Cleavage identification

An alternative approach to peptide sequencing uses a dry method in which the whole sequence is obtained from a mass spectrum, thereby obviating the need for multiple reactions. Mass spec-trometrically, a chain of amino acids breaks down predominantly through cleavage of the amide bonds, similar to the result of chemical hydrolysis. From the mass spectrum, identification of the molecular ion, which gives the total molecular mass, followed by examination of the spectrum for characteristic fragment ions representing successive amino acid residues allows the sequence to be read off in the most favorable cases. 

It is important to recognize that the following analytical methods essentially determine EO-PO ratio ( H NMR, IR, cleavage methods) or even simply alkylene oxide content (compleximetric methods) of the analyte, and as such are not specific quantitative or qualitative methods for poloxamers, since EO-PO copolymers of a different structure (for instance, random copolymers, or PO-EO-PO block copolymers) may respond to the methods in a way indistinguishable from poloxamers. The principal technique that permits definitive identification of a sample as a poloxamer is C NMR, which allows structural details, such as the distribution of EO and PO units along the polymer chain, to be elucidated [10]. 

B. The direct identification of such microscopic fracture modes as transgranular cleavage, radial fracture, intergranular separation or ductile dimpled rupture, was shown to be considerably more dependable by SEM than by OM... 

Thus, under suitable experimental conditions, all aromatic sulphones are cleaved, in most cases by a two-electron process summarized by equations 1 and 2. Such reactions have been established1-5 by means of coulometric titration, isolation of cleavage residues ArH and RH and chemical identification of the anion ArS02- (e.g. by treatment of the... 

Culley FJ, Brown A, Conroy DM et al (2000) Eotaxin is specifically cleaved by hookworm metal-loproteases preventing its action in vitro and in vivo. J Immunol 165 6447-6453 Davis DA, Singer KE, De La Luz Sierra M et al (2005) Identification of carboxypeptidase N as an enzyme responsible for C-terminal cleavage of stromal cell-derived factor-lalpha in the circulation. Blood 105 4561 568... 

For cinnamic acid at 9.6 °C, a = 0.107, b = 1.25 and k = 0.69 l.mole .sec E = 26.7 0.5 kcal.mole" and AS = 34.5 eu. Identification of products of oxidation of a number of acids indicates two concurrent mechanisms. Predominating is direct attack on the double bond to give, ultimately, cleavage products, e.g. benzaldehyde from cinnamic acid (some phenylacetaldehyde is also found, indicating oxidative decarboxylation to occur) and also acetophenone from 3-phenylcrotonic acid. 

The second pathway is the eccentric cleavage that occurs at double bonds other than the central 15,15 -double bond of the P-carotene molecule to produce different products called P-apocarotenals with various chain lengths. Because only trace amounts of apocarotenals were detected in vivo from tissues of animals fed P-carotene and these compounds can be formed non-enzymatically from P-carotene auto-oxidation, the existence of this pathway was controversial until recently. The identification of P-carotene 9, 10 -oxygenase (BC02), which acts specifically at the 9, 10 double bond of P-carotene to produce P-apo-lO -carotenal and P-ionone, provided clear evidence of the eccentric cleavage pathway in vivo. Lycopene was also reported as a substrate for BC02 activity. 

Kiefer, C. et al.. Identification and characterization of a mammalian enzyme catalyzing the asymmetric oxidative cleavage of provitamin A, J. Biol. Chem., 276, 14110, 2001. 

Redmond, T.M. et al.. Identification, expression, and substrate specificity of a mammalian beta-carotene 15,15-dioxygenase, J. Biol. Chem., 276, 6560, 2001. Leuenberger, M.G., Engeloch-Jarret, C., and Woggon, W.D., The reaction mechanism of the enzyme-catalyzed central cleavage of beta-carotene to retinal, Ang. Chem. Int. Ed., 40, 2614, 2001. 

Proteolytic cleavage has proven to be an efficient tool for exploring the structure and function of the Na,K-ATPase. Exposure and protection of bonds on the surface of the cytoplasmic protrusion provides unequivocal evidence for structural changes in the a subunit accompanying E1-E2 transition in Na,K-ATPase [52]. Localization of the proteolytic splits provided a shortcut to identification of residues involved in E1-E2 transition [33,53,54] and to detection of structure-function correlations [33]. Further proteolysis identifies segments at the surface of the protein and as the cytoplasmic protrusion is shaved off all ATP-dependent reactions are abolished. 

Definition of Ej and E2 eonformations of the a subunit of Na,K-ATPase involves identification of cleavage points in the protein as well as association of cleavage with different rates of inactivation of Na,K-ATPase and K-phosphatase activities [104,105]. In the Ei form of Na,K-ATPase the cleavage patterns of the two serine proteases are clearly distinct. Chymotrypsin cleaves at Leu (C3), Fig. 3A, and both Na,K-ATPase and K-phosphatase are inactivated in a monoexponential pattern [33,106]. Trypsin cleaves the E form rapidly at Lys ° (T2) and more slowly at Arg (T3) to produce the characteristie biphasic pattern of inactivation. Localization of these splits was determined by sequencing N-termini of fragments after isolation on high resolution gel filtration columns [107]. 

This discussion of the structures of diene polymers would be incomplete without reference to the important contributions which have accrued from applications of the ozone degradation method. An important feature of the structure which lies beyond the province of spectral measurements, namely, the orientation of successive units in the chain, is amenable to elucidation by identification of the products of ozone cleavage. The early experiments of Harries on the determination of the structures of natural rubber, gutta-percha, and synthetic diene polymers through the use of this method are classics in polymer structure determination. On hydrolysis of the ozonide of natural rubber, perferably in the presence of hydrogen peroxide, carbon atoms which were doubly bonded prior to formation of the ozonide... 

Marasco, E. and C. Schmidt-Dannert (2008). Identification of bacterial carotenoid cleavage dioxygenase homologs that cleave the interphenyl u,(J double bond of stilbene derivatives via a monooxygenase reaction. Chembiochem. 9(9) 1450-1461. 

Marasco, E. K., K.-l. Vay et al. (2006). Identification of carotenoid cleavage dioxygenases from Nosloc sp. PCC 7120 with different cleavage activities. J. Biol. Chem. 281(41) 31583-31593. 

Prado-Cabrero, A., A. F. Estrada et al. (2007). Identification and biochemical characterization of a novel carotenoid oxygenase Elucidation of the cleavage step in the Fusarium carotenoid pathway. Mol. Microbiol. 64(2) 448 160. 

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