 1567 cm-1 absorption is assigned to the heme propionates. For the proteins, the carboxylate absorption band is inhomogeneous, i.e., there is a distribution of frequencies. Both the amide I' and carboxylate bands are sensitive to protein conformation as shown by their different pH, salt, and redox dependence.

Amino Acid Sequence↗

PubMed1997

Conformational effects of calcium release from parvalbumin: comparison of computational simulations with spectroscopic investigations.

The effect of Ca2+ binding to parvalbumin was monitored by probes of conformation including absorption, fluorescence, circular dichroism (CD), infrared (IR) spectroscopy and differential scanning calorimetry. These experimental studies were compared with molecular dynamics computations on the structures of the Ca-bound and Ca-free forms of cod parvalbumin. The UV CD spectra show that removal of calcium results in a decrease in the alpha-helical content of the protein. The IR amide I' and III' regions are very much affected by Ca removal and are indicative of significant perturbation of secondary structure. The fluorescence of tryptophan, the IR markers, and UV ellipticity all show changes with temperature, pointing to a lowering of protein stability upon Ca removal. These results are consistent with the structures obtained for both the Ca-bound and Ca-free proteins after 200 ps of solvated molecular dynamics simulations which show a decrease in the secondary structure upon Ca removal.

Calcium↗

PubMed1997

Fluorescence line narrowing spectroscopy: a tool for studying proteins.

Perhaps the most important contribution of FLN is that it provides an experimental approach to relate physical changes in the protein to predicted dynamical behavior. It is clear that the sample is inhomogeneously broadened in a continuous manner, consistent with the damped motion of proteins. At the same time configurational substates can be selected, suggesting that there is indeed a hierarchy of protein motion and structure. As yet, identification of the structure, and relating it to the spectra, has not been achieved. It is clear that the electric field exerted by neighboring atoms shifts the electronic transition, and the inhomogeneity is greater when the surrounding disorder is greater. The inhomogeneity for the chromophore in the protein is dependent on the protein conformation and is intermediate between that of a crystal and a glass. The phonon coupling also depends on the chromophore and the protein. Fluorescence line narrowing provides in addition ground- and excited-state vibrational frequencies, thereby allowing for structural differences between the excited-state and the ground-state molecule to be detected.

Animals↗

PubMed1996

Spectral splitting in the alpha (Q0,0) absorption band of ferrous cytochrome c and other heme proteins.

The alpha or Q0,0 absorption band of horse iron(II) cytochrome c splits and shifts to the blue as temperature decreases over the temperature range of 290-10 K. At room temperature, its maximum is at 18 150 cm-1 and the spectral width is 273 cm-1, whereas at 10 K, the two bands of the Q0,0 transition occur at 18 364 and 18 253 cm-1 and the width of the lowest-energy band is 96 cm-1. Temperature dependent splitting also occurs for zinc cytochrome c, a derivative in which Fe has been replaced by Zn; at 10 K, the peaks in the Q0,0 band region occur at 17 106 and 16 996 cm-1. The peak positions are independent of the cryosolvent (aqueous ethylene glycol or glycerol mixtures). The splitting of the Q0,0 band seen in the protein (approximately 110 cm-1 for iron and zinc cytochrome c) is comparable to the crystal field splitting observed for metalloporphyrins in mixed crystals. In contrast, the Q0,0 band of zinc coproporphyrin III in a glassy solvent (dimethylformamide/ethylene glycol) or in poly(vinyl chloride) shows a blue shift with temperature decrease but no evidence of Q0,0 splitting. Available spectral data show that the Q0,0 band is composed of two nearly degenerate electronic transitions and the split is due to the asymmetry in the heme pocket of the protein that arises from the surrounding polypeptide chain. This asymmetry results in the stabilization of one form of the excited state over the other, according to a Jahn-Teller mechanism.

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

Spectroscopic characterization of bendazac and benzydamine: possible photochemical modes of action.

The involvement of near-UV light in cataract development suggests that potential anti-cataract drugs may display unusual spectroscopic properties. As bendazac impedes certain effects associated with lens opacification, we have characterized the singlet and triplet states of bendazac and its analog, benzydamine, by fluorescence and phosphorescence methods. These compounds have much shorter triplet state lifetimes compared to the triplet state lifetimes observed in proteins. Our results raise the possibility that the photoprotective action of these compounds may result from their ability to dissipate energy through the triplet state. We propose alternative modes for the photoprotective actions of these compounds.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed1996

Stark effect experiments in cytochrome c-type proteins: structural hierarchies.

We performed hole-burning Stark effect experiments on cytochrome c in which the iron of the herne was either removed or replaced by Zn. According to the experiments, the free-base compound has an effective inversion center, even in the protein. The Zn compound, on the other hand, shows quite peculiar features: in the low-frequency range of the inhomogeneous band, it definitely has a dipole moment, as indicated by a splitting of the hole in the external field. However, in the maximum of the inhomogeneous band, a severe charge redistribution occurs, as the experiments show. In addition to the Stark experiments, we performed calculations of the electrostatic fields at the pyrrole rings and at the metal site of the heme group. We interpret our findings with a model based on structural hierarchies: the protein can exist in a few subconformations, which can be distinguished through the structure of the heme pocket. The different pocket structures support different structures of the chromophore, which, in turn, can be distinguished through their behavior in an external field. These distinct structures, in turn, correspond to a rather broad distribution of protein structures, which leave, however, the pocket structure largely unchanged. These structures show up in inhomogeneous broadening.

Animals↗

PubMed1996

Hydrogen atoms are produced when tryptophan within a protein is irradiated with ultraviolet light.

The UV photolysis of the aromatic amino acid, tryptophan (Trp), in the Ca(2+)-binding protein, cod parvalbumin, type III, was studied using electron paramagnetic resonance (EPR) spectroscopy in the temperature range 4-80 K. For the Ca(2+)-bound protein, irradiation with UV light (250-400 nm) resulted in the generation of atomic hydrogen with a hyperfine splitting of 50.9 mT, whereas in the Ca(2+)-free form, where the Trp is exposed to solvent, the trapped atomic hydrogen was not in evidence. In the same spectra, the radical signal in the g = 2.00 region could be detected. The line shape of the Ca(2+)-bound form is similar to the EPR line shape obtained for Trp in micellar systems. In contrast, the EPR line shape for the Ca(2+)-free form is essentially featureless up to 80 K. The EPR spectra of the photoproducts of Trp and the nature of the photoreactions are therefore sensitive to the environment of Trp within the protein.

Animals↗

PubMed1995

Interaction of polyamines with the Ca(2+)-binding protein parvalbumin.

The interaction of spermine, spermidine and putrescine with the Ca(2+)-binding protein, parvalbumin, was studied at pH 6 and 7, with the help of the intrinsic fluorescence properties of tryptophan and circular dichroic spectroscopy of the protein in the ultraviolet region. Polyamines bind to parvalbumin that is either Ca(2+)-free or partially saturated with Ca2+, as indicated by a change in the emission maximum and intensity of tryptophan fluorescence. The binding affinities for the interactions are about 4 mM, 8 mM and > 20 mM for spermine, spermidine and putrescine, respectively. No alterations in fluorescence properties were detected when the polyamines were added to fully Ca(2+)-bound parvalbumin. An increase in the ellipticity of the circular dichroic spectrum in the region where tryptophan absorbs was observed when polyamines were added to Ca(2+)-free parvalbumin. This finding indicates that polyamine binding affects the segment of the protein where tryptophan is located. Based on these results it is postulated that polyamines bind to the Ca(2+)-free or partially saturated parvalbumin and stabilize its structure.

Animals↗

PubMed1995

Structure of zinc-substituted cytochrome c: nuclear magnetic resonance and optical spectroscopic studies.

Optical and proton nuclear magnetic resonance (NMR) studies were carried out to assess the structure of the polypeptide chain and metal ligation in zinc-substituted horse heart cytochrome c (Zn Cyt c). The 1D- and 2D-NMR (COSY, TOCSY, and NOESY) spectra allowed the assignment of proton resonances in 67 amino acid residues. These residues arose from all structural elements of the protein, alpha-helices, beta-turns, and segments of the protein with no defined secondary structure. Small deviations of the chemical shifts of Zn Cyt c proton resonances from native Fe(II) Cyt c of less than 0.1 ppm are due to not fully matching solvent conditions. Differences in the chemical shifts between the two proteins in the range 0.10-0.20 ppm are not clustered and are observed not only in the vicinity of the Zn porphyrin but also on distant surface locations of the cytochrome. The resonance positions of the bridge protons, from the thioether bonds of the porphyrin with Cys 14 and Cys 17, were conserved in Zn Cyt c. Similarly, the Met 80 and His 18 protons had chemical shifts supporting the proposal that His 18 and Met 80, as for Fe(II) Cyt c, may provide the axial ligation in the Zn protein and that zinc may be in an unusual hexacoordinated geometry. Chemical shifts from proton resonances of alternative axial ligands of misfolded cytochrome like His 33, Lys 79, and Phe 82 were found to be the same as in the Fe(II) protein, excluding the possibility of their axial ligation to Zn. The His 18-Zn-Met 80 ligation was also consistent with data from absorption and luminescence studies. We conclude that Zn Cyt c is an adequate structural model for Fe(II) Cyt c as both share the same overall structure, including axial ligands, environment in the porphyrin vicinity, and the same binding interface with redox partners.

Animals↗

PubMed1995

Dynamics of parvalbumin studied by fluorescence emission and triplet absorption spectroscopy of tryptophan.

Fluorescence emission and triplet-triplet absorbance spectroscopy of the single tryptophan in cod parvalbumin were used to study the stability and dynamics of the protein as influenced by Ca2+ binding and interaction with a chaotropic agent. The concentrations for half-saturation for Ca binding were 3.6 x 10(-9), 3.3 x 10(-4), 7.1 x 10(-3), and 0.14 M in the presence of 0, 2, 3, and 4 M guanidine hydrochloride, respectively. As predicted for thermodynamic reversibility, the guanidine hydrochloride unfolding reaction depends upon Ca2+, and the delta G are as follows: 22.9, 29.3, 35.2, and 44.2 kJ/mol for no added Ca2+, 1, 2, and 5 mM Ca2+, respectively. The stability toward denaturation imparted by the binding of two Ca2+ is about -60 kJ/mol. For Ca(2+)-bound parvalbumin in the presence of excess Ca2+, the decay of the triplet state tryptophan is approximately exponential, and the lifetime decreases from 6.5 to 3.8 ms as the temperature increases from 10 to 40 degrees C. In contrast, the triplet decay of the calcium-free protein is nonexponential over the time range of microseconds to milliseconds, a result that may indicate that the Ca-free protein is molten-globule-like. At Ca2+ concentrations where the protein is partially saturated with Ca2+, the lifetime of the longest decay component is less than that for the Ca-saturated protein; this finding suggests an exchange of Ca2+ and a conformational change during the triplet lifetime. From these data, a rate constant for the process that includes calcium-related protein conformational change can be surmised to range between 200 and 500 s-1.

Animals↗

PubMed1995

Electron paramagnetic resonance of the excited triplet state of metal-free and metal-substituted cytochrome c.

The photoactivated metastable triplate states of the porphyrin (free-base, i.e., metal-free) zinc and tin derivatives of horse cytochrome c were investigated using electron paramagnetic resonance. Zero-field splitting parameters, line shape, and Jahn-Teller distortion in the temperature range 3.8-150 K are discussed in terms of porphyrin-protein interactions. The zero-field splitting parameters D for the free-base, Zn and Sn derivatives are 465 x 10(-4), 342 x 10(-4) and 353 x 10(-4) cm-1, respectively, and are temperature invariant over the temperature ranges studied. AN E value at 4 K of 73 x 10(-4) cm-1 was obtained for Zn cytochrome c, larger than any previously found for Zn porphyrins derivatives of hemeproteins, showing that the heme site of cytochrome c imposes an asymmetric field. Though the E value for Zn cytochrome c is large, the geometry of the site appears quite constrained, as indicated by a spectral line shape showing a single species. Intersystem crossing occurred predominantly to the T2 > zero-field spin sublevel. EPR line shape changes with respect to temperature of Zn cyt c are interpreted in terms of vibronic coupling, and a maximum Jahn-Teller crystal-field splitting of approximately 180 cm-1 is obtained. Sn cytochrome c in comparison with the Zn protein exhibits a photoactivated triplet line shape that is less well resolved in the X-Y region. The magnitude of E value is approximately 60 x 10(-4) cm-1 at 4 K; its value rapidly tends toward zero with increasing temperature, from which a value for the Jahn-Teller crystal-field splitting of > or = 40 cm-1 is estimated. In contrast to those for the metal cytochromes, the magnitude of E value for the free-base derivative was essentially zero at all temperatures studied. This finding is discussed as a consequence of an excited-state tautomerization process that occurs even at 4 K.

Animals↗

PubMed1995

Effects of NO-generating compounds on synaptosomal energy metabolism.

The effects of nitroprusside and S-nitrosocysteine, compounds that generate nitric oxide (NO), on synaptosomal energy-producing pathways and energy level were investigated. The decrease in respiration was much faster and more pronounced with S-nitrosocysteine than with nitroprusside. S-Nitrosocysteine, at 10 microM, inhibited by 80% respiration with glucose and succinate (plus rotenone) in intact synaptosomes and with ascorbate/cytochrome c in broken preparations. Oxygenated hemoglobin reversed and/or prevented the inhibition, whereas glutathione (GSH) prolonged it. Under aerobic conditions, the synaptosomal energy level (creatine phosphate/creatine and ATP/ADP ratios) was reduced by the presence of S-nitrosocysteine, whereas lactate generation was enhanced. The effects on energy parameters were greater at 5 min than at 15 min of incubation and were more pronounced in the presence of GSH. Under strictly anaerobic conditions, lactate production was reduced by the NO-generating compounds in a concentration-dependent manner. It is concluded that (a) inhibition of oxidative phosphorylation by NO leads to a fall in the synaptosomal energy level, which in turn stimulates glycolysis; (b) glycolysis can be inhibited by higher concentrations of the radical; and (c) inhibitory effects on the energy-generating pathway and ATP level could contribute to NO toxicity under some in vivo situations.

Animals↗

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

Nitric oxide diffusion coefficients in solutions, proteins and membranes determined by phosphorescence.

The reactivity of nitric oxide under a given condition is a complex function of its diffusivity and the concentration of reacting partners. Quenching by NO of luminescence from Ru and Pd chelates of mesoporphyrin IX, two molecules which exhibit phosphorescence at room temperature, was utilized to evaluate the gas concentration and apparent diffusion coefficients. The properties of Ru-mesoporphyrin, a dye not previously employed as a probe for O2 or NO, were determined and the assay was verified and used to quantify NO produced by decomposition of nitrosocysteine. The pseudo-second order quenching constants were obtained from Stern-Volmer plots measured under various conditions and used to calculate diffusion coefficients for nitric oxide in solutions, proteins and membranes. The diffusion coefficients were greater at 37 than at 25 degrees C and, at a given temperature, smaller in proteins and membranes than in water. The conclusion is that NO and O2 closely resemble each other in diffusivity but that NO is slightly less lipophilic, resulting in somewhat faster apparent diffusion in protein and slower diffusivity in lipid, relative to O2. Taking a mean diffusion coefficient for NO of 10(-7) cm2s-1, then within 10 s the mean path is 10(-3) cm, or less than the diameter of a single cell. However, at low NO and O2 concentrations, the halflife of NO will be considerably longer than 10 s, and consequently the path of NO diffusion much greater.

Animals↗

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↗

PubMed1993

Native and denatured Zn cytochrome c studied by fluorescence line narrowing spectroscopy.

Fluorescence Line Narrowing (FLN) spectroscopy was employed to compare the environment around the porphyrin in folded and unfolded Zn-substituted cytochrome c (Zn cyt c). Parameters of the resolved spectra, including the inhomogeneous energy-distribution function, vibrational energy levels, and phonon coupling, were compared for guanidine-denatured Zn cyt c and native Zn cyt c. The spectra of denatured Zn cyt c showed increased broad background and decreased peak resolution when compared to the native protein, indicating that denaturation results in increased phonon coupling. The energy-distribution function for the unfolded protein was fitted to a single Gaussian centered at 17,230 cm-1 with a width of approx. 360 cm-1, which proved to be blue shifted and much wider than that for native Zn cyt c (approx. 65 cm-1). Vibrational frequencies of the ground-state for Zn cyt c were identified and shown to change upon denaturation. Temperature-dependence of the FLN spectra of native Zn cyt c was analyzed and found to have step-like broadening between 40 K and 50 K. Such discontinuous spectral broadening behavior suggests that a discrete conformational change occurs in the protein at these temperatures.

Animals↗