Peptide Environments

The ability of this hydrophobic peptide environment to effect the flavin reactivity was assessed by monitoring the oxidation ofN-alkyl-l,4-dihydronicotina-mides (N-alkyl-NAH) using conditions similar to those reported in the Kaiser experiments. Under these conditions, both systems exhibited slight enhancements in the rate of oxidation of either J -benzyl-NAH or N-hexyl-NAH. Hypothesizing that the lack of performance of the system may have been due to the occlusion of the flavin from interacting with the substrate, the assays were... 

Some characteristic properties of iron-sulfur clusters in proteins result from interactions with invariant amino acid fragments around the clusters. In particular, clusters in peptide environments exhibit positive shifts in redox potentials relative to those in nonpeptide environments. Such shifts are observed for a variety of oligopeptide model complexes of IFe, 2Fe-2S, and 4Fe-4S proteins. 

Active centers of metalloproteins are presently better understood than ever before, and their unique properties are being further explored by application of modern techniques and theories of inorganic chemistry. Peptide environments exist around active centers and are thought to have significant control on their properties. Peptide sequence data are available which indicate that specific amino acids near the active centers dictate the spectroscopic as well as chemical reactivities. 

The relationship between the structure of the peptide environment and active site chemical properties is thus of considerable interest and to a large extent awaits future studies. In this article, some examples of such specific relationships are described, particularly in the case of iron-sulfur proteins, because this class of proteins is distributed widely in living organisms ranging from bacterial cells to mammals. The major function of the proteins is now known to be electron transfer and the... 

Reichardt, P. et al., Identification and quantification of in vitro adduct formation between protein reactive xenobiotics and a lysine-containing model peptide, Environ. Toxicol., 18 (1), 29, 2003. 

Figure 17.23 The 3.4 A resolution structure of the oxygen evolving complex (OEC) and the immediate peptide environment. The directions of proposed PT and ET pathways are indicated with arrows. Figure adapted from Ref [206].

This synthetic protein fixates heme and zinc protoporphyrin IX very well in water < 10 M). The heme s iron(II) is a mixture of high spin and low spin, but no oxygen fixation is possible in water. Such a relatively simple designed protein may, however, fixate various redox- and photoactive chromophores and may be combined with anionic redox systems at its open end. Fast electron transfer may be achieved. The redox potential of the Fe /Fe° pair drops by 90 mV if the peptide environment of the heme changes from hydrophilic to hydrophobic. Hydrophobic-ity increases the binding constants of the peptides to the heme iron. They scale with more negative reduction potentials (Huffmann et al., 1998). 

To understand the mechanism by which the peptide environment around Dha might affect its specificity toward nucleophiles, it is useful to consider the unique chemical environment of dehydro residues. Whereas the dehydro residues can he considered simply as novel amino acid side chains, a close examination of their relationship with the polypeptide backbone reveals that they are much more profound than this. C e of the essential structural features of polypeptides is that the peptide backbone consists of a... 

UV spectroscopy is a sensitive probe for the environment of the UV chromophore, resulting in slightly different UV transition frequencies for each conformation. Shifts in the UV absorption band induced by the peptide environment and the intramolecular interactions are typically <100 cm for UV transitions around 37,000 cm . The combination of a narrow-band UV laser source (e.g. a frequency-doubled pulsed dye laser) and a coUisionless low-temperature environment (molecular beam) minimizes line broadening, allowing UV transitions of different conformers to be resolved. 

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