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Hoshino M, Sonoki H, Suzuki H, Adachi H, Miyazaki Y, Yamanaka K. Laser Photolysis Studies of Oxy- and Carbonylhemoglobin in Red Blood Cells. Effects of Cell Membrane on Reversible Binding of O2 and CO. J Phys Chem B 2001. [DOI: 10.1021/jp010762w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mikio Hoshino
- The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuda-machi, Midori-ku, Yokohama, Kanagawa 226-8502, Japan, Department of Chemistry, Faculty of Engineering, Toyo University, Kujirai, Kawagoe, Saitama 350-8585, Japan, and Department of Biochemical Toxicology, Nihon University College of Pharmacy, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Hirotaka Sonoki
- The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuda-machi, Midori-ku, Yokohama, Kanagawa 226-8502, Japan, Department of Chemistry, Faculty of Engineering, Toyo University, Kujirai, Kawagoe, Saitama 350-8585, Japan, and Department of Biochemical Toxicology, Nihon University College of Pharmacy, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Hiroyuki Suzuki
- The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuda-machi, Midori-ku, Yokohama, Kanagawa 226-8502, Japan, Department of Chemistry, Faculty of Engineering, Toyo University, Kujirai, Kawagoe, Saitama 350-8585, Japan, and Department of Biochemical Toxicology, Nihon University College of Pharmacy, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Haruna Adachi
- The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuda-machi, Midori-ku, Yokohama, Kanagawa 226-8502, Japan, Department of Chemistry, Faculty of Engineering, Toyo University, Kujirai, Kawagoe, Saitama 350-8585, Japan, and Department of Biochemical Toxicology, Nihon University College of Pharmacy, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Yoshio Miyazaki
- The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuda-machi, Midori-ku, Yokohama, Kanagawa 226-8502, Japan, Department of Chemistry, Faculty of Engineering, Toyo University, Kujirai, Kawagoe, Saitama 350-8585, Japan, and Department of Biochemical Toxicology, Nihon University College of Pharmacy, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
| | - Kenzo Yamanaka
- The Institute of Physical and Chemical Research, Wako, Saitama 351-0198, Japan, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuda-machi, Midori-ku, Yokohama, Kanagawa 226-8502, Japan, Department of Chemistry, Faculty of Engineering, Toyo University, Kujirai, Kawagoe, Saitama 350-8585, Japan, and Department of Biochemical Toxicology, Nihon University College of Pharmacy, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan
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Sauro HM, Barrett J. In vitro control analysis of an enzyme system: experimental and analytical developments. Mol Cell Biochem 1995; 145:141-50. [PMID: 7675034 DOI: 10.1007/bf00935486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this paper we describe a flow-through system for reconstituting parts of metabolism from purified enzymes. This involves pumping continuously into a reaction chamber, fresh enzymes and reagents so that metabolic reactions occur in the chamber. The waste products leave the chamber via the outflow so that a steady state can be setup. The system we chose consisted of a single enzyme, lactate dehydrogenase. This enzyme was chosen because it consumes NADH in the chamber which could be monitored spectrophotometrically. The aim of the work was to investigate whether a steady state could be achieved in the flow system and whether a metabolic control analysis could be done. We measured two control coefficients, CLDH and Cpump for the enzyme flux and NADH concentration and confirmed that the summation theorem applied to this system. The advantage of a flow-through system is that the titrations necessary to estimate the control coefficients can be easily and precisely controlled; this means that accurate estimates for the control coefficients can be obtained. In the paper, we discuss some statistical aspects of the data analysis and some possible applications of the technique, including a method to determine the presence of metabolic channelling between two different enzymes.
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Affiliation(s)
- H M Sauro
- Institute of Biological Sciences, University of Wales, Aberystwyth, Dyfed, UK
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Abstract
Monte Carlo simulations of neighbor exclusion models have been used to demonstrate the importance of collecting and fitting data over a wide range of saturation. Low saturation data are important for good estimates of the affinity K of a drug or protein for the lattice site. High saturation data are important for distinguishing between negatively cooperative and noncooperative binding modes. Neglect of negative cooperativity (omega < 1) has in general little effect on the estimation of K. The error is mostly absorbed by increasing the value of n. This kind of behavior was previously observed with the fitting of nonideal, monomer-dimer, ultracentrifugation data where variations in B, the second virial coefficient, and K2, the dimerization equilibrium constant, are highly correlated, thus making their individual determination difficult. Within experimental error the distinction between a noncooperative model [Eq. (1)] and a negatively cooperative model [Eq. (3) or (4) with omega < 1] may require additional evidence to justify the choice of one model over another. For example, for homogeneous lattices of synthetic deoxyoligonucleotides, n may be constrained with some validity, thus allowing a more accurate and precise determination of K and omega. In fact, n may be established independently, for example, by nuclear magnetic resonance (NMR) methods. However, the assumption of an integral value of n for natural DNA samples may not be valid because of sequence heterogeneity. Unconstrained fitting of negatively cooperative data to Eq. (4) will thus be a very difficult problem (Table V). At an experimental error of only 2.3%, n and K can be reasonably determined but with a large error in omega. Data from the final 20% of saturation are essential in extracting omega. This may in part explain the absence of more reports of negatively cooperative behavior in the literature. This analysis is independent of the systematic error that may be induced by the transformation of data to the Scatchard plot, or the omission of drug self-association, or the occurrence of wall binding by ligand, or variable point density, or non-Gaussian noise, or the occurrence of another mode of binding distinct from the models of McGhee and von Hippel. Each of these will introduce additional error, possibly biased error, in the parameters estimated; however, this does not obviate our conclusion. Even under these ideal circumstances there are serious limitations that must be considered when fitting neighbor exclusion model data. The direct fitting of absorbance data [to Eq. (2) or functions that incorporate other parameters] will also be sensitive to these considerations.
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Affiliation(s)
- J J Correia
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216
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Ackers GK, Johnson ML. Analysis of hemoglobin oxygenation from combined equilibrium and kinetic data. Is quaternary enhancement necessary? Biophys Chem 1990; 37:265-79. [PMID: 2285788 DOI: 10.1016/0301-4622(90)88026-o] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An experimental approach based on four independent techniques, in which kinetic and equilibrium measurements of subunit assembly reactions are combined with concentration-dependent oxygen-binding curves, has previously been used to resolve parameters of the linkage system for human hemoglobin over a wide range of conditions [(G.K. Ackers and H.R. Halvorson, Proc. Natl. Acad. Sci. U.S.A. 71 (1974) 4312; F.C. Mills et al., Biochemistry 15 (1976) 1093; M.L. Johnson et al., Biochemistry 15 (1976) 5363). Throughout this extensive body of results it has been found that the affinity for binding oxygen to tetramers at the fourth step exceeds the mean affinity of dissociated dimers. The existence of this "quaternary enhancement" effect has recently been questioned by Gibson and Edelstein (J. Biol. Chem. 262 (1987) 516) and by Philo and Lary (J. Biol. Chem. 265 (1990) 139) on the basis of kinetically derived oxygen-binding constants that do not exhibit quaternary enhancement. These authors have also suggested that quaternary enhancement might not be necessary to explain the oxygen-binding data mentioned above. In this study, we have explored the effect of constraining the numerical analysis of oxygen-binding data against the new kinetically derived binding constants. It is found that the sets of linkage constants which are compatible with both the oxygen-binding data and the new kinetically derived dimer binding constant require both quaternary enhancement and substantial dimer cooperativity. Increasing the dimer cooperativity to compensate completely for quaternary enhancement requires both dimeric and tetrameric binding constants that disagree with the kinetically derived values. Thus, the quaternary enhancement effect cannot be eliminated by readjustment of the remaining constants of the linkage system. Possible sources of the discrepancy between the kinetically derived binding constants and the otherwise self-consistent data from the other four techniques are discussed.
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Affiliation(s)
- G K Ackers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
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