Current issues and future problems in transplantation in East Asia.
Explore the source record for details and available documents.
Asia, Southeastern↗
Biomedical subjects
A Naqui
Publications and source records attributed to A Naqui.
Comparison of the SimPlate coliform and Escherichia coli test with Petrifilm, three-tube MPN, and VRBA + MUG methods for enumerating coliforms and E. coli in food.
SimPlate for coliforms and Escherichia coli (CEc) is a new method for the detection and quantification of coliforms and E. coli in food. Internal validation of the method was carried out at IDEXX Laboratories (Westbrook, ME) with 180 food samples representing a variety of different food matrices and compared against three-tube MPN (most probable number), VRBA (violet red bile agar) + MUG, and Petrifilm (E. coli count) methods. SimPlate CEc was highly correlated with each of these methods for the quantification of coliform bacteria (r > or = 0.90). An insignificant number of food samples were found to contain E. coli; therefore, no meaningful correlation data could be generated. Four hundred forty-four additional food samples were tested at five collaborating laboratories for the presence of coliforms E. coli using SimPlate CEc and either VRBA + MUG or Petrifilm (E. coli count). Regression analysis of data from SimPlate for CEc versus Petrifilm E. coli count plates generated correlation coefficients (r) of at least 0.89 for total coliforms and at least 0.90 for generic E. coli. Correlation coefficients between SimPlate for CEc and VRBA + MUG data were at least 0.90 for coliforms and at least 0.86 for E. coli. SimPlate for CEc demonstrated better recovery of E. coli than Petrifilm when high populations of bacteria were present. E. coli was not detected in 20 or 50 (40%) raw milk samples tested by the Petrifilm method due to the presence of interfering coliform and noncoliform bacteria. It is concluded that SimPlate for CEc is a suitable alternative for determining numbers of coliform bacteria and E. coli in food.
Bacteriological Techniques↗
On the environment of zinc in beef heart cytochrome c oxidase: an x-ray absorption study.
The role of zinc in beef heart cytochrome c oxidase has been studied by using x-ray absorption spectroscopy, zinc depletion and secondary structure predictions of subunits of beef heart cytochrome c oxidase. The stoichiometry of zinc in cytochrome oxidase has been determined in 35 different preparations and found to be one-half of copper (Cu:Zu = 2:1). Zinc is tightly bound to this enzyme and cannot be removed by dialysis against EDTA. However, zinc could be partially (up to 50%) depleted by treating the enzyme with either dipicolinic acid or by trypsin digestion. This partial depletion of zinc does not change the O2 uptake rate. X-ray absorption spectroscopy shows that the atom is in a distorted tetrahedral environment with mostly sulfur ligands. Since subunit VIa removed by the digestion removes about one-half the zinc, a possible binding site involves the two S sites present in that subunit with an appropriate folding in a structural role.
Animals↗
Does the peroxide compound of cytochrome oxidase contain a ferryl iron?
The reaction of peroxide with cytochrome oxidase generates a peroxide compound having a Soret maximum at 428 nm. X-ray absorption spectroscopy analysis of the local structure of the active site iron shows marked similarity to that of the cytochrome c peroxidase intermediate Compound ES, which contains a short iron to proximal nitrogen distance compared to globins. Reductive titration of the 580 nm band of this compound indicates that the iron is one oxidizing equivalent above the resting oxidized form. These results support the presence of a ferryl iron (Fe(IV) = O) in the peroxide compound similar to that found for the peroxidases.
Animals↗
Kinetic, structural, and spectroscopic identification of geminate states of myoglobin: a ligand binding site on the reaction pathway.
Elementary steps or geminate states in the reaction of gaseous ligands with transport proteins delineate the trajectory of the ligand and its rebinding to the heme. By use of kinetic studies of the 765-nm optical "conformation" band, three geminate states were identified for temperatures less than approximately 100 K. MbCO, which is accumulated by photolysis between 1.2 and approximately 10 K, was characterized by our previous optical and X-ray absorption studies [Chance, B., Fischetti, R., & Powers, L. (1983) Biochemistry 22, 3820-3829]. Between 10 and approximately 100 K, geminate states that are also identified that have recombination rates of approximately 10(3) s-1 and approximately 10(-5) s-1 (40 K). Thus, it is possible to maintain a steady-state nearly homogeneous population of the slowest recombining geminate state, Mb, by regulated continuous illumination (optical pumping). Both X-ray absorption and resonance Raman studies under similar conditions of optical pumping show that the heme structure around the iron in Mb is similar to that of MbCO. In both geminate states, the iron-proximal histidine distance remains unchanged (+/- 0.02 A) from that of MbCO while the iron to pyrrole nitrogen average distance has not fully relaxed to that of the deoxy state. In MbCO the CO remains close to iron but not bound, and the Fe...CO angle, which is bent in MbCO (127 +/- 4 degrees C), is decreased by approximately 15 degrees [Powers, L., Sessler, J. L., Woolery, G. L., & Chance, B. (1984) Biochemistry 23, 5519-5523]. The CO molecule in Mb, however, has moved approximately 0.7 A further from iron. Computer graphics modeling of the crystal structure of MbCO places the CO in a crevice in the heme pocket that is just large enough for the CO molecule end-on. Above approximately 100 K resonance Raman studies show that this structure relaxes to the deoxy state.
Binding Sites↗
A new procedure for the purification of monodisperse highly active cytochrome c oxidase from bovine heart.
A simple and rapid method for the isolation of a large quantity of cytochrome c oxidase from bovine heart mitochondria was developed, based on selective solubilization of mitochondrial protein with first Triton and then lauryl maltoside. Gel filtration shows that the lauryl maltoside-solubilized oxidase preparation is in a hydrodynamically homogeneous state with a Stokes radius of 7.5 +/- 0.2 nm. It contains 8.0 mumol of haem (with an a/a3 ratio of 1)/g of protein. The catalytic constant (maximum turnover number) with respect to cytochrome c approaches 600 S-1. After further purification of the solubilized enzyme on a sucrose-gradient centrifugation, the purified enzyme has a haem content of 10.3 mumol/g of protein and eight major polypeptide bands shown on SDS/polyacrylamide-gel electrophoresis.
Animals↗
Steady-state kinetic approaches to complex biological systems.
Steady-state kinetic approaches to study the biochemical systems have been extremely useful. In this paper we use this approach to explain the inhibition of electron transport in structurally bound multienzyme systems and in applying the work-energy cost transfer function to living tissues as studied by 31P NMR spectroscopy. We show that in both systems the steady-state approach leads to equations and predictions that are in accordance with the experimental data.
Animals↗
Enhanced superoxide dismutase activity of pulsed cytochrome oxidase.
The superoxide dismutase (SOD) activity of beef heart cytochrome oxidase, both in the resting (as isolated) and pulsed (reduced and reoxidized) states, has been investigated using their ability to inhibit the autoxidation rate of pyrogallol and epinephrine. Resting oxidase showed variable SOD activity, while in the pulsed state the SOD activity of cytochrome oxidase (CcO) increased by an order of magnitude. These results are discussed in terms of a physiological role for the pulsed oxidase.
Animals↗
Reactive oxygen intermediates in biochemistry.
Explore the source record for details and available documents.
Cytochrome P-450 Enzyme System↗
Resonance Raman spectroscopy and enhanced photoreducibility for the 420 nm pulsed form of cytochrome oxidase.
Resonance Raman (RR) spectra, with 413.1 nm Kr+ laser excitation, are reported for cytochrome oxidase in resting, reduced, and 428 nm (oxygenated) forms, and for the first time, in the 420 nm (pulsed) forms [(1984) J. Biol. Chem. 259, 2073-2076]. The differences between the resting, 420 nm, and 428 nm forms' RR spectra are small. All these forms contain FeIII only, as indicated by single v4 bands at approximately 1371 cm-1, and the reoxidized forms show partial conversion from high- to intermediate- or low-spin heme a3 (intensity shift from 1575 to 1588 cm-1 for v2). The 420 nm form differs strikingly from both the 428 nm and resting forms, however, in being much more readily photoreduced by the laser illumination. This property is linked to the protein conformational change believed to be responsible for the greater accessibility to exogenous ligands of the heme a3 in the 420 nm form.
Animals↗
Structure and reactivity of multiple forms of cytochrome oxidase as evaluated by X-ray absorption spectroscopy and kinetics of cyanide binding.
The extended X-ray absorption fine structure (EXAFS) data show differences between the active site structures of different cytochrome oxidase preparations. In the resting (as isolated) state of the Yonetani preparation, the bridging atom between Fe3+a3 and Cu2+a3 is present [Powers, L., Chance, B., Ching, Y., & Angiolillo, P. (1981) Biophys. J. 34, 465], whereas in another preparation (e.g., Hartzell-Beinert), this atom seems to be bound only to Fe3+a3 in a significant fraction of the molecules. Both preparations bind cyanide in a multiphasic fashion, suggesting that the resting cytochrome oxidase is not homogeneous but rather is a mixture of several forms. The proportion of these forms as detected by cyanide binding kinetics differs for different preparations. However, upon reduction and reoxidation (conversion to the "oxygenated" form) the cyanide binding kinetics become monophasic and all preparations of the oxygenated form bind cyanide at the same rate. Thus, a combination of structural and kinetic approaches seems necessary for evaluation of the nature of the active site of cytochrome oxidase in its various forms.
Animals↗
Pulsed cytochrome c oxidase from the thermophilic bacterium PS3.
A caa3-type terminal cytochrome c oxidase (EC 1.9.3.1) from the thermophilic bacterium PS3 containing three subunits showed conversion from resting into pulsed form. Upon pulsing (reduction and re-oxidation), the cytochrome c oxidase activity increased over 10-fold. This enhanced activity of the pulsed enzyme gradually decayed. Addition of phospholipids, necessary for the enzyme activity, did not affect this decay process. Small changes in the absorption spectrum were observed for the resting-into-pulsed transition and for H2O2 ligation to the pulsed enzyme. The e.p.r. spectrum of the resting enzyme was very similar to that of mitochondrial enzyme, but the transient g = 5, 1.78 and 1.69 set of e.p.r. signals, associated with the pulsed bovine heart oxidase, were not observed in the case of pulsed bacterium-PS3 enzyme.
Bacteria↗
Peroxide interaction with pulsed cytochrome oxidase. Optical and EPR studies.
EPR and optical analysis of the 420 nm form of cytochrome oxidase (Kumar, C., Naqui, A., and Chance, B. (1984) J. Biol. Chem. 259, 2073-2076) shows that 1) the 420 nm form possesses a 605 nm band, g = 5 EPR signals, and a slightly blue shifted 655 nm band; 2) the reaction of H2O2 with the 420 nm form generates the peroxide complex (Soret band at 427 nm) with the formation of a 580 nm band and abolition of both the 655 nm band and the g = 5 EPR signal. Comparison of our results with past data shows that various forms of oxidase formed from the resting oxidase through different protocols may be identified to be either the 420 nm or the 427 nm form and leads to identification of a peroxy intermediate during oxidase turnover.
Electron Spin Resonance Spectroscopy↗
A semi-integrated method for the determination of enzyme kinetic parameters and graphical representation of the Michaelis-Menten equation.
A semi-integrated method for the determination of the enzyme kinetics parameters (Km and V) and graphical representation of the Michaelis-Menten equation is proposed as a variation of determination of initial reaction rate (v) as a function of initial substrate concentration ([S]0). The method is based on the determination of the time required to exhaust half of the initial substrate concentration as a function of the initial substrate concentration. The advantages and limitations of this method are discussed.
Enzyme Inhibitors↗
Reaction of caa3-type terminal cytochrome oxidase from the thermophilic bacterium PS3 with oxygen and carbon monoxide at low temperatures.
Reaction of O2 and CO with a caa3-type terminal cytochrome oxidase (EC 1.9.3.1) from the thermophilic bacterium PS3 grown with high aeration was studied at low temperatures. The CO recombination at the temperature range studied (-50 degrees C to -80 degrees C) followed first-order kinetics with an activation energy of 29.3 kJ/mol (7.0 kcal/mol). In the presence of O2 at -113 degrees C the photolysed reduced form binds O2 to form an 'oxy' intermediate similar to Compound A. At a higher temperature (-97 degrees C) another intermediate, similar to Compound B, is formed as a result of electron transfer from the enzyme to the liganded O2.
Carbon Monoxide↗
The identity of pulsed cytochrome oxidase.
Reduction and reoxidation of beef heart cytochrome oxidase, under conditions that ensure the strict absence of hydrogen peroxide, produce a fully oxidized form of the enzyme that has the Soret band at 420 nm, as opposed to the 428 nm band normally associated with the pulsed or oxygenated enzyme. The 420 nm form shows the enhancement of catalytic activity associated with the pulsed enzyme. Addition of hydrogen peroxide to the 420 nm form gives rise to the 428 nm band of the oxygenated enzyme, thereby clearly establishing that the 428 nm form is a peroxide derivative of the fully oxidized enzyme. Previous data from other groups are re-evaluated in the light of our experiments.
Animals↗
An analysis of amino acid composition of a few oxidoreductases by different methods.
Explore the source record for details and available documents.
Amino Acids↗