Coenzyme conformation

The similarities of the coenzyme conformation when bound to the dehydrogenases reflect the similarities of the fold in the dinucleotide binding domains and of detailed similarities in those regions that are actually involved in binding. Unfortunately, details on the interaction between... 

FIGURE 14.22 Glutamate aspartate aminotransferase, an enzyme conforming to a double-displacement bisnbstrate mechanism. Glutamate aspartate aminotransferase is a pyridoxal phosphate-dependent enzyme. The pyridoxal serves as the —NH, acceptor from glntamate to form pyridoxamine. Pyridoxamine is then the amino donor to oxaloacetate to form asparate and regenerate the pyridoxal coenzyme form. (The pyridoxamine enzyme is the E form.)... 

This thiol-disulfide interconversion is a key part of numerous biological processes. WeTJ see in Chapter 26, for instance, that disulfide formation is involved in defining the structure and three-dimensional conformations of proteins, where disulfide "bridges" often form cross-links between q steine amino acid units in the protein chains. Disulfide formation is also involved in the process by which cells protect themselves from oxidative degradation. A cellular component called glutathione removes potentially harmful oxidants and is itself oxidized to glutathione disulfide in the process. Reduction back to the thiol requires the coenzyme flavin adenine dinucleotide (reduced), abbreviated FADH2. 

B. Nicotinamide and Flavin Coenzymes.—High-frequency (220 MHz) H n.m.r. spectroscopy shows that there are differences in conformation between oxidized and reduced pyridine coenzymes. A preliminary report on the P n.m.r. spectra of NAD+ and NADH confirms these observations, as the spectrum of NAD+ consists of an AB quartet while there is only a single resonance discernible in the spectrum of NADH. 

A difference in the solid state and solution conformation of 5 -de-oxyadenosylcobinamide (cobinamide coenzyme) has been inferred from the NMR spectrum of cobinamide coenzyme 123) which indicates that the resonance due to the proton at carbon R-l of the ribose is shifted significantly upfield from its expected position. Such an upfield shift would probably have to arise from the ring current of the adenine ring. 

The term coenzyme is a poor one. Compounds such as ATP, ADP, NADH are better seen as co-substrates because clearly they do not conform to two of the criteria which define an enzyme catalyst, that is ... 

In the crystal structures of TDP-dependent enzymes, the coenzyme is generally tightly packed within the active site and is maintained in a specific conformation which is conserved in all TDP-dependent enzymes but which is... 

A number of conformationally restricted fluorinated inhibitors have been synthesized and evaluated. These smdies show that (1) subtle conformational differences of the substrates affect the inhibition (potency, reversible or irreversible character) (Figure 7.50), (2) a third inhibition process involving an aromatization mechanism could take place (Figure 7.51). When the Michael addition and enamine pathways lead to a covalently modified active site residue, the aromatization pathway produces a modified coenzyme able to produce a tight binding complex with the enzyme, responsible for the inhibition (Figure 7.51). ... 

Enzymes, composed of various amino acids, constitute hydrophobic interior and hydrophilic exterior by arranging in space the appropriate amino acid residues. The hydrophobic receptor site is usually located inside and the hydrophilic amino acid residues located on the surface of enzyme are heavily solvated by water molecules in aqueous solution. Then, the supramolecular interactions with specific coenzymes, substrates, and inhibitors inevitably accompany extensive dehydration and conformational change of both enzyme and ligand. 

Fluorescence determinations are important to analyze cysteine, guanidine, proteins, (LSD), steroids, a number of enzymes and coenzymes, and some vitamins, as well as several hundred more substances. A fluorometer can be used to verify conformational changes in multipartite operator recognition by. -repressor as explained in a journal article by Deb et al. (2000). Upon titration with single operators site, the tryptophan fluorescence quenches to different degrees, suggesting different conformations of the DNA-protein complexes. 

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