Biomolecular rate constant

Anbar, M. and Neta, P. (1967). A compilation of specific biomolecular rate constants for the reaction of hydrated electrons, hydrogen atoms and hydroxyl radicals with inorganic and organic compounds in aqueous solutions. Int. J. Appl. Radiat. Isot. 18, 493-497. 

Table 2.4 Approximate Expressions and Values for Biomolecular Rate Constants for Different Types of Reactants and Complexes...

A detailed electrokinetic analysis of osmium mediator/laccase biocathodes was published in 2008 by GaUaway and Calabrese Barton [31]. In their work, the authors described the biomolecular rate constants for mediation to be between 250 and 9.4 X10" s when the redox potentials of mediator and laccase are close or far... 

Table II. Affinity Equilibrium (K ), Phopshorylation Rate (1 2) and Biomolecular Rate (Ic,) Constants for the Inhibition of AChE by ANTX-A(S) and DFP...

Finally, in Sect. 7.6, we have discussed how various free energy calculation methods can be applied to determine free energies of ensembles of pathways rather than ensembles of trajectories. In the transition path sampling framework such path free energies are related to the time correlation function from which rate constants can be extracted. Thus, free energy methods can be used to study the kinetics of rare transitions between stable states such as chemical reactions, phase transitions of condensed materials or biomolecular isomerizations. 

X = 0, CH2, CHCOOH, C(COOH)2, NH, NCH3 N(CH2CH=CH2), N(CHs)2 Cl Bobrowski and Das published a series of papers on the transients in the pulse radiolysis of retinyl polyenes31-37, due to their importance in a variety of biomolecular processes. They studied32 the kinetics and mechanisms of protonation reaction. The protons were released by pulse radiolysis, on a nanosecond time scale, of 2-propanol air-saturated solutions containing, in addition to the retinyl polyenes, also 0.5 M acetone and 0.2 M CCI4. Within less than 300 ns, the electron beam pulse results in formation of HC1. The protonated products of retinyl polyenes were found to absorb optically with Xmax at the range of 475-585 nm and were measured by this absorption. They found that the protonation rate constants of polyene s Schiff bases depend on the polyene chain... 

The reaction scheme in Fig. 26 gives a detailed picture of the main reactions initiated by the excitation of the dye molecule at the surface of an organic crystal. The rate constants connecting the reactants with the products are given in the dimensions s 1 for monomolecular reactions and in the dimensions cm3 s 1 for biomolecular reactions. Going from left to right in the first line a J describes the... 

To treat more realistic models for the kinetics of biomolecular encounters, a simulation approach has been developed and applied to proteins.370,371,3718 This approach merges stochastic dynamics methodology (Chapt. IV.D) with the analytic result for the Debye rate constant for a pair of particles, moving diffusively through solvent with a centrosymmetric interaction potential.365 The analytical expression for the Debye rate constant, ko(,R), to first achieve a separation, R, is given by... 

The solvent relaxes not with the expected Ti time constant (i.e. small rate constant), but instead with a much smaller observed time constant Tird that is proportional to the quality factor (Q), filing factor (77, ratio of sample volume over coil volume), ° and the magnetization (equilibrium being Mq). Room temperature probes typically have a Q of perhaps a few hundred units but cryogenically cooled probes can push this value to 1500 (or even upwards of 40 000 is possible though not applied in biomolecular probes). The increased rate of relaxation due to radiation dampening is immediately evident. 

The biomolecular inhibition rate constant (ifj) describes both the affinity and the rate of cholinesterase phosphorylation and is an indicator of inhibitory potency (Kousba et al 2004 Kardos and Sultatos, 2000 Amitai et al., 1998 Carr and Chambers, 1996). A typical determination is illustrated in Fig. 10 for the in vitro inhibition of rat BuChE with chlorpyrifos-oxon. In this example, the Kj was determined by incubating BuChE with varying concentrations of ehloropyrifos-oxon (0.25-5 nAf) the maximum inhibition ranged from 10 to 90% during a 7- to 30-min incubation period (Kousba et al., 2003). The slopes obtained from this analy.sis were then analyzed by linear regression to calculate a K (Fig. lOB). Similar in vitro approaches have been used to calculate the spontaneous first-order reactivation... 

Disregarding the tunnel effects (see Sect. 1.5) and staying within the approximation rigid rotator-harmonic oscillator, one may, for the biomolecular reaction A -h B), calculate the kinetic isotopic effect (ratio between the reaction rate constant of the compound with the light isotope and the rate constant K2 of the compound containing the heavy isotope) from the Bigeleisen equation ... 

The measured dissociation constants of biomolecular protein-protein complexes cover a range from roughly 10-3 to 10-13 M, corresponding to binding affinities up to about 18 kcal/mol. Association rates fall in the range 103 to 1010 M-1 s-1, and dissociation rates range from 103 to 10-8 s-1. 

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