Protein Relative Abundance

Figure 5.17 Correlations between mRNA and protein relative abundance. (From Chen, G. et al.. Mol. Cell. Proteomics, 1, 304—313, 2002. With permission.)...

Similarly, in developing Drosophila the response to wg is influenced by the relative abundance and ligand affinity of receptors expressed in the target tissue. A synthesis of the available data from all species suggests that the response to a specific Wnt signal in vivo is influenced both by the particular Wnt protein secreted and by the receptors and other downstream molecules present in the target tissue. 

In vivo studies in animals suggest that endosulfan may disrupt normal reproductive hormone levels in male animals, but that it is not an endocrine disrupter in females. Persistent depressed testicular testosterone was seen in male rats after intermediate duration oral exposures to endosulfan. In ovariectomized female rats, orally administered endosulfan did not induce normal development of female reproductive tissues, and in female mice and immature female rats, acute parenteral exposure to endosulfan did not affect several endocrine-related end points. In vitro studies have evaluated endosulfan for estrogen receptor (ER) and cytosolic protein binding affinity, ER-mediated reporter gene expression, estrogenic induction of cell proliferation, and alteration of relative abundance of active estradiol metabolites. Overall, in vitro evidence in favor of endosulfan estrogenicity indicates relatively weak potency compared to 17[3-estradiol. Apparently contradictory results were reported in different... 

The isotopic composition of carbon in the proteins, which are one of the main components of animal tissues, reflects the nature of the food resources in the diet of the animals. Determining the relative abundance of the stable isotopes of carbon in the proteins of bones or hair, for example, can facilitate understanding of the effects that different types of plants or animal food resources had on ancient diets (Katzenberg 2000 Burton 1996). 

According to the predominant component, the binders are usually divided into protein, oil, polysaccharide, and resin binders. In this section we shall focus on protein binders but it is worth mentioning that in the majority of natural non-protein binders a minority protein component is usually present as well. Thus many of the analytical techniques described here can be (with certain limitations) applied to them as well. Although in colour layers of artworks and particularly in paintings protein binders are relatively abundant (up to 10%), their identification is often limited by a small amount of sample that is usually available for analysis (tens or hundreds of micrograms at most [6]). 

Several factors indicate that the amino acids detected in all of these carbonaceous chondrites are indigenous and that they must have originated abiotically. First, the presence of protein and non-protein amino acids, with approximately equal quantities of D and L enantiomers points to a nonbiological origin and precludes terrestrial contamination. In addition, the non-extractable fraction of the Murchison is significantly heavier in 13C than terrestrial samples. Finally, the relative abundances of some compounds detected resemble those of products formed in prebiotic synthesis experiments. The aliphatic hydrocarbons are randomly distributed in chain length, and the C2, C3, and C4 amino acids have the highest concentrations (i.e., the most easily synthesized amino acids with the least number of possible structures are most abundant) [4]. 

Quantitation and qualification of large molecules follow similar principles as procedures for small molecules but involve different foci and approaches. The quantitation of proteins and peptides includes relative and absolute amount evaluations. Most proteomic applications in drug discovery are concerned with relative abundances of proteins. 

Quantitative studies comparing the relative abundances of proteins in different cellular states may be performed with MS. Methods such as 2D-GE have been utilized extensively with great success and differentially represent spots excised and then subjected to MS/MS for final identification of the differentially expressed proteins. 2D-GE requires approximately 50 pg of starting material and is limited by its bias toward high abundance proteins and propensity to detect proteins with extreme pi values. Furthermore, proteins at both extremes of molecular weight and those associated with membrane fractions are not well represented by 2D-GE.10... 

FIGURE 15.3 Outline of experimental protocol used for ICAT differential protein expression profiling. Protein mixtures from two cell populations are labeled with light or heavy isotopic versions of a cleavable ICAT reagent. Labeled proteins are combined, subject to multidimensional separation by SCX, RP, and avidin affinity chromatography, then analyzed by tandem MS for peptide and protein identification. Based on the relative ratio of the two isotopically labeled peptides, a relative abundance of protein expression can be determined. 

Synchronous fluorescence has the potential to provide useful information regarding the relative abundance of protein-like vs. fulvic-like DOM (Peak I / Peak II) and humic-like vs. fulvic-like DOM (Peak Ill/Peak II). Figure 4 shows the... 

Much of the early work which would lead to the identification of proteins as defined chemical entities started from observations on enzymes, either those involved in fermentation or on the characterization of components in gastric secretions which powerfully catalyzed the hydrolysis of different foodstuffs. As well as the digestive enzymes, a number of relatively pure proteins could be isolated from natural sources where they made up the major component (Table 1). Because of the importance and difficulty of isolating pure proteins and demonstrating their homogeneity, functionally active and relatively abundant... 

Following the separation process, the individual proteins must be identified and characterized. The 2-D separation has provided Mr, pi, and relative abundance data but no information on protein identities or functions. Computer algorithms are available for matching the Mr, pi, and relative abundance data... 

The basic principle behind the ChIP method is relatively simple It is based on the selective enrichment of a chromatin fraction containing a specific antigen (e.g. transcription factors, DNA binding proteins, modified histones, etc.) by an immunoprecipitation step. Specific (important, see below ) antibodies that recognize a protein of interest or the modified form of a protein can be used to determine the relative abundance of it within DNA regions. 

Some amino acids such as aspartic acid and glutamic acid contain an additional acid functional group, while amino acids such as lysine, arginine, and histidine contain additional basic groups. The presence of these units will confer to the protein tendencies to move toward the anode or cathode. The rate of movement is dependent on a number of factors including the relative abundance and accessibility of these acid and base functional groups. 

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