Equivalence of Mg2+ and Na+ ions in salt dependence of the equilibrium binding and dissociation rate constants of Escherichia coli RNA polymerase open complex

2009 ◽  
Vol 142 (1-3) ◽  
pp. 65-75 ◽  
Author(s):  
Tomasz Łoziński ◽  
Krystyna Bolewska ◽  
Kazimierz L. Wierzchowski
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Rate Constants ◽  
Dissociation Rate ◽  
Salt Dependence ◽  
Equilibrium Binding ◽  
Na Ions ◽  
Dissociation Rate Constants

scholarly journals Kinetics and thermodynamics of the binding of forskolin to the galactose-H+ transport protein, GalP, of Escherichia coli

1995 ◽  
Vol 308 (1) ◽  
pp. 261-268 ◽  
Author(s):  
G E M Martin ◽  
N G Rutherford ◽  
P J F Henderson ◽  
A R Walmsley
Keyword(s):  
Escherichia Coli ◽  
Rate Constants ◽  
Binding Sites ◽  
Cytochalasin B ◽  
Equilibrium Dialysis ◽  
Dissociation Rate ◽  
Protein Fluorescence ◽  
Time Resolved ◽  
Fluorescence Measurements ◽  
Dissociation Rate Constants

The binding of the transport inhibitor, forskolin, to the galactose-H+ symporter, GalP, of Escherichia coli was evaluated by equilibrium and time-resolved fluorescence measurements. A quench in protein fluorescence of 8-12% was observed upon the binding of forskolin. The overall dissociation constant (Kd) for forskolin determined by fluorescence titration ranged between 1.2 and 2.2 microM, which is similar to that reported from equilibrium dialysis measurements of the binding of [3H]forskolin (Kd = 0.9-1.4 microM). The kinetics of forskolin binding were measured by stopped-flow fluorescence methods. The protein fluorescence was quenched in a biphasic manner; the faster of these two rates was dependent on the concentration of forskolin and was interpreted as the initial binding step from which both the association (kon) and dissociation (koff) rate constants were determined. The association and dissociation rate constants were 5.4-6.2 microM-1.s-1 and 5.1-11.5 s-1 respectively, and the Kd was calculated to be 1.5 microM. The binding of forskolin was inhibited by D-galactose, but not by L-galactose, and displacement by sugar provided an additional method to calculate the dissociation rate constant for forskolin (koff = 12.4-13.0 s-1). The rate of the slow change in protein fluorescence (3-5 s-1) was independent of the forskolin concentration, indicating an isomerization of the transporter between different conformations, possibly outward- and inward-facing forms. These kinetic parameters were determined at a series of temperatures, so that the thermodynamics of forskolin binding and transporter re-orientation could be analysed. The binding process was entropically driven (delta S = 83.7 J.K-1.mol-1; delta H = 8.25 kJ.mol-1), similar to that for cytochalasin B, which is also an inhibitor of GalP. Measurements of the binding of [3H]forskolin by equilibrium dialysis revealed competitive displacement of bound forskolin by cytochalasin B, possibly suggesting that the sugar, forskolin and cytochalasin B binding sites are overlapping; the Kds for forskolin and cytochalasin B were calculated to be 0.85 microM and 4.77 microM respectively, and the concentration of binding sites was 10.2 nmol.mg-1.

scholarly journals Dissociation Rate Constants of Human Fibronectin Binding to Fibronectin-binding Proteins on LivingStaphylococcus aureusIsolated from Clinical Patients

2012 ◽  
Vol 287 (9) ◽  
pp. 6693-6701 ◽  
Author(s):  
Nadia N. Casillas-Ituarte ◽  
Brian H. Lower ◽  
Supaporn Lamlertthon ◽  
Vance G. Fowler ◽  
Steven K. Lower
Keyword(s):  
Rate Constants ◽  
Binding Proteins ◽  
Dissociation Rate ◽  
Human Fibronectin ◽  
Fibronectin Binding ◽  
Dissociation Rate Constants

scholarly journals Head-to-tail polymerization of microtubules in vitro. Electron microscope analysis of seeded assembly.

1980 ◽  
Vol 84 (1) ◽  
pp. 141-150 ◽  
Author(s):  
L G Bergen ◽  
G G Borisy
Keyword(s):  
Electron Microscope ◽  
Rate Constants ◽  
Dissociation Constants ◽  
Dissociation Rate ◽  
Association Constants ◽  
Directional Growth ◽  
Microtubule Protein ◽  
Electron Microscope Analysis ◽  
Dissociation Rate Constants

Microtubules are polar structures, and this polarity is reflected in their biased directional growth. Following a convention established previously (G. G. Borisy, 1978, J. Mol. Biol. 124:565--570), we define the plus (+) and minus (-) ends of a microtubule as those equivalent in structural orientation to the distal and proximal ends, respectively, of the A subfiber of flagellar outer doublets. Rates of elongation were obtained for both ends using flagellar axonemes as seeds and porcine brain microtubule protein as subunits. Since the two ends of a flagellar seed are distinguishable morphologically, elongation of each end may be analyzed separately. By plotting rates of elongation at various concentrations of subunit protein, we have determined the association and dissociation rate constants for the plus and minus ends. Under our conditions at 30 degrees C, the association constants were 7.2 X 10(6) M-1 s-1 and 2.25 X 10(6) M-1 s-1 for the plus and minus ends, respectively, and the dissociation constants were 17 s-1 and 7 s-1. From these values and Wegner's equations (1976, J. Mol. Biol. 108:139--150), we identified the plus end of the microtubule as its head and calculated "s," the head-to-tail polymerization parameter. Surprisingly small values (s = 0.07 +/- 0.02) were found. The validity of models of mitosis based upon head-to-tail polymerization (Margolis et al., 1978, Nature (Lond.) 272:450--452) are discussed in light of a small value for s.

scholarly journals Mechanism of a Disassembly Driven Sensing System Studied by Stopped-Flow Kinetics

2021 ◽  
Author(s):  
Cara Gallo ◽  
Suma S. Thomas ◽  
Allison Selinger ◽  
Fraser Hof ◽  
Cornelia Bohne
Keyword(s):  
Steady State ◽  
Rate Constants ◽  
Artificial Saliva ◽  
Global Analysis ◽  
Dissociation Rate ◽  
Stopped Flow ◽  
Steady State Fluorescence ◽  
Saliva Analysis ◽  
Binding Isotherms ◽  
Dissociation Rate Constants

<div> Mechanistic studies were carried out on the kinetics for the assembly of a DimerDye (DD12) and the binding of the monomeric DimerDye (DD1) with nicotine in aqueous buffer and artificial saliva. DD12 is non-fluorescent, while monomeric DD1 and DD1-nicotine fluoresce. Binding isotherms were determined from steady-state fluorescence experiments. The report includes measurements of the steady-state fluorescence at pHs 2.2, 6.3 and 12.1, and stopped-flow kinetic data for the homodimerization forming DD12 and DD1-nicotine formation in buffer and artificial saliva. Analysis of the homodimerization kinetics led to the recovery of the association and dissociation rate constants for DD12. These rate constants were used in the global analysis for the coupled kinetics for DD1-nicotine formation, which led to the determination of the association and dissociation rate constants for nicotine binding to DD1.</div>

The Master Equation for the Dissociation of a Dilute Diatomic Gas. VIII. The Rotational Contribution to Dissociation and Recombination

1973 ◽  
Vol 51 (2) ◽  
pp. 237-259 ◽  
Author(s):  
Tom Ashton ◽  
D. L. S. McElwain ◽  
H. O. Pritchard
Keyword(s):  
Master Equation ◽  
Rate Constant ◽  
Rate Constants ◽  
Transition Probabilities ◽  
Rotational Transition ◽  
Dissociation Rate ◽  
Third Body ◽  
Rotational States ◽  
Dissociation Rate Constants ◽  
Very High

The dissociation of the J = 21 state of H2, and the recombination of atoms into that state, have been examined in detail. The J = 21 state of H2 has two quasi-bound levels, one long-lived and the other short-lived, but the rate constants for dissociation or recombination involving this state are almost completely independent of the tunnelling rates into and out of the quasi-bound levels, and are in fact determined by bottleneck effects occurring lower down the vibrational ladder. Direct integration of the relaxation equations shows that, either excluding or including tunnelling, the dissociation and recombination rate constants obey the rate-quotient law, and that in the latter case the lowest eigenvalue of the relaxation matrix properly reflects the pressure dependence of the dissociation rate constant. Less extensive examination of the dissociation properties of other rotational states indicates that these conclusions are general, except that there is no strong bottleneck effect for very high rotational states (J ≥ 30).It is shown that if full rotational equilibration is assumed, the sum, weighted over all J, of the individual dissociation rate constants leads to an overall dissociation rate constant which is much too high, suggesting strongly that rotational equilibration cannot occur amongst the very high J states.A factored form of the master equation is then examined in which either only T–V or only T–R processes take place, over the temperature range 1500–5000 °K. It is found that in this approximation the upper rotational states are very strongly depleted, and that the Arrhenius temperature coefficients of the dissociation rate constants are between 92 and 94 kcal mol−1, depending upon the choice of rotational transition probabilities. The calculation suggests that one contributory cause of "low activation energies" in dissociation reactions is strong rotational depopulation of the very high rotational states, and its importance in relation to other possible causes is discussed.The smallest eigenvalues of the 177th order matrix representing the dissociation of para-H2 and of the 172nd order matrix representing the dissociation of ortho-H2 confirm that the factored model gives an acceptable representation of the dissociation rate of H2 in this temperature range; hence the conclusions of the factored model in respect of strong rotational depopulation are probably valid. Finally, it is shown that the second smallest eigenvalue of the full relaxation matrix changes by a factor of three at 1500 °K or by a factor of ten at 5000 °K when only rotational transition probabilities are varied, thus identifying the relaxation which immediately precedes the dissociation reaction in a shock wave as a T–VR rather than a T–V relaxation.An exploratory series of calculations for deuterium was carried out for the range of temperatures 700–5000 °K, using the latter model which includes full coupling between rotation, vibration, and dissociation, i.e., using matrices of order 348 and 355 for ortho- and para-deuterium, respectively. These calculations predict that there should be a reversal in the isotope effect for both dissociation and recombination of hydrogen and deuterium as follows: (i) with helium as third body, deuterium should dissociate faster than hydrogen at high temperatures, but below about 2000 °K, the dissociation of deuterium will become the slower of the two processes; (ii) with argon as third body, deuterium should recombine faster than hydrogen at high temperatures, but below about 1000 °K, the recombination of deuterium will become the slower of the two processes; (iii) the rate constants for the recombination of hydrogen by hydrogen and for the recombination of deuterium by deuterium will probably cross over near 1000 °K, indicating a need for experiments in this region of temperature.

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