SMD-Based Interaction-Energy Fingerprints Can Predict Accurately the Dissociation Rate Constants of HIV-1 Protease Inhibitors

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.

Download Full-text

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

10.26434/chemrxiv.14410775.v1 ◽

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>

Download Full-text

Direct Chromatographic Determination of Dissociation Rate Constants of Ligand−Receptor Complexes: Assessment of the Interaction of Noncompetitive Inhibitors with an Immobilized Nicotinic Acetylcholine Receptor-Based Liquid Chromatography Stationary Phase

Analytical Chemistry ◽

10.1021/ac0504464 ◽

2005 ◽

Vol 77 (16) ◽

pp. 5421-5426 ◽

Cited By ~ 28

Author(s):

Ruin Moaddel ◽

Krzysztof Jozwiak ◽

Rika Yamaguchi ◽

Irving W. Wainer

Keyword(s):

Liquid Chromatography ◽

Nicotinic Acetylcholine Receptor ◽

Rate Constants ◽

Chromatographic Determination ◽

Dissociation Rate ◽

Nicotinic Acetylcholine ◽

Receptor Complexes ◽

Dissociation Rate Constants ◽

Noncompetitive Inhibitors

Download Full-text

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

Canadian Journal of Chemistry ◽

10.1139/v73-037 ◽

1973 ◽

Vol 51 (2) ◽

pp. 237-259 ◽

Cited By ~ 31

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.

Download Full-text

Constancy and variability of contractile efficiency as a function of calcium and cross-bridge kinetics: simulation

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.1996.270.4.h1501 ◽

1996 ◽

Vol 270 (4) ◽

pp. H1501-H1508 ◽

Cited By ~ 1

Author(s):

H. Yamaguchi ◽

M. Takaki ◽

H. Matsubara ◽

S. Yasuhara ◽

H. Suga

Keyword(s):

Rate Constants ◽

Mechanical Energy ◽

Muscle Length ◽

Dissociation Rate ◽

Twitch Contraction ◽

Cross Bridge ◽

Cardiac Contractile ◽

Total Mechanical Energy ◽

Isometric Twitch ◽

Dissociation Rate Constants

We simulated myocardial Ca2+ (Ca) and cross-bridge (CB) kinetics to get insight into the experimentally observed constancy and variability of cardiac contractile efficiency in generating total mechanical energy under various inotropic and pathological conditions. The simulation consisted of a Ca transient, Ca association and dissociation rate constants of troponin C, and CB on and off rate constants. We evaluated sarcomere isometric twitch contractions at a constant muscle length. We assumed that each CB cycle hydrolyzes one ATP and that the force-length area (FLA) quantifies the total mechanical energy generated by CB cycles in a twitch contraction. FLA is a linear version of pressure-volume area, which quantifies the total mechanical energy of cardiac twitch contraction and correlates linearly with cardiac oxygen consumption (H. Suga, Physiol. Rev. 70: 247-277, 1990). The simulation shows that the contractile efficiency varies with changes in the Ca transient and Ca and CB kinetics except when they simultaneously speed up or slow down proportionally. These results point to possible mechanisms underlying the constancy and variability of cardiac contractile efficiency.

Download Full-text