Catalysts, proteins

While hydrolysis is a thermodynamically favored reaction, the amide and phosphoester bonds of polypeptides and ohgonucleotides are stable in the aqueous environment of the cell. This seemingly paradoxic behavior reflects the fact that the thermodynamics governing the equihbrium of a reaction do not determine the rate at which it will take place. In the cell, protein catalysts called enzymes are used to accelerate the rate... 

Higher organisms often elaborate several physically distinct versions of a given enzyme, each of which catalyzes the same reaction. Like the members of other protein families, these protein catalysts or isozymes arise through gene duplication. Isozymes may exhibit subtle differences in properties such as sensitivity to... 

During the development phase of the RNA world, there were no functioning processes which were influenced by protein catalysts. 

The information crisis , i.e., the fact that, because of the error frequency, longer RNA chains have so many errors after only a few reproduction steps that they can no longer be replicated, cries out for catalysts which can guarantee more exact replication. While only protein catalysts (enzymes) had been discussed until recently, ri-bozymes are now possible candidates. More complex catalysts would have required more complex matrices but where did the matrix molecules come from This serious problem, referred to by Eigen himself as an information crisis, is sometimes referred to as Eigen s dilemma (Blomberg, 1997). 

Significant advances have been made in the preparation of discrete macromolecules that include both coenzyme function and a defined polypeptide or protein architecture. Preliminary, but promising, functional studies have been carried out and assay methods developed. While in many cases rather modest effects have been observed, what is significant is that the methodology exists to prepare, characterize, and study defined macromolecular constructs. With new information becoming available on co enzyme-dependent protein catalysts from structural biology and mechanistic enzymology, it should be possible to more fully exploit the remarkable breadth of coenzyme reactivity in tailored synthetic systems. 

The problem to be solved with respect to the chemical reactions that constitute metabolism and sustain life is that, without the action of catalysts, they are far too slow. Let s consider the digestion of the proteins themselves, an important constituent of our diet. In an enviromnent similar to that of our digestive system, several tens of thousand years would be required to digest half of the protein content of a typical meal in the absence of a catalyst. Clearly, this will not do. In reality, the stomach secretes one protein catalyst, the enzyme pepsin, and the pancreas secretes several enzymes that catalyze the digestion of proteins. In the presence of these enzymes, dietary proteins are fully digested and reduced to their basic constituents, the amino acids, in a matter of hours. Obviously, these enzymes are enormously potent catalysts." ... 

Scheme 2.19 Asymmetric reduction of alkene 46 using a hybrid transition metal/protein catalyst.

Cieus M, Ward TR. Designed evolution of artificial metalloenzymes protein catalysts made to order. Org Biomol Chem 2007 5 1835-1844. 

Primitive translation system develops, with RNA genome and RNA-protein catalysts... 

DNA genome, translated on RNA-protein complex (ribosome) with protein catalysts... 

Virtually all reactions in the body are mediated by enzymes, which are protein catalysts that increase the rate of reactions without being changed in the overall process. Among the many biologic reactions that are energetically possible, enzymes selectively channel reactants (called substrates) into useful pathways. Enzymes thus direct all metabolic events. This chapter examines the nature of these catalytic molecules and their mechanism of action. 

Enzymes are protein catalysts that increase the velocity of a chemical reaction, and are not consumed during the reaction they catalyze. [Note Some types of RNA can act like enzymes, usually catalyzing the cleavage and synthesis of phosphodiester bonds. RNAs with catalytic activity are called ribozymes (see p. 436), and are much less commonly encountered than protein catalysts.]... 

Self-splicing KNA. The precursor to the 26S rRNA of Tetrahymena contains a 413-nucleotide intron, which was shown by Cedi and coworkers to be selfsplicing, i.e., not to require a protein catalyst for maturation.581 582 This pre-rRNA is a ribozyme with true catalytic properties (Chapter 12). It folds into a complex three-dimensional structure which provides a binding site for free guanosine whose 3-OH attacks the phosphorus at the 5 end of the intron as shown in Fig. 28-18A, step a. The reaction is a simple displacement on phosphorus, a transesterification similar to that in the first step of pancreatic ribonuclease action (Eq. 12-25). The resulting free 3-OH then attacks the phosphorus atom at the other end of the intron (step b) to accomplish the splicing and to release the intron as a linear polynucleotide. The excised intron undergoes... 

Rothman, J. E., Polypeptide chain binding proteins Catalysts of protein folding and related processes in cells. Cell 59 591, 1989. A description of the proteins that are thought to be involved promoting the formation of three-dimensional structure in proteins. 

Additional reaction components can be used that may enhance or be essential for catalytic activity in a particular system. These components may serve functions analogous to the cofactors used by protein catalysts (e. g., ATP, NADH, or metal ions). These components can be supplied free in solution or incorporated into the RNA library as previously described. As an example, Figure 8.5 oudines the RNA-catalyzed carbon-carbon bond-forming [4 + 2] cycloadclition reaction between a tethered diene substrate, (2E.4E)-hexa-2,4-clien-l-0-PEG (1), and 1-biotinamido-4-[A -(maleimidomethyl)cyclohexanecarboxamido] butane (BMCC-biotin, 2), a clienophile that is free in solution. The RNA catalyzes the formation of (3), which contains biotin for partitioning purposes. 

Enzymes are protein catalysts of remarkable efficiency and specificity. Lipid, carbohydrate, nucleotide, or metal-containing prosthetic groups may be attached to these enzymes and serve as essential components of their catalyses by enhancing specificity and/or stability (8—13). Each enzyme has a specific temperature and pH range where it functions to its optimal capacity the optima for these proteins usually He between 37—47°C, and pH optima range from acidic, ie, 1.0 in the case of gastric pepsin, to alkaline, ie, 10.5 in the case of alkaline phosphatase. However, enzymes from extremely thermotolerant bacteria have become available these can function at or near the boiling point of water, and therapeutic use of these ultrastable proteins can be anticipated. 

Over the last 20 years, many reservations with respect to biocatalysis have been voiced, contending that (i) enzymes only feature limited substrate specificity (ii) there is only limited availability of enzymes (iii) only a limited number of enzymes exist (iv) protein catalyst stability is limited (v) enzyme reactions are saddled with limited space-time yield and (vi) enzymes require complicated cosubstrates such as cofactors. 

Protein catalyst stability is limited. This is one of major drawbacks of enzymes. They commonly require temperatures around ambient to perform (15-50°C), pH values around neutral (pH 5-9), and aqueous media. In addition, any number of system components or features such as salts, inhibitors, liquid-gas or liquid-solid interfaces, or mechanical stress can slow down or deactivate enzymes. Under almost any condition, native proteins, with their Gibbs free enthalpy of stability of just a few kilojoules per mole, are never far away from instability. In this book, we cover inhibitors (Chapter 5, Section 5.3) or impeding system parameters (Chapter 17) and successful attempts at broadening the choice of solvents (Chapter 12). 

The enzymes used to generate reactive quinone methides often undergo inactivation by addition of this electrophile to essential nucleophilic amino acid side chains of the protein catalyst. This is a type of suicide enzyme inhibition.80 This was observed for the acid phosphatase and ribonuclease catalysts used to generate 43.76 79 Alkaline phosphatase has been used to remove the phosphate protecting group from a derivative of an o-difluoromethyl phenyl phosphate that was covalently attached to a solid support. Breakdown of the immobilized 4-hydroxybenzyl difluoride gives an immobilized quinone methide that, in principle, will react irreversibly with proteins and lead to their attachment to the solid support.81... 

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