Meaning of diffusion-controlled association rate constants in enzymology

Abstract

In the first stage of enzyme-ligand interactions diffusion-controlled association occurs which may be the most common and simplest elementary process. The rate constant for the diffusion-controlled association can be calculated by using suitable theoretical equations. The deviation of experimental values from results calculated by using the Smoluchowski equation suggests the existence of a restricted target area on the enzyme surface. Recently, a crevice or capture-window model has been proposed which appears more realistic in terms of known enzyme structures. A simple alternative capture window model is proposed. The viscosity dependence of an apparent association rate constant is interpreted in terms of diffusion-controlled formation and dissociation (fe-i) of an encounter complex followed by a nondiffusion-controlled reaction (k2). For the reaction of pnitroperbenzoic acid with horseradish peroxidase, km = 1.3 X 108 M"1 s'1 and k^/k2 = 2,2 in water at 25 °C. Publication costs assisted by Tohoku UniversityThe binding of alkali metal cation with poly(oxyethylene) was studied by means of conductometry in methanol. Apparent binding constants, KA, were determined by assuming the existence of discrete binding sites distributed every a monomer units along the polymer chain. KA increased in the order Li < Na < K < Cs < Rb. For large anions, such as thiocyanate or perchlorate, the formation of an ion pair complex was indicated. KA and a increased rapidly with decreasing salt concentration. This result was interpreted by the increased electrostatic repulsion between bound ions. The linear relationship between a1/2 and Cs"1/2 conforms to the Gaussian distribution of the segment between charges as well as to the partial retention of crystalline conformation of the poly-(oxyethylene)-ion complex.

Structure of Horseradish Perosidase Compound I

“…This value is consistent with literature values of 4.0 x lo7 M-' s-' and 3.7 x lo' M-' s-' which were obtained at acidicpH values [13,14]. The secondorder rate constant for horseradish peroxidase compound I formation using p-nitroperbenzoic acid as the oxidizing substrate has been reported to decrease with increase in pH.…”

The Complete Pathway for Catalytic Activation of the Mitogen-activated Protein Kinase, ERK2

“…In such experiments, initial-rate measurements are performed in buffer containing increasing concentrations of a microviscosogen (8,11). We have employed sucrose as the microviscosogenic agent and, under such conditions, all kinetic steps (Scheme 1) can be resolved (9). Scheme 1 depicts the addition of substrate MBP to the enzyme⅐ATP complex.…”

Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions

“…Effect of Solvent Viscosity on AGAO Activity-To further probe the equilibrium shift between TPQ amr and TPQ sq , we examined the dependence of catalytic activity on solvent viscosity, which can perturb diffusion-controlled steps, including substrate binding, product release, and conformational changes of the enzyme (58,59). Glycerol (M r ϭ 92.1) and sucrose (M r ϭ 342.3) were used as viscogens.…”