Attributes of Proteins

Knowledge of protein primary sequence, quantities, posttranslational modifications (PTMs), structures, protein-protein (P-P) interactions, cellular spatial relationships, and functions are seven important attributes (see Table 4.2) needed for comprehensive protein expression analysis. It is this multifold and complex nature of protein attributes that has spawned the development of so different many proteomic technologies. Some of these challenges in proteomic analysis include defining the identities and quantities of an entire proteome in a particular spatial location (i.e., serum, liver mitochondria, brain), the existence of multiple protein forms and complexes, the evolving structural and functional annotations of the human and rodent 

Molecular and Biochemical Toxicology, Fourth Edition, edited by Robert C. Smart and Ernest Hodgson Copyright 2008 John Wiley Sons, Inc. 

Proteome That portion of the genome expressed as proteins in cell or organism over time. Proteomics Global protein analysis to study the structure and function of the proteome. 

All proteomic platforms generally involve separation and identification of proteins. Toxicoproteomics Proteomics applied to toxicology with the aims of identifying critical proteins and pathways affected by chemical and environmental exposures. 

Identity Based on amino acid sequence of protein 

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These considerations about protein composition and structure are helpful for understanding key properties and attributes of proteins in proteomic analysis. The isoelectric point (pi) and the molecular mass are two important properties used in... 

The many attributes of proteins mentioned in Table 4.2 make complete global analysis of proteins from cells, tissues, organs, or organisms a formidable analytical challenge. A primary aim of proteomic analysis is to provide researchers with as much data as possible about one or more protein attributes. Flowever, to many researchers, proteomic analysis usually involves the three attributes of identification and quantitation of all proteins in a defined sample space. Only the highlights of each platform will be summarized here. A critical appraisal of capabilities, advantages, and drawbacks are summarized in Figure 4.13 (Section 4.5.6). 

Both order and native disorder are well-characterized structural attributes of protein chains [16]. However, the highly vulnerable regions in a soluble fold described in this chapter belong to the novel category of tamed disorder because they can acquire and maintain a structured state only upon association. Neither order nor disorder is an adequate category to describe such dehydron-rich protein regions. 

Typically proteins and especially enzymes contain only a few residues that are absolutely vital for function. In contrast there are usually many other residues of the same type in the protein that do not fulfill any special role. In many cases the catalytic residues have different chemical and physical properties from the same amino acid in solution for example, the pKa of the side chain might be several pH units higher or lower than the free amino acid. It is generally found that the behavior of an amino acid is profoundly influenced by the context of that amino acid within the protein. Altering the chemical properties of a functional group is one of the major attributes of protein structure and appears to be essential for the activity of most enzymes. There are many ways in which this is achieved however, a simple example is placement of a charged residue in the interior of a protein such that the deionized state is favored. This serves to raise the pKa of aspartate and glutamate and lower the pKa of lysine. 

Regulation of enzyme activity is achieved in a variety of ways, ranging from controls over the amount of enzyme protein produced by the cell to more rapid, reversible interactions of the enzyme with metabolic inhibitors and activators. Chapter 15 is devoted to discussions of enzyme regulation. Because most enzymes are proteins, we can anticipate that the functional attributes of enzymes are due to the remarkable versatility found in protein structures. 

In oxidized Rieske proteins, a larger number of peaks are observed that have been attributed to vibrations of the iron-sulfur core this is indicative of the reduced symmetry of the iron-sulfur core in Rieske proteins since ungerade vibrations are Raman-inactive in the centro-symmetric (in first approximation) [2Fe-2S]-Cys4 core (point group D2h or Cih) while the corresponding modes are Raman-active in C2 symmetry. The characteristic peak of the SL mode of proteins con-... 

Fig. 4. Representation of the ligand sphere of the [2Fe-2S] cluster of the Rieske protein from spinach and the attribution of g-tensor to moleculEir axes as discussed in the text. Ser 130 has been observed to influence the redox potentiEd of the cluster via hydrogen interactions with the acid-labile bridging sulfur.

Release of tetracycUne hydrochloride from PCL fibers was evaluated as a means of controlled administration to periodontal pockets (69). Only small amounts of the drug were released rapidly in vitro or in vivo, and poly(ethylene-co-vinyl acetate) gave superior results. Because Fickian diffusion of an ionic hydrochloride salt in a UpophiUc polymer is unlikely, and because PCL and EVA have essentially identical Fickian permeabilities, we attribute this result to leaching of the charged salt by a mechanism similar to release of proteins from EVA (73). Poly-e-caprolactone pellets have been found unsuitable for the release of methylene blue, another ionic species (74,75). In this case, blending PCL with polyvinyl alcohol (75% hydrolyzed) increased the release rate. 

This asymmetry can be partially attributed to the irregular distribution of proteins within the membranes. An inside-outside asymmetry is also provided by the external location of the carbohydrates attached to membrane proteins. In addition, specific enzymes are lo-... 

Exposure of protein amino groups to MDA (formed by the degradation of lipid peroxides) or to oxygen radicals directly, generated by transition metals and hydrogen peroxide, induce fluorescence indistinguishable from that attributed to Amadori-adduct formation (Chio and Tappel, 1969), and leads to the formation of cross-links (Lunec a al., 1985). 

Figure 11.5 Positive ion DIESMS spectra of the crude cell extract of an E. coli strain that expresses the GFP protein, showing protein peaks. The inset is the MaxEnt decon-voluted spectrum that shows more than three peaks attributable to proteins from the extract.

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