Abundance abundant proteins

Immunophillins are abundant proteins that catalyze the cis-trans isomerization of proline residues within proteins, generally to aid in protein folding. Immunophillins are not essential proteins, are the intracellular binding proteins of several immunosuppressive drugs. Cyclosporin A exerts its action after binding to cyclophilin. Tacrolimus and sirolimus predominantly bind to the protein FKBP-12 (FK binding protein-12). 

Many other peptides are synthesized as proproteins that require modifications before attaining biologic activity. Many of the posttranslational modifications involve the removal of amino terminal amino acid residues by specific aminopeptidases. Collagen, an abundant protein in the extracellular spaces of higher eukaryotes, is synthesized as procollagen. Three procol-... 

COLLAGEN IS THE MOST ABUNDANT PROTEIN IN THE ANIMAL WORLD... 

Collagen is the most abundant protein in the animal kingdom approximately 19 types have been isolated. All collagens contain greater or lesser stretches of triple helix and the repeating stmcture (Gly-X-Y). ... 

It is clear that both intact cell MALDI-TOF and PFGE have their limitations. PFGE analyses probes the chromosomal DNA of microorganisms for variations in the locations of specific restriction enzyme cleavage sites, while MALDI-TOF mass spectrometry of intact cells primarily examines abundant proteins such as ribosomal proteins35 and those associated with or near bacterial cell walls.58 In order for MALDI-TOF to detect a variation, a mutation must lead to noticeable changes in the expression of cell wall—associated... 

Figure 10.4 All spectra obtained between 20 and 66 minutes are combined into a single spectrum and then deconvoluted using MaxEnt 1. The resulting molecular weight spectrum is noisy and hampers the identification of low abundance proteins. The asterisks indicate where proteins of mass 7274 and 10652 should be observed but are not.

As is the case with identifications based on protein molecular masses, it appears that the use of tryptic or other peptide masses as the basis for identification is extended with difficulty to mixtures of microorganisms. This reflects unpredictable suppression. Another limitation is redundancy of peptide masses across several microorganisms. For example, the most abundant proteins (SASPs), and thus the most abundant peptides, in spores of Bacillus anthracis and the closely related pesticide Bacillus thuringiensis have extensive sequence homology.25,82... 

Wienkoop, S., Glinski, M., Tanaka, N., Tolstikov, V.V., Fiehn, O., Weckwerth, W. (2004). Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins. Rapid Commun. Mass Spectrom. 18, 643-650. 

The proteins of high abundance are often identified by multiple peptides and high statistical confidence. On the contrary, many medium and low abundant proteins are typically identified by only a single peptide. This is a direct result of the semirandom nature of the DDA algorithm (Liu et al., 2004), as discussed above. In addition, these peptide hits often cannot be confirmed by subsequent DDA experiments conducted... 

Figure 12.5 illustrates a typical problem of analysis of minor components present in a matrix of highly abundant ones. Despite the availability of large LC-MS peak capacity (Table 12.3), the number of peptides detected in a semm/plasma digest does not exceed several hundreds (Kapp et al., 2005). These peptides typically match 30-50 high abundant proteins. We believe that the maj ority of remaining proteins/peptides in the sample are present at concentrations well below the LOD of MS instrument. 

Zolotaijova, N., Martosella, J., Nicol, G., Bailey, J., Boyes, B.E., Barrett, W.C. (2005). Differences among techniques for high-abundant protein depletion. Proteomics 5, 3304-3313. 

Gill et al.21 Archival FFPE spinal cord tissue both paraformaldehyde-fixed frozen rat spinal cord tissue and paraffin-embedded same tissue To establish an optimal protocol for detection of low-abundance protein (NeuN) in human spinal cord FFPE tissue sections, testing three AR solutions of pH 6, alkaline, and acidic buffer, with three heating conditions 95,100, and 105°C Heating FFPE tissue sections in an alkaline buffer yields most effective AR-IHC staining results. 

Egg white contains, apart from water (88%), mainly proteins (-11%), saccharides, mineral compounds and traces of lipids. The most abundant proteins (mostly glycoproteins) are ovoalbumin (54%), ovotransferin (13%), ovomocoid (11%), lysozyme (3.5%), other globulins (4%) and ovomucin (1.5 2%) some other proteins, e.g. ovoinhibitor, ovoflavoprotein, ovomicroglobulin and avidin [1], are present in traces (<1%). 

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