Enzyme general acid-base catalysis

Enzymes are often considered to function by general acid-base catalysis or by covalent catalysis, but these considerations alone cannot account for the high efficiency of enzymes. Proximity and orientation effects may be partially responsible for the discrepancy, but even the inclusion of these effects does not resolve the disparity between observed and theoretically predicted rates. These and other aspects of the theories of enzyme catalysis are treated in the monographs by Jencks (33) and Bender (34). 

No large conformational changes occur in the enzyme during catalysis, but many small movements take place. The structural basis for the catalytic power of ribonuclease thus resides in several different features tight, specihc binding of a strained conformation of the substrate, general acid-base catalysis by His-12 and His-119, and preferential stabilization of the transition state by ionic interactions with Lys-41. 

Most enzymes employ a combination of several catalytic strategies to bring about a rate enhancement. A good example of the use of both covalent catalysis and general acid-base catalysis is the reaction catalyzed by chymotrypsin. The first step is cleavage of a peptide bond, which is accompanied by formation of a covalent linkage between a Ser residue on the enzyme and part... 

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. 

Bovine pancreatic chymotrypsin (Mr 25,191) is a protease, an enzyme that catalyzes the hydrolytic cleavage of peptide bonds. This protease is specific for peptide bonds adjacent to aromatic amino acid residues (Trp, Phe, Tyr). The three-dimensional structure of chymotrypsin is shown in Figure 6-18, with functional groups in the active site emphasized. The reaction catalyzed by this enzyme illustrates the principle of transition-state stabilization and also provides a classic example of general acid-base catalysis and covalent catalysis. 

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. 

Effective concentration 65-72 entropy and 68-72 in general-acid-base catalysis 66 in nucleophilic catalysis 66 Elastase 26-30, 40 acylenzyme 27, 40 binding energies of subsites 356, 357 binding site 26-30 kinetic constants for peptide hydrolysis 357 specificity 27 Electrophiles 276 Electrophilic catalysis 61 metal ions 74-77 pyridoxal phosphate 79-82 Schiff bases 77-82 thiamine pyrophosphate 82-84 Electrostatic catalysis 61, 73, 74,498 Electrostatic effects on enzyme-substrate association rates 159-161... 

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. 

Ribonuclease A is a member of a group of enzymes that cleave RNA using general acid-base catalysis without a metal ion in the enzyme. In ribonuclease A, such catalysis is performed by two imidazoles of histidine units, one as the free base (Im) and the other, protonated, as the acid (ImH+). To mimic this in an artificial enzyme, we prepared (3-cyclodextrin bis-imidazoles 41 [124]. The first one was a mixture of the... 

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. 

Enzymes adopt conformations that are structurally and chemically complementary to the transition states of the reactions that they catalyze. Sets of interacting amino acid residues make up sites with the special structural and chemical properties necessary to stabilize the transition state. Enzymes use five basic strategies to form and stabilize the transition state (1) the use of binding energy, (2) covalent catalysis, (3) general acid-base catalysis, (4) metal ion catalysis, and (5) catalysis by approximation. Of the enzymes examined in this chapter, three groups of enzymes catalyze the addition of water to their substrates but have different requirements for catalytic speed and specificity, and a fourth group of enzymes must prevent reaction with water. 

Figure 37.2 depicts the action of chymolrypsin, with the imidazole group of histidine-57 playing the same role of general base as that just described—and with protonated imidazole necessarily acting as general acid. There is general acid-base catalysis of both reactions involved first, in the formation of the acyl enzyme, and then in its hydrolysis. 

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. 

W.P. Jencks, Structure-Reactivity Correlations and General Acid-Base Catalysis in Enzymic Transacylation Reactions, Cold Spring Harbor Symp. Quant. Biol, 1971, 36, 1. 

The information within an enzyme s active site (its shape and charge distribution) constrains the motions and allowed conformations of the substrate, making it appear more like the transition state. In other words, the information in the structure of the enzyme is used to optimally orient the substrate. As a result of this information transfer, the energy of the enzyme-substrate complex becomes closer to the AG, which means that the energy needed for the reaction to proceed to product is reduced. Consequently there is an increase in the rate of the enzyme-catalyzed reaction. Other factors, such as electrostatic effects, general acid-base catalysis, and covalent catalysis (discussed on pp. 177-180), also contribute to the increased rates of enzyme-catalyzed reactions over non-enzyme catalyzed reactions. 

FIGURE 6-9 Amino acids in general acid-base catalysis. Many organic reactions are promoted by proton donors (general acids) or proton acceptors (general bases). The active sites of some enzymes contain amino acid functional groups, such as those shown here, that can participate in the catalytic process as proton donors or proton acceptors. 

The main parts of this scheme were proposed earlier by Theorell and co-workers 119,291) on the basis of inhibitor binding and steady-state kinetic studies. Other suggested mechanisms based on general acid-base catalysis 297), reduction of the enzyme 362), or direct participation of histidine 363) or cysteine 364) in the hydride transfer step are highly unlikely in view of the crystallographic and kinetic results reviewed in this chapter. Contrary to expectations the mechanism described here is in most details very different from that proposed for lactic dehydrogenase 126). 

There is an interesting contrast between the large contribution (a factor of ca. 10 ) to the rate enhancement of intramolecular and enzyme-catalysed reactions by nucleophilic catalysis and the much smaller contribution (ca. 1-10) of general acid-base catalysis. 

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