The effect of binding ions on the oxidation of horse heart ferrocytochrome c

1979 ◽  
Vol 57 (5) ◽  
pp. 372-377 ◽  
Author(s):  
B. F. Peterman ◽  
R. A. Morton

The effect of various specific binding ions on the rate of oxidation by potassium ferricyanide of electrodialyzed horse heart ferroeytochrome c was studied. The ionic strength was kept constant using Tris–cacodylate buffer, pH 7.0. Either the Tris or cacodylate ion was replaced by the binding ion studied. At an ionic strength of 0.194 M (24 °C), replacing cacodylate by chloride decreased the bimolecular oxidation rate constant from about 13.3 × 106 (Tris–cacodylate) to about 8.8 × 106 M−1 s−1 (Tris–chloride). Comparable decreases were found when cacodylate was replaced by phosphate or when Tris was replaced by potassium. When picrate replaced cacodylate (ionic strength 0.0485 M) a larger decrease was found, from about 5.2 × 107 to about 0.8 × 107 M−1 s−1. Data at intermediate ion concentrations were consistent with a simple cooperative binding model. The calculated association constants for chloride, potassium, and phosphate were in the range of 2–20 M−1, while for picrate it was 500 M−1. The data were consistent with one bound ion per ferroeytochrome c molecule, except for picrate, for which two binding sites were suggested. The results were interpreted by the hypothesis that the picrate ion binds near the solvent-exposed heme edge. The electron transfer reaction of ferricyanide was also presumed to take place through this region. The other ions probably bind at some distance from the heme edge and were suggested to exert their effect by perturbing the proteins' solvent shell. Consistent with this was the effect of replacing H2O by D2O which decreased the oxidation rate constant by about 50%.

Soil Research ◽  
1993 ◽  
Vol 31 (1) ◽  
pp. 67
Author(s):  
JH Watkinson

An equation is proposed that describes the oxidation rate of elemental sulfur particles with a wide range of sizes, such as would be found in fertilizers. The only information needed is the mean oxidation rate constant over the period of interest and, from a sieve analysis, the proportions of the total mass in each sieve fraction (ratio of upper to lower size < to 2).


Soil Research ◽  
1993 ◽  
Vol 31 (1) ◽  
pp. 67
Author(s):  
JH Watkinson

An equation is proposed that describes the oxidation rate of elemental sulfur particles with a wide range of sizes, such as would be found in fertilizers. The only information needed is the mean oxidation rate constant over the period of interest and, from a sieve analysis, the proportions of the total mass in each sieve fraction (ratio of upper to lower size < to 2).


2020 ◽  
Vol 48 (16) ◽  
pp. 8914-8926
Author(s):  
Erin E Cutts ◽  
J Barry Egan ◽  
Ian B Dodd ◽  
Keith E Shearwin

Abstract The Apl protein of bacteriophage 186 functions both as an excisionase and as a transcriptional regulator; binding to the phage attachment site (att), and also between the major early phage promoters (pR-pL). Like other recombination directionality factors (RDFs), Apl binding sites are direct repeats spaced one DNA helix turn apart. Here, we use in vitro binding studies with purified Apl and pR-pL DNA to show that Apl binds to multiple sites with high cooperativity, bends the DNA and spreads from specific binding sites into adjacent non-specific DNA; features that are shared with other RDFs. By analysing Apl's repression of pR and pL, and the effect of operator mutants in vivo with a simple mathematical model, we were able to extract estimates of binding energies for single specific and non-specific sites and for Apl cooperativity, revealing that Apl monomers bind to DNA with low sequence specificity but with strong cooperativity between immediate neighbours. This model fit was then independently validated with in vitro data. The model we employed here is a simple but powerful tool that enabled better understanding of the balance between binding affinity and cooperativity required for RDF function. A modelling approach such as this is broadly applicable to other systems.


1995 ◽  
Vol 73 (7) ◽  
pp. 1181-1186 ◽  
Author(s):  
Eddy Cheung ◽  
Ann M. English

The kinetics of reduction of ferricyanide by yeast ferrocytochrome c peroxidase (CPPII) were investigated as a function of ionic strength in phosphate buffers at pH 7.0 and 25 ± 1 °C. The observed bimolecular rate constant (k12) is 8.4 × 104 M−1 s−1 in 0.1 M phosphate. The dependence of the reaction rate on ionic strength indicates a change of −9 on the protein at pH 7.0, which is in good agreement with the total charge of −11 estimated for CCPII from its amino acid content. Substituting k12 at infinite ionic strength [Formula: see text] into the Marcus cross relation yields an electron self-exchange rate constant [Formula: see text] for the FeIII/FeII couple of CCP of 7.2 × 10−5 M−1 s−1. This value is over four orders of magnitude higher than that calculated for the FeIV/FeIII couple of CCP from literature data for cross-reactions with ferrocyanide at pH 7.0. Possible reasons for the large difference in the two CCP [Formula: see text] values are discussed. Literature data also allowed [Formula: see text] values for various other heme proteins to be determined from their cross-reactions with ferricyanide. The calculated rate constants vary by eight orders of magnitude, and the variation of [Formula: see text] with protein structure suggests that the redox reactivity of ferrous heme proteins towards ferricyanide is dependent on the spin state and coordination of iron, as well as on the accessibility of the heme. Keywords: cytochrome c peroxidase, ferricyanide, Marcus cross relation, electron self-exchange.


1983 ◽  
Vol 96 (2) ◽  
pp. 229-239 ◽  
Author(s):  
Kenneth Smith ◽  
Sam Shuster ◽  
Michael Rawlins

Using an exchange assay to measure occupied and unoccupied binding sites the interaction between [3H]triamcinolone acetonide and rat skin cytosol proteins was studied. A binding site with a high affinity (dissociation constant = 7 × 10−10 mol/l) and a low capacity (400–600 fmol/mg protein) for triamcinolone acetonide was detected. The binding was specific to corticosteroids; fluorinated steroids showed a higher affinity than natural steroids. Non-corticosteroids, with the exception of progesterone, had little or no affinity for the binding site. At 0 °C the second-order rate constant of association was 2·23 × 106 mol/l per min and the first-order rate constant of dissociation was 1·6 × 10−4 per min. In the absence of dithiothreitol and molybdate the specific binding was rapidly abolished. The binding was also labile to heating and proteolytic enzymes. One day after adrenalectomy there was a significant increase in the number of assayable binding sites in the cytosol. The results are consistent with the binding protein being the physiological glucocorticoid receptor in rat skin.


2017 ◽  
Vol 24 (35) ◽  
pp. 27366-27375 ◽  
Author(s):  
Erlinda V. Ortiz ◽  
Daniel O. Bennardi ◽  
Daniel E. Bacelo ◽  
Silvina E. Fioressi ◽  
Pablo R. Duchowicz

2019 ◽  
Author(s):  
Erin Cutts ◽  
J. Barry Egan ◽  
Ian Dodd ◽  
Keith Shearwin

AbstractThe Apl protein of bacteriophage 186 functions both as an excisionase and as a transcriptional regulator; binding to the phage attachment site (att), and also between the major early phage promoters (pR-pL). Like other recombination directionality factors (RDFs), Apl binding sites are direct repeats spaced one DNA helix turn apart. Here, we use in vitro binding studies with purified Apl and pR-pL DNA to show that Apl binds to multiple sites with high cooperativity, bends the DNA, and spreads from specific binding sites into adjacent non-specific DNA; features that are shared with other RDFs. By analysing Apl’s repression of pR and pL, and the effect of operator mutants in vivo with a simple mathematical model, we were able to extract estimates of binding energies for single specific and non-specific sites and for Apl cooperativity, revealing that Apl monomers bind to DNA with low sequence specificity but with strong cooperativity between immediate neighbours. This model fit was then independently validated with in vitro data. The model we employed here is a simple but powerful tool that enabled better understanding of the balance between binding affinity and cooperativity required for RDF function. A modelling approach such as this is broadly applicable to other systems.


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