Proteomes, mammalian

Conrads, T. P., Alving, K., Veenstra, T. D., Belov, M. E., Anderson, G. A., Anderson, D. )., Lipton, M. S., Pasa-Tolic, L, Udseth, H. R., Cheislee,W. B., etal. (2001). Quantitative analysis of bacterial and mammalian proteomes using a combination of cysteine affinity tags and 15N-metabolic labeling. Anal. Chem. 73, 2132-2139. 

The abundance of experimentally determined protein structures should not, however, obscure the fact that for the majority of protein domains, no structural information is available at all. The coverage of the mammalian proteome by experimentally determined structures is still only about 10-15% and varies between the protein families. Structures of only four G-protein coupled receptors (GPCR), out of about 900, have been determined by crystallography, and only about one-third of the human kinases and the same fraction of the nuclear receptors. For many of those proteins, models by homology can be built (5), although the... 

Frith MC, Forrest AR, Nourbakhsh E et al 2006 The abundance of short proteins in the mammalian proteome. PLoS Genet 2 e52... 

Choi, S.S., VaUender, E.J., Lahn, B.T Systematically assessing the influence of 3-dimensional structural context on the molecular evolution of mammalian proteomes. Mol. Biol. Evol. 2006, 23(11), 2131-3. 

The strategy described has been demonstrated by the in vivo labeling of proteins in both bacterial and mammalian systems thereby making it potentially useful for future bioimaging and proteomics applications [163],... 

The approach recruited to chemical proteomics in Reference [17] is called SILAC (stable isotope labeling with amino acids in cell culture) and is important in comparative proteomics (Figure 1). SILAC works well with cultured mammalian cells, but prokaryotes defeat it by metabolizing the label (usually supplied in lysine and arginine) into other amino acids. For applications beyond cultured eukaryotic cells, the reductive methylation route to differential labeling [18] is among the alternatives [15]-... 

An important factor in all these experiments is the choice of bead used to immobilize the probe. Biochemists have considered cross-linked agarose beads to be exceptionally hydrophilic with a low tendency to bind proteins nonspecifically, and these beads have the further attraction of being commercially available in activated forms (succinimidyl esters, epoxides, and maleimides, for example). However, early trials of bead-based chemical proteomics have shown that many proteins in mammalian cell lysates bind tenaciously to agarose beads. This was unimportant in many studies in which protein-protein interactions were detected by coimmunoprecipitation with immunochemical... 

Yi, Y., Song, Y., and Loscalzo, J. (2007) Regulation of the protein disulfide proteome by mitochondria in mammalian cells. PNAS 104, 10813-10817. 

This multidimensional protein identification technology (MudPIT) specifically incorporates a strong cationic exchange (SCX) column in tandem with an RP column to achieve maximal resolution and exquisite sensitivity. MudPIT is effective for studying complex proteomes such as mammalian cellular samples. It has been applied to large-scale protein characterization with identification of up to 1484 proteins from yeast in a single experiment.12... 

Finally, it is a pleasure to acknowledge the very considerable behind the scenes help from all those who helped make the conference a success. We would like to thank Anne Tuson and Marg Hedges, as well as all the members of the Mammalian Behaviour and Evolution Group and the Proteomics and Functional Genomics Group at the University of Liverpool. We would also like to express our thanks to the University of Chester Conference Team for their support and efforts at the venue. 

Protein functions and interactions are infinitely varied in biological species— one of the major problems associated with complete classification of any proteome. Proteins may transport substances myoglobin and hemoglobin (discussed in Chapter 7) transport oxygen, and carbon dioxide, in mammalian blood. Proteins called enzymes catalyze necessary biochemical reactions. The active site of an enzyme contains those amino acids that come in direct contact... 

Smith MA, Richey Harris PL, Sayre LM, Beckman JS, Perry G (1997) Widespread peroxynitrite-mediated damage in Alzheimer s disease. J Neurosci 17 2653-2657 Stadtman ER, Levine RL (2003) Free radical-mediated oxidation of free amino acids and amino acid residues in proteins. Amino Acids 25 207-218 Stuehr DJ (1999) Mammalian nitric oxide synthases. Biochim Biophys Acta 1411 217-230 Sultana R, Boyd-Kimball D, Poon HF, Cai J, Pierce WM, Klein JB, Markesbery WR, Zhou XZ, Lu KP, Butterfield DA (2006c) Oxidative modification and down-regulation of Pinl in Alzheimer s disease hippocampus A redox proteomics analysis. Neurobiol Aging 27(7) 918-925... 

Before the application of proteomics to the NE, proteins of this stmcture were identified through a wide variety of approaches. Lamins were the first NE proteins characterized (roughly 30 years ago) because their solubility characteristics as intermediate filament proteins and their abundance facilitated easy biochemical enrichment (Aaronson and Blobel 1975 Gerace et al. 1978). It is estimated that there are 3 million lamin molecules in the average mammalian nucleus (Gerace and Burke 1988). 

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