Enzyme compartmentalization

Normal functioning of a cell, however, also requires the segregation of proteins to particular compartments such as the mitochondria, nucleus, and lysosomes. In regard to enzymes, compartmentation not only provides an opportunity for controlling the delivery of substrate or the exit of product but also permits competing reactions to take place simultaneously in different parts of a cell. We describe the mechanisms that cells use to direct various proteins to different compartments in Chapters 16 and 17. 

Nonallosterlc mechanisms for regulating protein activity Include proteolytic cleavage, which irreversibly converts inactive zymogens into active enzymes, compartmentation of proteins, and signal-Induced modulation of protein synthesis and degradation. 

In order to address the characteristics of biological models, we have to first define the basic principles of biological systems that a supramolecular model may mimic. Among the most important are selective molecular recognition of a molecular entity selective and highly accelerated modification of a substrate (typieal role of enzymes) compartmentalization and selective translocation of chemical species across boundaries (typieal role of biomembranes) harvesting and transformation of energy and self-replication. 

Many alkaloid biosynthetic enzymes have been localized to subcellular compartments other than the cytosol 260). Enzyme compartmentalization sequesters toxic alkaloids and pathway intermediates away from sensitive areas of the cell. The subcellular trafficking of biosynthetic intermediates might also create an important level of metabolic regulation. Understanding the subcellular compartmentalization of alkaloid pathways will show whether enzyme characteristics observed in vitro represent bona fide regulatory mechanisms in vivo. 

Since no small mediators are involved, it is possible to determine the specific accessibility to the electroactive electron-carrier protein, of various enzymes compartmentalized in intact membrane-bound environments. 

Two particularly interesting aspects of the pyruvate carboxylase reaction are (a) allosteric activation of the enzyme by acyl-coenzyme A derivatives and (b) compartmentation of the reaction in the mitochondrial matrix. The carboxy-lation of biotin requires the presence (at an allosteric site) of acetyl-coenzyme A or other acylated coenzyme A derivatives. The second half of the carboxylase reaction—the attack by pyruvate to form oxaloacetate—is not affected by CoA derivatives. 

COMPARTMENTALIZED PYRUVATE CARBOXYLASE DEPENDS ON METABOLITE CONVERSION AND TRANSPORT The second interesting feature of pyruvate carboxylase is that it is found only in the matrix of the mitochondria. By contrast, the next enzyme in the gluconeogenic pathway, PEP carboxykinase, may be localized in the cytosol or in the mitochondria or both. For example, rabbit liver PEP carboxykinase is predominantly mitochondrial, whereas the rat liver enzyme is strictly cytosolic. In human liver, PEP carboxykinase is found both in the cytosol and in the mitochondria. Pyruvate is transported into the mitochondrial matrix, where it can be converted to acetyl-CoA (for use in the TCA cycle) and then to citrate (for fatty acid synthesis see Figure 25.1). /Uternatively, it may be converted directly to 0/ A by pyruvate carboxylase and used in glu-... 

Pathways are compartmentalized within the cell. Glycolysis, glycogenesis, glycogenolysis, the pentose phosphate pathway, and fipogenesis occur in the cytosol. The mitochondrion contains the enzymes of the citric acid cycle, P-oxidation of fatty acids, and of oxidative phosphorylation. The endoplasmic reticulum also contains the enzymes for many other processes, including protein synthesis, glycerofipid formation, and dmg metabolism. 

In bacteria and plants, the individual enzymes of the fatty acid synthase system are separate, and the acyl radicals are found in combination with a protein called the acyl carrier protein (ACP). However, in yeast, mammals, and birds, the synthase system is a multienzyme polypeptide complex that incorporates ACP, which takes over the role of CoA. It contains the vitamin pantothenic acid in the form of 4 -phosphopan-tetheine (Figure 45-18). The use of one multienzyme functional unit has the advantages of achieving the effect of compartmentalization of the process within the cell without the erection of permeability barriers, and synthesis of all enzymes in the complex is coordinated since it is encoded by a single gene. 

Figure 34-7 summarizes the roles of the intermediates and enzymes of pyrimidine nucleotide biosynthesis. The catalyst for the initial reaction is cytosolic carbamoyl phosphate synthase II, a different enzyme from the mitochondrial carbamoyl phosphate synthase I of urea synthesis (Figure 29-9). Compartmentation thus provides two independent pools of carbamoyl phosphate. PRPP, an early participant in purine nucleotide synthesis (Figure 34-2), is a much later participant in pyrimidine biosynthesis.

Life originated in an aqueous environment enzyme reactions, cellular and subcellular processes, and so forth have therefore evolved to work in this milieu. Since mammals live in a gaseous environment, how is the aqueous state maintained Membranes accomplish this by internalizing and compartmentalizing body water. 

Chlorophyll b occurs as an accessory pigment of the light-harvesting systems in land plants and green algae, and comprises one-third (or less) of total chlorophyll. The biosynthesis of chlorophyll b has been an area of active research particularly regarding its compartmentalization in chloroplast membranes, identification of the gene for chlorophyllide a oxidase, and characterization of the enzymes involved. ... 

When the initial LA concentration is large, the quantity of substrate transferred to the aqueous phase allows the lipoxygenation to progress. This reaction consumes LA and produces HP, which favor the transfer of residual substrate between the two phases. Then catalysis and transfer have a reciprocal influence on each other. We demonstrated that the use of a non-allosteric enzyme in a compartmentalized medium permits the simulation of a co-operativity phenomenon. The optimal reaction rate in the two-phase system is reached for a high initial LA concentration 14 mM. Inhibition by substrate excess is observed in two-phase medium. 

A common characteristic of metabolic pathways is that the product of one enzyme in sequence is the substrate for the next enzyme and so forth. In vivo, biocatalysis takes place in compartmentalized cellular structure as highly organized particle and membrane systems. This allows control of enzyme-catalyzed reactions. Several multienzyme systems have been studied by many researchers. They consist essentially of membrane- [104] and matrix- [105,106] bound enzymes or coupled enzymes in low water media [107]. 

PBPK and classical pharmacokinetic models both have valid applications in lead risk assessment. Both approaches can incorporate capacity-limited or nonlinear kinetic behavior in parameter estimates. An advantage of classical pharmacokinetic models is that, because the kinetic characteristics of the compartments of which they are composed are not constrained, a best possible fit to empirical data can be arrived at by varying the values of the parameters (O Flaherty 1987). However, such models are not readily extrapolated to other species because the parameters do not have precise physiological correlates. Compartmental models developed to date also do not simulate changes in bone metabolism, tissue volumes, blood flow rates, and enzyme activities associated with pregnancy, adverse nutritional states, aging, or osteoporotic diseases. Therefore, extrapolation of classical compartmental model simulations... 

Another approach, developed in our laboratory, consists of the compartmentalization of the sensing layer25"27. This concept, only applicable for multi-enzyme based sensors, consist in immobilizing the luminescence enzymes and the auxiliary enzymes on different membranes and then in stacking these membranes at the sensing tip of the optical fibre sensor. This configuration results in an enhancement of the sensor response, compared with the case where all the enzymes are co-immobilized on the same membrane. This was due to an hyperconcentration of the common intermediate, i.e. the final product of the auxiliary enzymatic system, which is also the substrate of the luminescence reaction, in the microcompartment existing between the two stacked membranes. 

Berger A., Blum L. J., Enhancement of the response of a lactate oxidase/peroxidase-based fiberoptic sensor by compartmentalization of the enzyme layer, Enzyme Microb. Technol. 1994 16 979-984. 

Of the large number of protein interactions that take place in cells, perhaps the vast majority may be described as transient. Most proteins that modify other molecules do so very rapidly and so interact only briefly with their substrates or binding partners (i.e., enzymes). In addition, since proteins within cells are highly compartmentalized, the affinity of most interactions doesn t have to be very great, because each potential binding partner is within short diffusion distances and the relative concentration of molecules within these small volumes is high. 

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