Proteomics Proteins

D. Hall and A. P. Minton, Macromolecular crowding qualitative and semiquantitative successes, quantitative challenges, Biochim. Biophys. Acta (Proteins Proteomics) 1649, 127 (2003). 

Warshel A, Sharma PK, Kato M, Parson WW (2006) Biochim Biophys Acta Proteins Proteom 1764 1647... 

Several observations lend credence to the rationale of monitoring cellular activities at the level of the proteins (proteomes) and metabolites (metabolomes). Some are listed below ... 

M. Yamada, M. Elias, K. Matsushita, C.T. Migita, and O. Adachi, Escherichia coli PQQ-containing quinoprotein glucose dehydrogenase its structure comparison with other quinoproteins. Biochim. Biophys. Acta Proteins Proteomics 1647, 185-192 (2003). 

Uversky, V. N., and Fink, A. L. (2004). Conformational constraints for amyloid fibrillation The importance of being unfolded. Biochim. Biophys. Acta Proteins Proteomics 1698, 131-153. 

The real value in the genome sequence is to find out the regions of the genome that encode proteins. Proteomics, the study of the structures and functions of proteins, further enhances our understanding of proteins and their functions, leading to insights on how they are affected in normal and disease conditions. Exhibit A2.3 shows some of the medical conditions due to genetic problems. 

MueUer, M., Martens, L. and Apweiler, R (2007) Annotating the Human Proteome Beyond Establishing a Parts list. Biochim Biophys Acta (BBA) -Proteins Proteomics, 1774,175. 

Mayer, M., et al. (2004) Micropatterned agarose gels for stamping arrays of proteins and gradients of proteins. Proteomics. 4, 2366-76. 

Georgiou HM, Rice GE, Baker MS. Proteomic analysis of human plasma Failure of centrifugal ultrafiltration to remove albumin and other high molecular weight proteins. Proteomics 2001 1(12) 1503-1506. 

Puhse M, Szweda RT, Ma YY et al (2009) Marasmius scorodonius extracellular dimeric peroxidase - Exploring its temperature and pressure stability. BBA Proteins Proteomics 1794 1091-1098... 

Jung C. The mystery of cytochrome P450 Compound I a mini-review dedicated to Klaus Ruckpaul. Biochim Biophys Acta Proteins Proteomics. 2011 1814 46-57. 

Fortunato, D., Giuffrida, M.G., Cavaletto, M., Garoffo, L.P., Dellavalle, G., Napolitano, L., Giunta, C., Fabris, C., Bertino, E., Coscia, A., Conti, A. 2003. Structural proteome of human colostral fat globule membrane proteins. Proteomics. 3, 897-905. 

Lin, D., Tabb, D.L. and Yates, J.R. (2003) Large-scale protein identification using mass spectrometry. Biochim. Biophys. Acta-Proteins Proteomics, 1646, 1-10. 

Synaptosomal proteins are involved in synaptic transmission, which is deranged in AD. The machinery consists of synaptosomal proteins, including soluble N-ethylmaleimide-sensitive factor attachment proteins (SNAPs) present as three isoforms, a, (3 and y, synaptosomal-associated protein 25 (SNAP 25), synapto-tagmin, and vesicular proteins. Proteomics studies showed reduced expression... 

Carbodiimides are the diimides derived from carbon dioxide, and they are extensively used in the formation of peptide amide bonds from carboxylic acids and amines. This reaction was utilized by the Nobel laureate Sheehan in the total synthesis of penicillin. He also was the first to use water soluble carbodiimides to crosslink gelatin. Khorana, another Nobel laureate, demonstrated that carbodiimides can also be used in the synthesis of nucleotides. Today, carbodiimides are used extensively in the synthesis and modification of proteins. Proteomics is the new frontier of chemical research. 

Moritz, R.L., Clippingdale, A.B., Kapp, E.A., Eddes, J.S., Ji, H., Gilbert, S., Connolly, L.M. and Simpson, R.J. (2005) Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins. Proteomics 5, 3402-3413. 

Galeva, N. and Altermann, M. (2002) Comparison of one-dimensional and two-dimensional gel electrophoresis as a separation tool for proteomic analysis of rat liver microsomes cytochromes P450 and other membrane proteins. Proteomics 2, 713-722. 

Scheurer, S.B., Roesli, C., Neri, D. and Elia, G. (2005) A comparison of different biotinylation reagents, tryptic digestion procedures, and mass spectrometric techniques for 2-D peptide mapping of membrane proteins. Proteomics 5, 3035-3039. 

The analytical approach applied in the PoweU et at. (2005) study represents a major advancement in our current study of the chemical structure of DOM. SDS-PAGE remains one of the few methods that wiU allow separation and purification of intact dissolved proteins proteomics, as applied by PoweU et at. (2005), is now routinely applied in the biochemical and biomedical fields but is rarely applied in the environmental sciences. A major advantage of these mass spectrometry based techniques (i.e., proteomics) is the relatively smaU quantity of material required for the analysis this opens up the possibility for analyzing peptides and proteins in total DOM with little or no pre-concentration. However, the presence of salts stUl needs to be minimized before effective mass spectra can be generated. A recent review by Mopper et at. (2007) highlights the application of high-resolution analytical techniques to study marine DOM composition, and we refer the reader to this review for a more comprehensive discussion of recent analytical advances. 

Functional Genomics Informatics for Proteins Proteomics Systems Biology... 

Pieper R, Gatlin CL, Makusky AJ, Russo PS, Schatz CR, Miller SS, Su Q, McGrath AM, Estock MA, Parmar PP, Zhao M, Huang ST, Zhou J, Wang F, Esquer-Blasco R, Anderson NL, Taylor J, Steiner S. The human serum proteome Display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins. Proteomics 2003 3(7) 1345-64. 

Y. Yamamoto, K. Koshikawa, N. Terui, M. Mita, A. Matsuoka and K. Shikima, Biochim. Biophys. Acta - Proteins Proteomics, 2003, 1652, 136. 

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