Peptides means

The peptides will now be considered individually in some detail. It must be noted that the large molecular size of the peptides means that they are even less likely to cross the blood-brain barrier than classical transmitters and the instability of peptides means that full functional studies require non-peptide agonists and antagonists. Whereas nature has provided morphine and medicinal chemists have made naloxone, tools are lacking for many other peptides. 

Peptides are a very heterogeneous group of compounds that share the common characteristic of being made up of chains of amino acids joined by an amide bond, also known as a peptide bond. The large number of different amino acids that exists in nature and the large variations in the number of amino acids in a given peptide mean that peptides can be highly diverse. 

Here and later peptide means either CPP or receptor ligand. 

Automated peptide sjmthesis is quite routine now, although the expense of the reagents and difficulty of purification when more than 20 amino acids are incorporated into a peptide means that it is only viable for smaller peptides. 

In synthetic target molecules esters, lactones, amides, and lactams are the most common carboxylic acid derivatives. In order to synthesize them from carboxylic acids one has generally to produce an activated acid derivative, and an enormous variety of activating reagents is known, mostly developed for peptide syntheses (M. Bodanszky, 1976). In actual syntheses of complex esters and amides, however, only a small selection of these remedies is used, and we shall mention only generally applicable methods. The classic means of activating carboxyl groups arc the acyl azide method of Curtius and the acyl chloride method of Emil Fischer. 

For nonvolatile or thermally labile samples, a solution of the substance to be examined is applied to the emitter electrode by means of a microsyringe outside the ion source. After evaporation of the solvent, the emitter is put into the ion source and the ionizing voltage is applied. By this means, thermally labile substances, such as peptides, sugars, nucleosides, and so on, can be examined easily and provide excellent molecular mass information. Although still FI, this last ionization is referred to specifically as field desorption (FD). A comparison of FI and FD spectra of D-glucose is shown in Figure 5.6. 

Mass spectral fragmentation patterns of alkyl and phenyl hydantoins have been investigated by means of labeling techniques (28—30), and similar studies have also been carried out for thiohydantoins (31,32). In all cases, breakdown of the hydantoin ring occurs by a-ftssion at C-4 with concomitant loss of carbon monoxide and an isocyanate molecule. In the case of aryl derivatives, the ease of formation of Ar—NCO is related to the electronic properties of the aryl ring substituents (33). Mass spectrometry has been used for identification of the phenylthiohydantoin derivatives formed from amino acids during peptide sequence determination by the Edman method (34). 

Evidence soon emerged that the endogenous opioids were peptides rather than simple morphine-like molecules (9). The first direct evidence for endogenous opioids in brain extracts was provided in 1975 when two pentapeptides were purified that differed only in the carboxyl terminal amino acids (10) (Table 1). These peptides were called methionine- (Met-) and leucine- (Leu-) enkephalin, from the Greek term meaning "in the head."... 

The succinimide derivative (234) can be used in peptide synthesis for conversion of amino acids into their succinimide esters (235 Scheme 41) (79CL1265). 3-Substituted mercapto-1,2-benzisothiazole 1,1-dioxides (236) have been recommended as an odourless means of storage of thiols. The latter are readily regenerated by the action of piperidine (81CL1457). 

Most of the 2D QSAR methods are based on graph theoretic indices, which have been extensively studied by Randic [29] and Kier and Hall [30,31]. Although these structural indices represent different aspects of molecular structures, their physicochemical meaning is unclear. Successful applications of these topological indices combined with multiple linear regression (MLR) analysis are summarized in Ref. 31. On the other hand, parameters derived from various experiments through chemometric methods have also been used in the study of peptide QSAR, where partial least square (PLS) [32] analysis has been employed [33]. 

Meador, W.E., Means, A.R., Quiocho, F.A. Target enzyme recognition by calmodulin 2.4 A stmcture of a calmodulin-peptide complex. Science 257 1251-1255, 1992. 

In order to examine whether this sequence gave a fold similar to the template, the corresponding peptide was synthesized and its structure experimentally determined by NMR methods. The result is shown in Figure 17.15 and compared to the design target whose main chain conformation is identical to that of the Zif 268 template. The folds are remarkably similar even though there are some differences in the loop region between the two p strands. The core of the molecule, which comprises seven hydrophobic side chains, is well-ordered whereas the termini are disordered. The root mean square deviation of the main chain atoms are 2.0 A for residues 3 to 26 and 1.0 A for residues 8 to 26. 

It should be emphasized here that the four major complexes of the electron transport chain operate quite independently in the inner mitochondrial membrane. Each is a multiprotein aggregate maintained by numerous strong associations between peptides of the complex, but there is no evidence that the complexes associate with one another in the membrane. Measurements of the lateral diffusion rates of the four complexes, of coenzyme Q, and of cytochrome c in the inner mitochondrial membrane show that the rates differ considerably, indicating that these complexes do not move together in the membrane. Kinetic studies with reconstituted systems show that electron transport does not operate by means of connected sets of the four complexes. 

The transmembrane potential derived from a concentration gradient is calculable by means of the Nemst equation. If K+ were the only permeable ion then the membrane potential would be given by Eq. 1. With an ion activity (concentration) gradient for K+ of 10 1 from one side to the other of the membrane at 20 °C, the membrane potential that develops on addition of Valinomycin approaches a limiting value of 58 mV87). This is what is calculated from Eq. 1 and indicates that cation over anion selectivity is essentially total. As the conformation of Valinomycin in nonpolar solvents in the absence of cation is similar to that of the cation complex 105), it is quite understandable that anions have no location for interaction. One could with the Valinomycin structure construct a conformation in which a polar core were formed with six peptide N—H moieties directed inward in place of the C—O moieties but... 

The peptide is removed from the polystyrene resin by means of hydrogen fluoride. The couplings were nearly complete by using a threefold excess of the N-protected tripeptide. A fractionation of the resulting oligotripeptide, however, has been performed. The folding behavior in water was much more pronounced than in the case of the polymers obtained by the old TEPP method13 . 

Since 1973, several authors have proved that there is a relationship between thermostability of collagen and the extent of hydroxylation of the proline residues31,34). Equilibrium measurements of the peptides al-CB 2 of rat tail and rat skin revealed a higher rm, for al-CB 2 (rat skin)157). The sequence of both peptides is identical except that in the peptide obtained from rat skin, the hydroxylation of the proline residues in position 3 has occurred to a higher extent than in the case of al-CB 2 (rat tail). Thus, a mere difference of 1.8 hydroxy residues per chain causes a ATm of 26 K. Obviously, there are different stabilizing interactions in the triple-helical state, that means al-CB 2 (rat skin) forms more exothermic bonds than al-CB 2 (rat tail) in the coil triple-helix transition. This leads to an additional gain of enthalpy which overcompensates the meanwhile occurring losses of entropy. 

Figure 5.31 LC-electrospray-MS-MS spectrum of the column eluate at around 22 min in the analysis of the peptide mixture from the tryptic digest of glycoprotein TIME-EA4 from silkworm diapause eggs. Reprinted from Bioorg. Med. Chem., 10, Kurahashi, T., Miyazaki, A., Murakami, Y., Suwan, S., Franz, T., Isobe, M., Tani, M. and Kai, H., Determination of a sugar chain and its linkage site on a glycoprotein TIME-EA4 from silkworm diapause eggs by means of LC-ESI-Q-TOF-MS and MS/MS , 1703-1710, Copyright (2002), with permission from Elsevier Science.

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