Terminal residues

Because oligosaccharides often branch, they can have more non-reducing than reducing terminals and the latter may anyway be blocked, for example by protein or lipid. Unfortunately, there is no simple method for labelling the non-reducing ends of chains and so their nature has often to be determined by indirect methods, such as methylation or oxidation (see below). 

Where reducing (aldehydic) terminals are available for reaction, they can be labelled by reduction with agents such as tritiated sodium borohydride or by conversion into a cyanohydrin with C-labelled sodium cyanide. Alternatively, labelling with reagents such as dansyl hydrazide is possible, to yield a fluorescent derivative. 

Another method for the stepwise degradation of a polypeptide chain has been suggested by Levy (1950). Here the A-terminal residue is split off as a 2-thiothiazolid-5-one derivative as follows  

Here again the process may be repeated on the peptide chain containing one residue less. This method has not yet been worked out on a small scale, but was found to give satisfactory results with synthetic peptides. 

The reaction of CS2 with amino groups has also been used by L onis (1948) as the basis for a titration method for estimating the total a-amino groups as well as -amino, imino, and thiol groups. CS2 reacts about ten times as rapidly with a-amino groups as with -amino groups, so that the two may be distinguished. 

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Example Molecular dynamics simulations of selected portions of proteins can demonstrate the motion of an amino acid sequence while fixing the terminal residues. These simulations can probe the motion of an alpha helix, keeping the ends restrained, as occurs n atiirally m transmembrane proteins. You can also investigate the conformations of loops with fixed endpoints. 

Several chemical methods have been devised for identifying the N terminal ammo acid They all take advantage of the fact that the N terminal ammo group is free and can act as a nucleophile The a ammo groups of all the other ammo acids are part of amide linkages are not free and are much less nucleophilic Sanger s method for N terminal residue analysis involves treating a peptide with 1 fluoro 2 4 dimtrobenzene which is very reactive toward nucleophilic aromatic substitution (Chapter 23)... 

When Sanger s method for N terminal residue analysis was discussed you may have wondered why it was not done sequentially Simply start at the N terminus and work steadily back to the C terminus identifying one ammo acid after another The idea is fine but It just doesn t work well m practice at least with 1 fluoro 2 4 dimtrobenzene... 

A major advance was devised by Pehr Edman (University of Lund Sweden) that has become the standard method for N terminal residue analysis The Edman degrada tion IS based on the chemistry shown m Figure 27 12 A peptide reacts with phenyl iso thiocyanate to give a phenylthwcarbamoyl (PTC) denvative as shown m the first step This PTC derivative is then treated with an acid m an anhydrous medium (Edman used mtromethane saturated with hydrogen chloride) to cleave the amide bond between the N terminal ammo acid and the remainder of the peptide No other peptide bonds are cleaved m this step as amide bond hydrolysis requires water When the PTC derivative IS treated with acid m an anhydrous medium the sulfur atom of the C=S unit acts as... 

This reaction forms the basis of one method of terminal residue analysis A peptide is treated with excess hydrazine in order to cleave all the peptide linkages One of the terminal amino acids is cleaved as the free amino acid and identified all the other ammo acid residues are converted to acyl hydrazides Which amino acid is identified by hydrazmolysis the N terminus or the C terminus ... 

It has been proposed to designate polymethine cations (9a) in an electron-deficient (N — 1) form, and anion (9b) in an electron-excessive (N + 1) form (17). As a rule, typical PMDs have only one stable form, in contrast to related polyenes with the same terminal residues which have two or even three relatively stable forms (17,18). 

Nucleophilic Reagents. In contrast to electrophilic reactions, nucleophiles attack positively charged, even carbons ia the chain. The reactions lead to the exchanging of substituents or terminal residues. Thus, SR and OR groups, or halogen atoms can be exchanged by other suitable nucleophiles (4,69,70), for example, by aniline ... 

If the dye contains no mobile substituents ia the chain, nucleophiles attack primarily the end carbon atoms (changing of terminal residues). Streptocyanines can be hydroly2ed ia aqueous alkaline solution to form the corresponding merocyanines and then the oxonoles (71,72). These processes are reversible. Nucleophilic reactions with the methylene bases of the corresponding heterocycles result ia polymethines containing new end groups (Fig. 

A two-site immunometric assay of undecapeptide substance P (SP) has been developed. This assay is based on the use of two different antibodies specifically directed against the N- and C-terminal parts of the peptide (95). Affinity-purified polyclonal antibodies raised against the six amino-terminal residues of the molecule were used as capture antibodies. A monoclonal antibody directed against the carboxy terminal part of substance P (SP), covalently coupled to the enzyme acetylcholinesterase, was used as the tracer antibody. The assay is very sensitive, having a detection limit close to 3 pg/mL. The assay is fiiUy specific for SP because cross-reactivity coefficients between 0.01% were observed with other tachykinins, SP derivatives, and SP fragments. The assay can be used to measure the SP content of rat brain extracts. 

J. M. Manning, ia E. Antonini, L. Rossi-Bemardi, and E. Chiancone, eds.. Methods in En mology, Hemoglobins, Academic Press, New York, 1981, pp. 159—167. Preparation of hemoglobin carbamylated at specific NH -terminal residues. 

Figure 8.3 The DNA-binding protein Cro from bacteriophage lambda contains 66 amino acid residues that fold into three a helices and three P strands, (a) A plot of the Ca positions of the first 62 residues of the polypeptide chain. The four C-terminal residues are not visible in the electron density map. (b) A schematic diagram of the subunit structure. a helices 2 and 3 that form the helix-turn-helix motif ate colored blue and red, respectively. The view is different from that in (a), [(a) Adapted from W.F. Anderson et al., Nature 290 754-758, 1981. (b) Adapted from D. Ohlendorf et al., /. Mol. Biol. 169 757-769, 1983.]...

The polypeptide chain of the 92 N-terminal residues is folded into five a helices connected by loop regions (Figure 8.6). Again the helices are not packed against each other in the usual way for a-helical structures. Instead, a helices 2 and 3, residues 33-52, form a helix-turn-helix motif with a very similar structure to that found in Cro. 

The side of the p sheet that faces away from DNA is covered by two long a helices. One of these helices contains a number of basic residues from the middle segment of the polypeptide chain while the second helix is formed by the C-terminal residues. Residues from these two helices and from the short loop that joins the two motifs (red in Figure 9.4) are likely candidates for interactions with other subunits of the TFIID complex, and with specific transcription factors. 

For the identification of the C-terminal residue of polypeptides, an enzymatic approach is commonly used. 

ENZYMATIC ANALYSIS WITH CARBOXYPEPTIDASES. Carboxypeptidases are enzymes that cleave amino acid residues from the C-termini of polypeptides in a successive fashion. Four carboxypeptidases are in general use A, B, C, and Y. Carboxypeptidase A (from bovine pancreas) works well in hydrolyzing the C-terminal peptide bond of all residues except proline, arginine, and lysine. The analogous enzyme from hog pancreas, carboxypeptidase B, is effective only when Arg or Lys are the C-terminal residues. Thus, a mixture of carboxypeptidases A and B liberates any C-terminal amino acid except proline. Carboxypeptidase C from citrus leaves and carboxypeptidase Y from yeast act on any C-terminal residue. Because the nature of the amino acid residue at the end often determines the rate at which it is cleaved and because these enzymes remove residues successively, care must be taken in interpreting results. Carboxypeptidase Y cleavage has been adapted to an automated protocol analogous to that used in Edman sequenators. 

FIGURE 9.19 Proteins containing the C-terminal sequence CAAX can undergo prenylation reactions that place thioether-linked farnesyl or geranylgeranyl groups at the cysteine side chain. Prenylation is accompanied by removal of the AAX peptide and methylation of the carboxyl group of the cysteine residue, which has become the C-terminal residue. 

What is the N-terminal residue on a peptide that gives the following PTH derivative on Edmau degradation ... 

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Proteins with destabilizing N-terminal residues such as arginine and leucine are recognized by a RING-type ubiquitin ligase (termed N-recognin or E3-a) that, together with a specific ubiquitin c, mediates poly-ubiquitylation. 

Threonine peptidases (and some cysteine and serine peptidases) have only one active site residue, which is the N-terminus of the mature protein. Such a peptidase is known as an N-terminal nucleophile hydrolase or Ntn-hydrolase. The amino group of the N-terminal residue performs the role of the general base. The catalytic subunits of the proteasome are examples of Ntn-hydrolases. 

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