Site-specific chemical

Figure 2.7. Identification ofphosphoproteins by site-specific chemical modification. A. Method of Zhou et al. (2001) involves trypsin digest of complex protein mixture followed by addition of sulfhydryl groups specifically to phosphopeptides. The sulfhydryl group allows capture of the peptide on a bead. Elution of the peptides restores the phosphate and the resulting phosphopeptide is analyzed by tandem mass spectrometry. B. Method of creates a biotin tag in place of the phosphate group. The biotin tag is used for subsequent affinity purification. The purified proteins are proteolyzed and identified by mass spectrometry.

The second method also relies on site-specific chemical modification ofphosphoproteins (Oda et al., 2001). It involves the chemical replacement of phosphates on serine and threonine residues with a biotin affinity tag (Fig. 2.7B). The replacement reaction takes advantage of the fact that the phosphate moiety on phosphoserine and phosphothreonine undergoes -elimination under alkaline conditions to form a group that reacts with nucleophiles such as ethanedithiol. The resulting free sulfydryls can then be coupled to biotin to create the affinity tag (Oda et al., 2001). The biotin tag is used to purify the proteins subsequent to proteolytic digestion. The biotinylated peptides are isolated by an additional affinity purification step and are then analyzed by mass spectrometry (Oda et al., 2001). This method was also tested with phosphorylated (Teasein and shown to efficiently enrich phosphopeptides. In addition, the method was used on a crude protein lysate from yeast and phosphorylated ovalbumin was detected. Thus, as with the method of Zhou et al. (2001), additional fractionation steps will be required to detect low abundance phosphoproteins. 

The site-specific chemical modification of post-translation... 

Yem, A.W. et al. (1992) Site-specific chemical modification of interleukin lb by Acrylodan at cysteine 8 and lysine 103./. Biol. Chem. 267, 3122. 

Scope of the CLL approach. Critical loads and levels can be calculated for various specified sensitive elements of the environment (UNECE CLRTAP 2004, V-l). However, terrestrial and aquatic ecosystems are most frequently referred to as receptors in this effect-based approach. In addition, specific parts of ecosystems (e.g., populations of most valuable species) or ecosystem characteristics can be defined as receptors as well (UNECE CLRTAP, 2004). Such flexibility and established provisions for ecosystem assessment makes the CLL concept a promising solution for ecosystem risk assessment and a potential substitute for site-specific chemical RA following the bottom-up approach. 

Classical carrier-linked prodrugs Site-specific chemical delivery systems Macromolecular prodrugs Drug-antibody conjugates... 

A special group of carrier-linked prodrugs are the site-specific chemical delivery systems [23], Macromolecular prodrugs are synthetic conjugates of drugs covalently bound (either directly or via a spacer) to proteins, polypeptides, polysaccharides, and other biodegradable polymers [24],... 

N. Bodor, Novel Approaches to the Design of Safer Drugs Soft Drugs and Site-Specific Chemical Delivery Systems , in Advances in Drug Research , Ed. B. Testa, Academic Press, London, Vol. 13, 1984, p. 255-331. 

Although many of the costs for chemical oxidation technologies will be site specific, chemical costs will generally average 15 to 30% of the total remediation costs. Factors that influence chemical costs will include the chemical oxygen demand (COD) of the contaminated media, pH, the size of the site, and initial contaminant concentrations (D22442A, pp. 19, D-1). 

Tsutsumi, Y., M. Onda, S. Nagata, B. Lee, R.J. Kreitman, and I. Pastan, Site-specific chemical modification with polyethylene glycol of recombinant immunotoxin anti-Tac(Fv)-PE38 (LMB-2) improves antitumor activity and reduces animal toxicity and immunogenicity. Proc Natl Acad Sci USA,... 

Novel approaches to the design of safer drugs Soft drugs and site-specific chemical delivery systems, 13, 255... 

Dunham, T. D., and Farrens, D. L. (1999). Conformational changes in rhodopsin. Movement of helix f detected by site-specific chemical labeling and fluorescence spectroscopy./. Biol. Chem. 274, 1683-1690. 

N. Bodor and J. J. Kaminski, Prodrugs and site-specific chemical delivery systems, Annu. Rep. Med. Chem. 22 303 (1987). 

Pennington, M. W. (1994) Site-specific chemical modification. In Peptide Synthesis Protocols (Pennington, M. W. and Dunn, B. M., eds.), Humana Press Totowa, NJ, p. 173. 

In terms of stability in the repetitive N -deprotection steps required for the synthesis of larger peptides and proteins, only the Z group and particularly its halogenated derivatives are compatible with the Boc/Bzl strategy for N -protection, while among the other groups discussed in Section 2.1.1.1.1, the Fmoc, Teoc, Msc, and particularly Aloe groups have found application in terms of an additional level of selectivity as required in special cases for postsynthetic site-specific chemical manipulations of the peptide chain on resin or in solution. 

When the crystal structure of a protein is not available, other techniques can be employed to identify the amino acids that are involved in its structure and function. Commonly used techniques include chemical cross-linking, site-specific chemical modifications, and mutagenesis. Chemical modifications of Met residues using oxidizing agents such as hydrogen peroxide, t-butyl hydroperoxide, chloramine T, and sodium periodate have been useful in identifying structure and function relationships in many proteins (1-7). 

The prodrug methenamine, described above in this chapter (Scheme S-17), can be considered a site-specific chemical delivery system for the urinary tract antiseptic agent fotmal-dehyde. The low pH of the urine promotes the hydrolysis... 

Puthenveetil S, Whitby L, Ren J, et al. Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification. Nucleic Acids Res. 2006 34 4900-4911. 

Recommendation 10a. Chemical demilitarization facilities should develop site-specific chemical event reporting procedures and an accompanying training program that tests and improves the implemented procedures and communication system. 

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