Enzyme diffusion-controlled

The quantity kcat/Km is a rate constant that refers to the overall conversion of substrate into product. The ultimate limit to the value of k at/Km is therefore set by the rate constant for the initial formation of the ES complex. This rate cannot be faster than the diffusion-controlled encounter of an enzyme and its substrate, which is between 10 to 10 per mole per second. The quantity kcat/Km is sometimes called the specificity constant because it describes the specificity of an enzyme for competing substrates. As we shall see, it is a useful quantity for kinetic comparison of mutant proteins. 

Enzymes Whose Acat/Approaches the Diffusion-Controlled Rate of Association with Substrate ... 

We have already mentioned the application of supercomputers to biochemical simulations. Internal dynamics may play an Important role In such simulations. An example would be enzyme binding-site fluctuations that modulate reactivity or the dynamics of antigen-antibody association (11). In the specific case of diffusion-controlled processes, molecular recognition may occur because of long-range sterlc effects which are hard to assess without very expensive simulations (12.)-... 

Approximation refers to the bringing together of the substrate molecules and reactive functionalities of the enzyme active site into the required proximity and orientation for rapid reaction. Consider the reaction of two molecules, A and B, to form a covalent product A-B. For this reaction to occur in solution, the two molecules would need to encounter each other through diffusion-controlled collisions. The rate of collision is dependent on the temperature of the solution and molar concentrations of reactants. The physiological conditions that support human life, however, do not allow for significant variations in temperature or molarity of substrates. For a collision to lead to bond formation, the two molecules would need to encounter one another in a precise orientation to effect the molecular orbitial distortions necessary for transition state attainment. The chemical reaction would also require... 

Simultaneous generation of nitric oxide and superoxide by NO synthases results in the formation of peroxynitrite. As the reaction between these free radicals proceeds with a diffusion-controlled rate (Chapter 21), it is surprising that it is possible to detect experimentally both superoxide and NO during NO synthase catalysis. However, Pou et al. [147] pointed out that the reason is the fact that superoxide and nitric oxide are generated consecutively at the same heme iron site. Therefore, after superoxide production NO synthase must cycle twice before NO production. Correspondingly, there is enough time for superoxide to diffuse from the enzyme and react with other biomolecules. 

The Bronsted relationship can be strictly accurate only over a certain range of acid and base strengths. When has diffusion-controlled values, which of course cannot be exceeded, the linear plot of log k/ y vs log must level off to a zero slope, that is a = 0. As well as being reported, although rarely, in simple metal complexes, the resultant curvature in the Bronsted plot is also shown by the zinc enzyme carbonic anhydrase (Chap. 8. Zn(II)). In... 

The cholinesterases, acetylcholinesterase and butyrylcholinesterase, are serine hydrolase enzymes. The biological role of acetylcholinesterase (AChE, EC 3.1.1.7) is to hydrolyze the neurotransmitter acetylcholine (ACh) to acetate and choline (Scheme 6.1). This plays a role in impulse termination of transmissions at cholinergic synapses within the nervous system (Fig. 6.7) [12,13]. Butyrylcholinesterase (BChE, EC 3.1.1.8), on the other hand, has yet not been ascribed a function. It tolerates a large variety of esters and is more active with butyryl and propio-nyl choline than with acetyl choline [14]. Structure-activity relationship studies have shown that different steric restrictions in the acyl pockets of AChE and BChE cause the difference in their specificity with respect to the acyl moiety of the substrate [15]. AChE hydrolyzes ACh at a very high rate. The maximal rate for hydrolysis of ACh and its thio analog acetyl-thiocholine are around 10 M s , approaching the diffusion-controlled limit [16]. 

Importantly, carbonic anhydrase II is one of the most efficient biological catalysts known and it catalyzes the hydration of CO2 with a turnover rate of 10 sec at 25 C (Khalifah, 1971 Steiner et al, 1975). With kcaJKm = 1.5 X 10 sec carbonic anhydrase II is one of a handful of enzymes for which catalysis apparently approaches the limit of diffusion control. Since transfer of the product proton away from the enzyme to bulk solvent comprises a kinetic obstacle [an enzyme-bound group with ap/C, of about 7 cannot transfer a proton to bulk solvent at a rate faster than 10 sec (for a review see Eigen and Hammes, 1963)], the observed turnover rate of 10 sec" requires the participation of buffer in the proton transfer. 

Since enzyme catalysis and regulation are dynamic processes, the dynamics of hydrogen bonding is also an important consideration. In relatively weakly hydrogen bonding solvents, such as the first four entries in Table I, the association rate is essentially diffusion controlled, whereas the association rate constants for the last two entries are considerably less than expected for a diffusion-controlled process. This can be understood... 

As noted earlier, peroxynitrite is formed with a diffusion-controlled rate from superoxide and nitric oxide (Reaction 10). As both these radicals are ubiquitous species, which present practically in all cells and tissues, peroxynitrite can be the most important species responsible for free radical-mediated damage in biological systems. Moreover, it is now known that NO synthases are capable of producing superoxide and nitric oxide simultaneously (see Chapter 22), greatly increasing the possible rate of peroxynitrite production. In addition, another enzyme xanthine dehydrogenase is also able to produce peroxynitrite in the presence of nitrite... 

TABLE 6-8 Enzymes for Which kcat/Km Is Close to the Diffusion-Controlled Limit (10s to 109 m H )... 

From this we see that kcat/Km is the apparent second-order rate constant for the reaction of free enzyme with substrate. As such it cannot exceed the diffusion controlled limit /cD of Eqs. 9-28 to 9-30 which falls in the range of 109 - 1011 M 1 s-1. Experimentally observed... 

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