Enzymes/nucleic acids, reactive sites

Phospholipids located in a membrane, phospholipids (as second messengers) in the cytosol, sphingomyelin, folded protein structures, reactive sites of enzymes, nucleic acids in the zinc finger of the chromosome. Wliat are tire assumptions and constraints for each of these molecular modeling systems (a) Force field methods, (b) Semi-empirical method, (c) Ab initio method. 

Photochemically reactive molecules have often been used as labels for specific sites in proteins and nucleic acids. Psoralen derivatives serve as relatively nonspecific photochemically activated crosslinking agents for DNA and double-stranded RNA.195 Aryl azides are converted by light to aryl nitrenes, which react in a variety of ways including insertion into C-H bonds (Eq. 23-27).200 201 In some cases UV irradiation can be used to join natural substrates to enzymes or hormones to receptors. For example, progesterone, testosterone, and other steroids have been used for direct photoaffinity labeling of their receptors.202 Synthetic benzophenones have also been used widely as photoactivated probes.203... 

These reactive metabolites can bind covalently to cellular macromolecules such as nucleic acids, proteins, cofactors, lipids, and polysaccharides, thereby changing their biologic properties. The liver is particularly vulnerable to toxicity produced by reactive metabolites because it is the major site of xenobiotic metabolism. Most activation reactions are catalyzed by the cytochrome P450 enzymes, and agents that induce these enzymes, such as phenobarbital and 3-methylcholanthrene, often increase toxicity. Conversely, inhibitors of cytochrome P450, such as SKF-525A and piperonyl butoxide, frequently decrease toxicity. 

With a small adjustment to this procedure, using thiophosphoryl chloride (PSCI3) in place of phosphoryl chloride (POCI3), the nucleoside 5 -(l-thio)triphosphates can be easily synthesized.7 These compounds have been used extensively for applications inter alia for site-directed mutagenesis, sequencing of nucleic acids and investigation of enzyme mechanisms.16 Phosphorylation with thiophosphoryl chloride is generally slower than with phosphoryl chloride but still occurs at a reasonable rate for purine nucleosides. However, for pyrimidine nucleosides, it is necessary to add 2,4,6-collidine as a catalyst, which forms a reactive intermediate with the thiophosphoryl chloride in situ. 

The superoxide free radical thus generated, 02, is very reactive and can damage enzymes, membrane lipids, and nucleic acids. Antimycin A, an inhibitor of Complex 111, may act by occupying the Q, site (Fig. 19-11), thus blocking the Q cycle and prolonging the binding of Q to the Qp site this would increase the likelihood of superoxide radical formation and cellular damage. From... 

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