Specificity, enzymatic

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Sulphones occur relatively rarely as natural products. Thus there is no reported specific enzymatic system for the formation of sulphones. However, there are several well-understood pathways for the oxidation of sulphides to sulphoxides and these do lead to sulphones in some cases. 

The previous chapters taught us how to ask questions about specific enzymatic reactions. In this chapter we will attempt to look for general trends in enzyme catalysis. In doing so we will examine various working hypotheses that attribute the catalytic power of enzymes to different factors. We will try to demonstrate that computer simulation approaches are extremely useful in such examinations, as they offer a way to dissect the total catalytic effect into its individual contributions. 

Another important specific enzymatic target is neuraminidase, which is found on the envelope of influenza viruses (see chapter by von Itzstein and Thomson, this... 

Drugs can also Interfere with laboratory results by negating certain nonspecific oxidation and reduction reactions essential for the chemical assay. Penicillin, streptomycin and ascorbic acid are known to react with cupric Ion thus, false positive results for glucose may occur If a copper reduction method Is used. If the specific enzymatic glucose-oxidase method Is employed, ascorbic acid can cause a false negative result by preventing the oxidation of a specific chromogen In the reaction. 

The file Is used routinely In the laboratory at the National Institutes of Health In an attempt to explain abnormal test results The resident physicians affiliated with the Clinical Chemistry Service discuss the results with the patient-care physicians and determine If the results were due to the patient s clinical state or to a drug effect This close monitoring of test results has led to recognition of deficiencies In what Is believed are specific enzymatic procedures for the measurement of glucose and uric acid Likewise, the gualac procedure for occult blood In feces was found to yield false negative results under certain circumstances This has prompted the development of a more specific procedure (Jaffe et al unpublished) ... 

Many antimicrobials undergo some degree of metabolism once ingested. Metabolism may occur via hepatic, renal, or non-organ-specific enzymatic processes. The route... 

The cAMP molecule serves as the second messenger, which carries out the effects of the hormone inside the cell. The primary function of cAMP is to activate protein kinase A. This kinase then attaches phosphate groups to specific enzymatic proteins in the cytoplasm. The phosphorylation of these enzymes enhances or inhibits their activity, resulting in the enhancement or inhibition of specific cellular reactions and processes. Either way, cellular... 

Mullis, K.B., Faloona, F., Scharf, S., Saiki, R., Horn, G. and Erlich, H. (1986) Specific enzymatic amplification of DNA in vitro the polymerase chain reaction. Cold Spring Harbor Symposium of Quantitative Biology 51, 263—273. 

Regarding the reductive debromination as the first step of deca-BDE degradation in mammals, Huwe and Smith [54] detected the formation of different PBDEs (three nona-BDEs, four octa-BDEs and one hepta-BDE) from deca-BDE degradation in rats, which also suggests the existence of a reductive debromination process as the first step in deca-BDE degradation in mammals. In this case, it was not identified whether the specific enzymatic system responsible for the reductive debromination and the corresponding analyses to detect the formation of hydroxylated metabolites were not carried out. 

F. Pouthas, C. Gentil, D. Cote, and U. Bockelmann, DNA detection on transistor arrays following mutation-specific enzymatic amplification. Appl. Phys. Lett. 84, 1594-1596 (2004). 

The enzymatic activities of O -chymotrypsin in solution and adsorbed at the different surfaces are presented in Fig. 11, where the specific enzymatic activity (defined as activity per unit mass of protein) is plotted as a function of temperature. The enzyme loses activity due to adsorption. On the hydrophobic Teflon and PS surfaces, the activity is completely gone, whereas on the hydrophilic silica surface, or-chymotrypsin has retained most of its biological function. These differences are in agreement with the adsorption isotherms and the circular dichroism spectra. The influence of the hydrophobicity of the sorbent surface on the affinity of the protein for the sorbent surface, as judged from the rising parts of the adsorption isotherms (Fig. 8), suggests that the proteins are more perturbed and, hence, less biologically active when adsorbed at hydrophobic surfaces. Also, the CD spectra indicate that adsorption-induced structural perturbations are more severe at hydrophobic surfaces. 

The diversity of functions within a microbial population is important for the multiple functions of a soil. The functional diversity of microbial communities has been found to be very sensitive to environmental changes (Zak et al. 1994 Kandeler et al. 1996,1999). However, the methods used mainly indicate the potential in vitro functionality. Functional diversity of microbial populations in soil may be determined by either expression of different enzymes (carbon utilization patterns, extracellular enzyme patterns) or diversity of nucleic acids (mRNA, rRNA) within cells, the latter also reflecting the specific enzymatic processes operating in the cells. Indicators of functional diversity are also indicators of microbial activity and thereby integrate diversity and function. 

Specific Enzymatic Activity of Rat Liver at Different Ages0... 

Most probably some fraction of the peptides appearing in urine represents small quantities of peptide hormones, such as vasopressin, oxytocin, glucagon, and the melanocyte-stimulating hormone, the occurrence of which in small amounts in normal urine has been occasionally reported. As the specific enzymatic decomposition of these hormones takes place... 

Figure 8.11 Specific enzymatic immunodetection of a blotted protein. Depicted are blocked binding sites on the membrane (1), a primary antibody (2) specifically bound to an antigenic protein, and a secondary antibody (3) bound to the primary antibody. The secondary antibody is conjugated to a reporter enzyme (4). Substrate (S) is converted to insoluble product (P) at the site of the antigen.

Genetic polymorphism may result in poor metabolizers (i.e., individuals who have only a limited or no capacity to metabolize a given chemical via a specific enzymatic pathway), and extensive metabolizers (i.e., individuals who have a sufficient capacity to metabolize a given chemical via a specific enzymatic pathway) and individuals of a particular group may therefore respond differently to exposure to chemicals. 

Protein phosphorylation is a specific enzymatic reaction in which one protein serves as a substrate for a protein kinase. Protein kinases are phophotransferases. They catalyze the transfer of a phosphate group from ATP to an acceptor amino acid in the substrate protein (fig. 2.10). A detailed discussion of protein kinases can be found in chapter 7. 

The ubiquitinylation of proteins is a complex process which involves several specific enzymatic reactions. Three sequential steps can be distinguished (fig. 2.15A) ... 

Both in nature and in test tubes many complicated reactions take place with apparent ease. Highly specific enzymatic reactions involving complementarity of substrate and receptor both with respect to their spatial structure and electrostatic fields lie outside the scope of this book. Here we would like only to mention a few... 

Immunoprecipitation followed by SDS-PAGE and immunoblotting, is routinely used in a variety of applications to determine the molecular weights of protein antigens, to study protein-protein interactions, to determine specific enzymatic activity, to monitor protein post-translational modifications and to determine the presence and quantity of proteins. The IP technique also enables the detection of rare proteins which otherwise would be difficult to detect since they can be concentrated up to... 

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