Amino acids, interactions with

The association of sulfur and iron into simple to more complex molecular assemblies allows a great flexibility of electron transfer relays and catalysis in metalloproteins. Indeed, the array of different structures, the interactions with amino-acid residues and solvent and their effect on redox potential and spectroscopic signatures is both inspiring for chemists and electrochemists, and of paramount importance for the study of these centers in native conditions. Most of the simpler natural clusters have been synthesized and studied in the laboratory. Particularly, the multiple redox and spin states can be studied on pure synthetic samples with electrochemical and spectroscopic techniques such as EPR or Fe Mossbauer spectroscopy. More complex assembhes still resist structural... 

McNeill, 1986). This is probably due to differences in the activities and types of enzymes that break down RNA. A synergistic effect is detected when 5 ribonucleotides interact with amino acids, especially glutamate. 

Proteases are enzymes catalyzing the hydrolysis of peptide bonds. They form one of the largest enzyme families encoded by the human genome, with more than 500 active members. Based on the different catalytic mechanisms of substrate hydrolysis, these enzymes are divided into four major classes serine/threonine, cysteine, metallo, and aspartic proteases. In serine, cysteine, and threonine proteases, the nucleophile of the catalytic site is a side chain of an amino acid in the protease (covalent catalysis). In metallo and aspartic proteases, the nucleophile is a water molecule activated through the interaction with amino acid side chains in the catalytic site (non-covalent catalysis) (Gerhartz et al., 2002). 

S.6.5.2 Interaction With Amino Acid, Peptide, and Protein... 

The role of structural zinc sites is likely two-fold. They maintain the structure of the protein in the immediate vicinity of the metal site. In this manner it may influence enzymatic activity by providing active-site residues involved in catalysis and/or effecting the chemical environment of catalytic groups through interaction with amino acids originating from within its metal-binding spacers. However, in many cases, these metal sites also effect the overall stability of the protein as judged by temperature and pH criteria. 

As discussed previously, the radicals produced upon irradiation of water [Eq. (I)] have very different characteristics. Primary radicals (OH, H and e q) and their interactions with amino acids will be addressed first. The two secondary radicals that will be discussed... 

Phenols are readily oxidized chemically or enzymatically to quinones which can interact with amino acids to form aminohydroquinones. The latter can then be oxidized to aminoquinones (Fig. 8). The resulting products are dark colored and release only low yields of amino acids when hydrolyzed with hot acid. 

In the capillary beds of most organs, a rapid passage of molecules occurs from the blood through the endothelial wall of the capillaries into the interstitial fluid. Thus, the composition of interstitial fluid resembles that of blood, and specific receptors or transporters in the plasma membrane of the cells being bathed by the interstitial fluid may directly interact with amino acids, hormones, or other compounds from the blood. In the brain, transcapillary movement of substrates in the peripheral circulation into the brain is highly restricted by the blood-brain barrier. This barrier hmits the accessibility of blood-borne toxins and other potentially harmful compounds to the neurons of the CNS. 

Deakyne and Allen (1979) have used semiempirical CNDO/2 calculations to attempt to define the amino acid residues at the active site of RNase involved in binding and catalysis in the cyclization step of the reaction. As these workers state, such calculations are not absolute, but demonstrate trends. They suffer from the limitations of the level of calculation and the minimal model structures that may be used for substrate and aetive site. The cyclization step is considered in two parts the first, attachment and partial protonation of the substrate the second, deprotonation/protonation of the TBP intermediate. For attachment and partial protonation, dimethyl phosphate is used as a model for the nucleotide substrate and interactions with amino acid models analysed. Several conclusions are drawn ... 

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