N-terminals

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

Identify the N terminal and the C terminal amino acid m the original peptide and m each fragment... 

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)... 

Acid hydrolysis cleaves the amide bonds of the 2 4 dimtrophenyl labeled peptide giving the 2 4 dimtrophenyl labeled N terminal ammo acid and a mixture of unlabeled ammo acids... 

FIGURE 27 12 Identifica tion of the N terminal ammo acid of a peptide by Edman degradation... 

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... 

Step 2 On reaction with hydrogen chloride m an anhydrous solvent the thiocarbonyl sulfur of the PTC derivative attacks the carbonyl carbon of the N terminal ammo acid The N terminal ammo acid is cleaved as a thiazolone derivative from the remainder of the peptide... 

Step 3 Once formed the thiazolone derivative isomerizes to a more stable phenylthiohydantom (PTH) derivative which IS isolated and characterized thereby providing identification of the N terminal ammo acid The remainder of the peptide (formed m step 2) can be isolated and subjected to a second Edman degradation... 

Only the N terminal amide bond is broken m the Edman degradation the rest of the peptide chain remains intact It can be isolated and subjected to a second Edman procedure to determine its new N terminus We can proceed along a peptide chain by beginning with the N terminus and determining each ammo acid m order The sequence is given directly by the structure of the PTH derivative formed m each successive degradation... 

Protect the ammo group of the N terminal ammo acid and the carboxyl group of the C terminal ammo acid... 

A related N terminal protecting group is tert butoxycarbonyl abbreviated Boc... 

Modem methods of peptide sequencing follow a strategy similar to that used to sequence insulin but are automated and can be carried out on a small scale A key feature is repetitive N terminal identification using the Edman degradation... 

Section 28 12 The start codon for protein biosynthesis is AUG which is the same as the codon for methionine Thus all proteins initially have methionine as their N terminal ammo acid but lose it subsequent to their formation The reaction responsible for extending the protein chain is nucleophilic acyl substitution... 

Edman degradation (Section 27 13) Method for determining the N terminal amino acid of a peptide or protein It in volves treating the material with phenyl isothiocyanate (CgH5N=C=S) cleaving with acid and then identifying the phenylthiohydantoin (PTH derivative) produced Elastomer (Section 10 11) A synthetic polymer that possesses elasticity... 

Sanger s reagent (Section 27 11) The compound 1 fluoro 2 4 dimtrobenzene used in N terminal ammo acid identifica tion... 

P-Endorphin. A peptide corresponding to the 31 C-terminal amino acids of P-LPH was first discovered in camel pituitary tissue (10). This substance is P-endorphin, which exerts a potent analgesic effect by binding to cell surface receptors in the central nervous system. The sequence of P-endorphin is well conserved across species for the first 25 N-terminal amino acids. Opiates derived from plant sources, eg, heroin, morphine, opium, etc, exert their actions by interacting with the P-endorphin receptor. On a molar basis, this peptide has approximately five times the potency of morphine. Both P-endorphin and ACTH ate cosecreted from the pituitary gland. Whereas the physiologic importance of P-endorphin release into the systemic circulation is not certain, this molecule clearly has been shown to be an important neurotransmitter within the central nervous system. Endorphin has been invaluable as a research tool, but has not been clinically useful due to the avadabihty of plant-derived opiates. 

Biosynthesis. Three separate genes encode the opioid peptides (see Fig. 1). Enkephalin is derived from preproenkephalin A, which contains six copies of Met-enkephalin and extended peptides, and one copy of Leu-enkephalin (62—66). ( -Endorphin is one of the many products of POMC, and represents the N-terminal 31 amino acids of P-Hpotropin (67,68). Three different dynorphin peptides are derived from the third opioid gene, preproenkephalin B, or preprodynorphin (69). The dynorphin peptides include dynorphin A, dynorphin B, and a-neo-endorphin. 

H-Tyr-D-Ala-Pile-Asp-Val-Val-Gly-NH2 (D-Ala -deltorpliiu I) and H-Tyr-D-Ala-Plie-Glu-Val-Val-Gly-NH2 (D-Ala -deltorpliiu II) display greater 5-selectivity than DPDPE owiag to their higher 5-receptor affinity (96). These compounds both contain the same N-terminal tripeptide sequence as the. -selective dermorphins, which underscores the importance of the C-terminal tetrapeptide sequence in conferring 5-selectivity. 

Figure 4.6 The bifunctional enzyme PRA-isomerase (PRAI) IGP-synthase (IGPS) catalyzes two sequential reactions in the biosynthesis of tryptophan. In the first reaction (top half), which is catalyzed by the C-terminal PRAI domain of the enzyme, the substrate N-(5 -phosphoribosyl) anthranilate (PRA) is converted to l-(o-carboxyphenylamino)-l-deoxyribulose 5-phosphate (CdRP) by a rearrangement reaction. The succeeding step (bottom half), a ring closure reaction from CdRP to indole-3-glycerol phosphate (IGP), is catalyzed by the N-terminal IGPS domain.

Figure S.7 The subunit structure of the neuraminidase headpiece (residues 84-469) from influenza virus is built up from six similar, consecutive motifs of four up-and-down antiparallel fi strands (Figure 5.6). Each such motif has been called a propeller blade and the whole subunit stmcture a six-blade propeller. The motifs are connected by loop regions from p strand 4 in one motif to p strand 1 in the next motif. The schematic diagram (a) is viewed down an approximate sixfold axis that relates the centers of the motifs. Four such six-blade propeller subunits are present in each complete neuraminidase molecule (see Figure 5.8). In the topological diagram (b) the yellow loop that connects the N-terminal P strand to the first P strand of motif 1 is not to scale. In the folded structure it is about the same length as the other loops that connect the motifs. (Adapted from J. Varghese et al.. Nature 303 35-40, 1983.)...

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