Simple Enzyme Models

From the rate studies the macrotricyclic quaternary ammonium host 25 emerges as an efficient though very simple enzyme model It is a water soluble compound of well defined structure and size which possesses one molecular cavity (active site). Substrate binding occurs there in a specific fashion and may initiate catalysis in certain reactions. The rate effects demonstrate reaction — as well as substrate specificity and originate in principal from entropic and enthalpic diminution of the rate limiting free enthalpy barrier. Even kinetic positive cooperativity can be observed. 

CD derivatives have wide applications in analogue enzyme and analysis chemistry. CD derivative with special functional group can be used as a simple enzyme model which is convenient for studying the action mode and functional groups of the enzyme. The fluorescent and chromophore groups linked to the CDs can be seen as an indicator or a probe which are beneficial for separating the isomers and enantiomers. 

The concept of electrostatic complimentarity is somewhat meaningless without the ability to estimate its contribution to AAg. Thus, it is quite significant that the electrostatic contribution to AAthat should be evaluated by rigorous FEP methods can be estimated with a given enzyme-substrate structure by rather simple electrostatic models (e.g., the PDLD model). It is also significant that calculated electrostatic contributions to A A g seem to account for its observed value (at least for the enzymes studied in this book). This indicates that simple calculations of electrostatic free energy can provide the correlation between structure and catalytic activity (Ref. 10). 

The carboxyl proteases are so called because they have two catalytically essential aspartate residues. They were formerly called acid proteases because most of them are active at low pH. The best-known member of the family is pepsin, which has the distinction of being the first enzyme to be named (in 1825, by T. Schwann). Other members are chymosin (rennin) cathepsin D Rhizopus-pepsin (from Rhizopus chinensis) penicillinopepsin (from Penicillium janthinel-lum) the enzyme from Endothia parasitica and renin, which is involved in the regulation of blood pressure. These constitute a homologous family, and all have an Mr of about 35 000. The aspartyl proteases have been thrown into prominence by the discovery of a retroviral subfamily, including one from HIV that is the target of therapy for AIDS. These are homodimers of subunits of about 100 residues.156,157 All the aspartyl proteases contain the two essential aspartyl residues. Their reaction mechanism is the most obscure of all the proteases, and there are no simple chemical models for guidance. 

The development of magnetic resonance techniques coupled with computer time averaging has made the study of enzyme structure and function by these techniques more fruitful. H NMR, 13C NMR and 19F NMR have been used successfully to determine the structure of B 12-compounds in solution. We are rapidly approaching the point where the structure and function of the B 12-coenzymes will be completely understood, and the need for the synthesis and study of simple Bi2-model compounds such as the cobaloximes (3) will be no longer necessary. However, even though studies on the chemistry of B 12-coenzymes is a necessary prerequisite to our understanding of their biochemical role, it is a wrong assumption to expect that the chemical properties of free coenzymes in aqueous solution should be duplicated in the enzymes. 

We take two cases in which mineral surfaces catalyze oxidation or reduction, and one in which a consortium of microbes, modeled as if it were a simple enzyme, promotes a redox reaction. In Chapter 33, we treat the question of modeling the interaction of microbial populations with geochemical systems in a more general way. 

As stated earlier, to make such a catalytic center is not a simple job. However, it can be said with confidence that, in view of the successes with some of the structures described here, the goal appears a great deal more attainable now than it was two decades ago when Morawetz, Bender, Bruice, and others began looking at enzyme models. 

This chapter aims to summarize our efforts to investigate the effects of fluorinated amino acid substitutes on the interactions with natural protein environments. In addition to a rather specific example concerning the interactions of small peptides with a proteolytic enzyme, we present a simple polypeptide model that aids for a systematic investigation of the interaction pattern of amino acids that differ in side chain length as well as fluorine content within both a hydrophobic and hydrophilic protein environment. Amino acid side chain fluoiination highly affects polypeptide folding due to steric effects, polarization, and fluorous interactions. 

Some energy diagram models of simple enzymic reactions are shown in Figure 8.1. A schematic model for an advantageous binding of the substrate on the enzyme active center is illustrated in Figure 8.2. 

Lehn and coworkers have profitably employed tartaric acid-containing crown ethers as enzyme models. The rate of proton transfer to an ammonium-substituted pyridinium substrate from a tetra-l,4-dihydropyridine-substituted crown ether was considerably enhanced compared to that for a simple 1,4-dihydropyridine. The reaction showed first order kinetic data and was inhibited by potassium ions. Intramolecular proton transfer from receptor to substrate was thus inferred via the hydrogen bonded receptor-substrate complex shown in Figure 16a (78CC143). 

A benzoyl benzoate substituent in 6-position of p-cyclodcxtrine can act as redox catalyst for the cathodic cleavage of a benzylester-cyclodextrine inclusion compound. Thus, a simple redox enzyme model was formed... 

In cases where the natural amino acid side chains of enzymes are insufficient to carry out a desired reaction, the enzyme frequently uses coenzymes. A coenzyme is bound by the enzyme along with the substrate, and the enzyme catalyses the bimolecular reaction between the coenzyme and the substrate (cf. Section 2.6.3). A simple model for a-amino acid synthesis by transamination was developed by substituting /I-cyclodextrin with pyridoxamine. Pyridoxamine is able to carry out the transformation of a-keto acids to a-amino acids even without the presence of the cyclodextrin, but with the cyclodextrin cavity as well, the enzyme model proves to be more selective and transaminates substrates with aryl rings bound strongly by the cyclodextrin much more rapidly than those having little affinity for the cyclodextrin. Thus (p-le/f-butylphenyl) pyruvic acid and phenylpyruvic acid are transaminated respectively 15 000 and 100 times faster then pyruvic acid itself, to give (p-le/f-butylphenyl) alanine and phenylalanine (Scheme 12.5). 

Understanding of how the nitrogenases work can be derived not only from studies on the reaction with N2 but also from investigation of the wide variety of other small, unsaturated molecules that the enzyme is capable of transforming, shown in Table 1. We will not discuss all the alternative substrates here, but restrict our attention to those areas investigated by using the complementary approach of studies on the enzyme and in simple chemical models. Although the reduction... 

There have been a few reports of first generation coordination complex structural models for the phosphatase enzyme active sites (81,82), whereas there are some examples of ester hydrolysis reactions involving dinuclear metal complexes (83-85). Kim and Wycoff (74) as well as Beese and Steitz (80) have both published somewhat detailed discussions of two-metal ion mechanisms, in connection with enzymes involved in phosphate ester hydrolysis. Compared to fairly simple chemical model systems, the protein active site mechanistic situation is rather more complex, because side-chain residues near the active site are undoubtedly involved in the catalysis, i.e, via acid-base or hydrogenbonding interactions that either facilitate substrate binding, hydroxide nucleophilic attack, or stabilization of transition state(s). Nevertheless, a simple and very likely role of the Lewis-acidic metal ion center is to... 

Ballester, Vidal-Ferran, and van Leeuwen evaluate concepts and strategies in the field of supramolecular catalysis. The authors describe what characterizes supramolecular catalysts, formulating a definition on the basis of the nature of interactions between catalyst and substrate or between building blocks of the catalyst. Examples are cited that demonstrate how supramolecular catalysts are superior to simple molecular catalysts in a broad range of reactions. Ballester et al. consider supramolecular catalysts as enzyme models, guided in their comparisons by the various mechanisms by which enzymes accelerate chemical transformations such as the binding of a reactant next to the catalytic site, the simultaneous complexation of two reactants, or desolvation. Addressing the synthesis of supramolecular catalysts, the authors describe how... 

For a variety of reasons (7) none of the [MoOS] " complexes described above constitute realistic enzyme models. The complexes in 2 and 3 do, however, demonstrate the feasibility of producing oxo-thio- and dithio-Mo(VI) complexes in addition to the simple thiomolybdates in 1. 

This chapter is a preview rather than a review. Most of the selective chemical methods for peptide cleavage have been thought about or tested only very recently. Although these methods have been applied to simple peptide models, only a few field studies with enzymes and proteins have been pursued. However, these chemical methods introduce a new challenging approach which may make possible structural work on more complex proteins with large molecular weights. 

Figure 10.16. Simple Sequential Model for a Tetrameric Allosteric Enzyme. The binding of a ligand (L) to a subunit changes the conformation of that particular subunit from the T (square) to the R (circle) form. This transition affects the affinity of the other subunits for the ligand.

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