Enzymic Function

For a long time erythrocuprein was thought to act exclusively as a copper-transporting protein. This was a very attractive conclusion since over 50% of the erythrocyte copper content is present in erythrocuprein (60). However, in the absence of any known function of a metalloprotein, it is always tempting to assign to it the role of storage or transport of the respective metal ions. For example, caeruloplasmin was considered to be the main copper-transporting protein in blood plasma. It subsequently turned out that this copper protein is a key enzyme in iron metabolism, responsible for the oxidation of Fe2+ to the Fe3+ bound in transferrin (130—132). 

The enzymic-catalyzed reduction of cytochrome cox using the xanthine - xanthine oxidase reaction led to the assumption that Oi- was the active reducing agent (133). Myoglobin and carboanhydrase were able 

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If a catalyst is to work well in solution, it (and tire reactants) must be sufficiently soluble and stable. Most polar catalysts (e.g., acids and bases) are used in water and most organometallic catalysts (compounds of metals witli organic ligands bonded to tliem) are used in organic solvents. Some enzymes function in aqueous biological solutions, witli tlieir solubilities detennined by the polar functional groups (R groups) on tlieir outer surfaces. 

Enzymes. Protein engineering has been used both to understand enzyme mechanism and to selectively modify enzyme function (4,5,62—67). Much as in protein stabiUty studies, the role of a particular amino acid can be assessed by replacement of a residue incapable of performing the same function. An understanding of how the enzyme catalyzes a given reaction provides the basis for manipulating the activity or specificity. 

Disease States. Rickets is the most common disease associated with vitamin D deficiency. Many other disease states have been shown to be related to vitamin D. These can iavolve a lack of the vitamin, deficient synthesis of the metaboUtes from the vitamin, deficient control mechanisms, or defective organ receptors. The control of calcium and phosphoms is essential ia the maintenance of normal cellular biochemistry, eg, muscle contraction, nerve conduction, and enzyme function. The vitamin D metaboUtes also have a function ia cell proliferation. They iateract with other factors and receptors to regulate gene transcription. 

The most numerous cases of homogeneous catalysis are by certain ions or metal coordination compounds in aqueous solution and in biochemistry, where enzymes function catalyticaUy. Many ionic effects are known. The hydronium ion and the hydroxyl ion OH" cat-... 

Proteins are the indispensable agents of biological function, and amino acids are the building blocks of proteins. The stunning diversity of the thousands of proteins found in nature arises from the intrinsic properties of only 20 commonly occurring amino acids. These features include (1) the capacity to polymerize, (2) novel acid-base properties, (3) varied structure and chemical functionality in the amino acid side chains, and (4) chirality. This chapter describes each of these properties, laying a foundation for discussions of protein structure (Chapters 5 and 6), enzyme function (Chapters 14-16), and many other subjects in later chapters. 

Enzymes are complex molecules, usually proteins, that speed up chemical reactions. Figure 2 illustrates in graphic form how enzymes function. To fully understand Figure 2, imagine a chemical reaction in which a part of one compound is transferred to another compound ... 

Handedness is also important in organic and biological chemistry, where it arises primarily as a consequence of the tetrahedral stereochemistry of 5p3-hybridized carbon atoms. Many drugs and almost all the molecules in our bodies, for instance, are handed. Furthermore, it is molecular handedness that makes possible the specific interactions between enzymes and their substrates that are so crucial to enzyme function. We ll look at handedness and its consequences in this chapter. 

Enzymes function through a pathway that involves initial formation of an enzyme-substrate complex E S, a multistep chemical conversion of the enzyme-bound substrate into enzyme-bound product E - P, and final release of product from the complex. 

If we consider natural synthetic processes, enzymes are seen to exert complete control over the enantiomeric purity of biomolecules (see Figure 8.2). They are able to achieve this because they are made of single enantiomers of amino adds. The resulting enantiomer of the enzymes functions as a template for the synthesis of only one enantiomer of the product Moreover, the interaction of an enzyme with the two enantiomers of a given substrate molecule will be different. Biologically important molecules often show effective activity as one enantiomer, the other is at best ineffective or at worst detrimental. 

Generally speaking we consider that most micro-organisms live and grow in aqueous environments, and that the cytoplasm within cells in which enzymes function is also aqueous. On die other hand, most lipids are only sparingly soluble in aqueous media. Cholesterol, for example, has a solubility of less than 2 mg l 1 (equivalent to a concentration of less than 5 pmol l 1). Even at much lower concentrations (25-40 nmol l 1) it tends to aggregate into micelles. There is, therefore, a general problem of how to supply lipid substrates at sufficient concentration to produce reaction kinetics that are appropriate for industrial purposes. 

McCord, J. M., and Fridovich, I. (1969). Superoxide dismutase an enzymic function for erythrocuprein (hemocuprein)./. Biol. Chem. 244 6049-6055. 

In addition, eNOS is subject to protein phosphorylation. It can be phosphotylated on several serine (Ser), threonine (Thr), and tyrosine (Tyr) residues however, major changes in enzyme function have been reported for the phosphorylation of amino acid residues Seri 177 and Thr495 (in the human eNOS sequence) (Fig. 3). 

Enzyme Functional effects of polymorphism and frequency Examples for the medical impact... 

In principle, numerous reports have detailed the possibility to modify an enzyme to carry out a different type of reaction than that of its attributed function, and the possibility to modify the cofactor of the enzyme has been well explored [8,10]. Recently, the possibility to directly observe reactions, normally not catalyzed by an enzyme when choosing a modified substrate, has been reported under the concept of catalytic promiscuity [9], a phenomenon that is believed to be involved in the appearance of new enzyme functions during the course of evolution [23]. A recent example of catalytic promiscuity of possible interest for novel biotransformations concerns the discovery that mutation of the nucleophilic serine residue in the active site of Candida antarctica lipase B produces a mutant (SerlOSAla) capable of efficiently catalyzing the Michael addition of acetyl acetone to methyl vinyl ketone [24]. The oxyanion hole is believed to be complex and activate the carbonyl group of the electrophile, while the histidine nucleophile takes care of generating the acetyl acetonate anion by deprotonation of the carbon (Figure 3.5). 

HIV integrase consists of three distinct domains. The N-terminal domain contains a HHCC motif that coordinates a zinc atom that is required for viral cDNA integration. Three highly conserved amino acids (D,D-35-E) are embedded in the core domain, which form the acidic catalytic triad coordinating one or possibly two divalent metals (Mn + or Mg +). The C-terminal domain (residues 213-288) is responsible for unspecific DNA binding and adopts an overall SH3 fold (Chiu and Davies 2004). The enzyme functions as a multimer and to this end all three domains can form homodimers. 

The enzyme systems responsible for fixing atmospheric N2 to form ammonia are known as the nitrogenases. These enzymes function at field temperatures and 0.8 atm N2 pressure, whereas the industrial Haber-Bosch process requires high temperatures (300-400°C) and high pressures (200-300 atm) in a capital-intensive process that relies on burning fossil fuel. Small wonder, then, that the chemistry of the nitrogenases has attracted considerable attention for many years. 

Bowlus, R.D. Somero, G.N. (1979). Solute compatibility with enzyme function and structure rationales for the selection of osmotic agents and end products of anaerobic metabolism in marine invertebrates. Journal of Experimental Zoology, 208, 137-52. 

Szklarz GD, Graham SE, Paulsen MD. Molecular modeling of mammalian cytochromes P450 application to study enzyme function. Vitamins Hormones 2000 58 53-87. 

Protein phosphorylation-dephosphorylation is a highly versatile and selective process. Not all proteins are subject to phosphorylation, and of the many hydroxyl groups on a protein s surface, only one or a small subset are targeted. While the most common enzyme function affected is the protein s catalytic efficiency, phosphorylation can also alter the affinity for substrates, location within the cell, or responsiveness to regulation by allosteric ligands. Phosphorylation can increase an enzyme s catalytic efficiency, converting it to its active form in one protein, while phosphorylation of another converts it into an intrinsically inefficient, or inactive, form (Table 9—1). 

Fischer F, S Kunne, S Fetzner (1999) Bacterial 2,4-dioxygenases new members of the a/p hydrolase-fold superfamily of enzymes functionally related to serine hydrolases. J Bacterial 181 5725-5733. 

The pathway of the metabolic process converting the original nutrients, which are of rather complex composition, to the simple end products of COj and HjO is long and complicated and consists of a large number of intermediate steps. Many of them are associated with electron and proton (or hydrogen-atom) transfer from the reduced species of one redox system to the oxidized species of another redox system. These steps as a rule occur, not homogeneously (in the cytoplasm or intercellular solution) but at the surfaces of special protein molecules, the enzymes, which are built into the intracellular membranes. Enzymes function as specific catalysts for given steps. 

N6. Neubauer, B. A., Pekrun, A., Eber, S. W Lakomek, M and Schroter, W., Relation between genetic defect, altered protein structure, and enzyme function in triose-phosphate isomerase (TPI) deficiency. Eur. J. Pediatr. 151,232a (1992). 

Until now our discussions of enzyme inhibition have dealt with compounds that interact with binding pockets on the enzyme molecule through reversible forces. Hence inhibition by these compounds is always reversed by dissociation of the inhibitor from the binary enzyme-inhibitor complex. Even for very tight binding inhibitors, the interactions that stabilize the enzyme-inhibitor complex are mediated by reversible forces, and therefore the El complex has some, nonzero rate of dissociation—even if this rate is too slow to be experimentally measured. In this chapter we turn our attention to compounds that interact with an enzyme molecule in such a way as to permanendy ablate enzyme function. We refer to such compounds as enzyme inactivators to stress the mechanistic distinctions between these molecules and reversible enzyme inhibitors. 

An affinity label is a molecule that contains a functionality that is chemically reactive and will therefore form a covalent bond with other molecules containing a complementary functionality. Generally, affinity labels contain electrophilic functionalities that form covalent bonds with protein nucleophiles, leading to protein alkylation or protein acylation. In some cases affinity labels interact selectively with specific amino acid side chains, and this feature of the molecule can make them useful reagents for defining the importance of certain amino acid types in enzyme function. For example, iodoacetate and A-ethyl maleimide are two compounds that selectively modify the sulfur atom of cysteine side chains. These compounds can therefore be used to test the functional importance of cysteine residues for an enzyme s activity. This topic is covered in more detail below in Section 8.4. 

Ethanolamine ammonia lyase has a molecular weight of 520,000 and consists of 8 or 10 subunits. Two 5 -deoxyadenosylcobalamin molecular bind per enzyme molecule, and recent kinetic studies by Babior show that these two molecules carry out catalysis independently. Evidence is available that this enzyme functions by a radical mechanism since both spin labeling and Co(II) esr experiments indicate that Co(II) is an intermediate during H-transfer. Also, 5 -deoxyadenosine has been detected as a product of oxygenation of the enzyme-substrate complex (99—101). 

Most enzymes are very specific in their activity, and each chemical reaction in a living organism requires a specific enzyme. Their specificity arises from what is known as an active site, a location in the enzyme s molecule that has a shape matching that of a part of the molecule with which it reacts. The activity of the enzymes is affected by such factors as temperature and pH, each enzyme functioning best within a specific range of temperatures and pH. Outside this range the enzymes are structurally altered and their activity is either impaired or terminated. 

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