General acid-base catalysis mechanisms

The Lysozyme Mechanism Involves General Acid-Base Catalysis... 

Carbonyl reactions are extremely important in chemistry and biochemistry, yet they are often given short shrift in textbooks on physical organic chemistry, partly because the subject was historically developed by the study of nucleophilic substitution at saturated carbon, and partly because carbonyl reactions are often more difhcult to study. They are generally reversible under usual conditions and involve complicated multistep mechanisms and general acid/base catalysis. In thinking about carbonyl reactions, 1 find it helpful to consider the carbonyl group as a (very) stabilized carbenium ion, with an O substituent. Then one can immediately draw on everything one has learned about carbenium ion reactivity and see that the reactivity order for carbonyl compounds ... 

Generally, HNLs utilize an acid-base catalysis mechanism. The amino acid residues at active sites of these enzymes differ significantly, but share the common motif for cyanogenesis. 

As we have seen (Section 4, p. 191) the range of effective molarities associated with ring-closure reactions is very much greater than that characteristic of intramolecular general acid-base catalysis the main classification is therefore in terms of mechanism. By far the largest section (I, Tables A-D) gives EM s for intramolecular nucleophilic reactions. These can be concerted displacements (mostly at tetrahedral carbon), stepwise displacements (mostly addition-elimination reactions at trigonal carbon), or additions, and they have been classified in terms of the nucleophilic and electrophilic centres. 

Additional catalytic mechanisms employed by enzymes include general acid-base catalysis, covalent catalysis, and metal ion catalysis. Catalysis often involves transient covalent interactions between the substrate and the enzyme, or group transfers to and from the enzyme, so as to provide a new, lower-energy reaction path. 

Chymotrypsin is a serine protease with a well-understood mechanism, featuring general acid-base catalysis, covalent catalysis, and transition-state stabilization. 

Other mechanisms The active site can provide catalytic groups that enhance the probability that the transition state is formed. In some enzymes, these groups can participate in general acid-base catalysis in which amino acid residues provide or accept protons. In other enzymes, catalysis may involve the transient formation of a covalent enzyme-substrate complex. 

Figure 16.7 Mechanism of aspartyl proteases involving general acid-base catalysis and the formation of a protonated terahedral intermediate. Bottom Proposal by T. J. Rodriguez. T. A. Angeles, and T. D. Meek, Biochemistry 32, 12380 (1993), that the first step is peptide bond isomerization. This accounts for the observed inverse 15N/14N kinetic isotope effect, which implies that bonding with the N atom becomes stiffer in the transition state.

Comprehensive discussions are to be found in (a) M. L. Bender, Mechanisms of Homogeneous Catalysis from Protons to Proteins, Wiley, New York, 1971 (b) W. P. Jencks, Catalysis in Chemistry and Enzymology, McGraw-Hill, New York, 1969 (c) M. L. Bender, Ckem. Rev., 60, 53 (1960). For more specialized treatments of particular aspects, see (d) W. P. Jencks, Chem. Rev., 72, 705 (1972), general acid-base catalysis (e) S. L. Johnson, Advan. Phys. Org. Chem., 5,237 (1967), ester hydrolysis (f) L. P. Hammett, Physical Organic Chemistry, 2nd ed., McGraw-Hill, New York, 1970, chap. 10, acid—base catalysis. 

General acid-base catalysis is often the controlling factor in many mechanisms and acts via highly efficient and sometimes intricate proton transfers. Whereas log K versus pH profiles for conventional acid-base catalyzed chemical processes pass through a minimum around pH 7.0, this pH value for enzyme reactions is often the maximum. In enzymes, the transition metal ion Zn2+ usually displays the classic role of a Lewis acid, however, metal-free examples such as lysozyme are known too. Good examples of acid-base catalysis are the mechanisms of carbonic anhydrase II and both heme- and vanadium-containing haloperoxidase. 

Enzymatic Mechanisms General Acid-Base Catalysis I 259... 

It is a major challenge to elucidate the mechanisms responsible for the efficiencies of enzymes. Jencks (1) offered the following classification of the mechanisms by which enzymes achieve transition state stabilization and the resulting acceleration of the reactions proximity and orientation effects of reactants, covalent catalysis, general acid-base catalysis, conformational distortion of the reactants, and preorganization of the active sites for transition state complementarity. 

Figure 3 Idealized pH dependence of a ribozyme reaction. Ideal pH-species plots and pH-/cobs profiles according to a kinetic model for general acid/base catalysis. The solid lines depict a mechanism in which the species with the lower pKa (pKa,1) acts as the general base (shown by blue lines), and the species with the higher pKa (pKa,2) acts as the general acid (shown by red lines). The black line indicates the observed pH dependence of the reaction rate. The dotted lines simulate a mechanism in which the catalytic roles of the species with pKa,1 and pKa,2 have been switched. Adapted from References 34 and 35.

Bevilacqua PC. Mechanistic considerations for general acid-base catalysis by RNA revisiting the mechanism of the hairpin ribozyme. Biochemistry 2003 42 2259-2265. 

Perrotta AT, Shih I, Been MD. Imidazole rescue of a cytosine mutation in a self-cleaving rihozyme. Science 1999 286 123-126. Nakano S, Chadalavada DM, Bevilacqua PC. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 2000 287 1493-1497. 

A rate maximum is predicted, the position of which depends upon the relative magnitude of Ki and k lk Kz for path A, or and k jk K for path B. As is so frequently the case in general acid-base catalysis, it is difficult to distinguish between the two mechanisms from solvent... 

PT step, AGpj. This quantity is determined by the difference between the pKa s of the donor and acceptor (ApKJ. The value of this ApKa in water is the "chemical part" of the general acid-base catalysis and is independent of the specific enzyme active site. In fact, this effect can be simply considered as the result of using different reaction mechanisms with different reactants rather than an actual catalytic effect. The change of the given ApKa from its value in water to the corresponding value in the enzyme active site is a true catalytic effect. This change reflects the electrostatic effect of the enzyme active site which is the subject of the next section. 

General acid-base catalysis provides mechanisms for bringing about the necessary proton transfers without involving hydrogen or hydroxide ions, which are present in water at concentrations of only about 10 M under physiological conditions. At pHs near neutrality relatively weak acids and bases can compete with lyo-nium or lyate species because they can be present in much higher concentrations. 

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