Isomeric peptides

Since amino acids can be assembled in any order, depending on which -C02H group joins with which -NH2 group, the number of possible isomeric peptides increases rapidly as the number of amino acid residues increases. There are six... 

This method is quite useful when distinguishing isomeric peptides, i.e., with the same amino acids but in a different sequence (Fig. 65). a, AcN-Val-Ala-Leu-COOMe b, AcN-Leu-Ala-Val-COOMe. 

Clearly, CTI leads to a periodic backbone contraction/expansion of the polypeptide chain involved, as could be inferred from the isomer-specific distances of the Ca atoms directly attached to the isomerizing peptide bond. For prolyl bonds in native proteins this distance is about 0.8 A shorter in the cis isomer when compared to the respective trans isomer [12]. This atomic translation produces a mechanical moment that was hypothesized to be involved in the functional cycle of motor proteins [13]. 

Wu, C. Siems, W.F. Klasmeier, J. Hill, H.H., Separation of isomeric peptides using electrospray ionization/high-resolution ion mobility spectrometry, Anal. Chem. 2000, 72, 391-395. 

The synthesis of these five isomeric peptides (I-V in Table VII) was carried out by a group working at Lederle Laboratories Division of the American Cyanamid Co. (24,81,82,83,426,427,428) (diagram 1 to 6.)... 

Wee, S. O Hair, R. A. J. McFadyen, W. D. Side-chain radical losses from radical cations allows distinction of leucine and isoleucine residues in the isomeric peptides Gly-XXX-Arg. S. Rapid Commun. Mass Spectrom. 2002,16, 884-890. 

R. J. Loncharich, B. R. Brooks, and R. W. Pastor. Langevin dynamics of peptides The frictional dependence of isomerization rates of N-acetylalanyl-N -methylamide. Biopolymers, 32 523-535, 1992. 

This reaction sequence is much less prone to difficulties with isomerizations since the pyridine-like carbons of dipyrromethenes do not add protons. Yields are often low, however, since the intermediates do not survive the high temperatures. The more reactive, faster but less reliable system is certainly provided by the dipyrromethanes, in which the reactivity of the pyrrole units is comparable to activated benzene derivatives such as phenol or aniline. The situation is comparable with that found in peptide synthesis where the slow azide method gives cleaner products than the fast DCC-promoted condensations (see p. 234). 

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... 

In the native protein these less stable ds-proline peptides are stabilized by the tertiary structure but in the unfolded state these constraints are relaxed and there is an equilibrium between ds- and trans-isomers at each peptide bond. When the protein is refolded a substantial fraction of the molecules have one or more proline-peptide bonds in the incorrect form and the greater the number of proline residues the greater the fraction of such molecules. Cis-trans isomerization of proline peptides is intrinsically a slow process and in vitro it is frequently the rate-limiting step in folding for those molecules that have been trapped in a folding intermediate with the wrong isomer. 

This isoxazolium salt (10 g.) (obtained from the Aldrich Chemical Company, Inc.) was dissolved in 45 ml. of aqueous 1 M hydrochloric acid and reprecipitated by the slow addition with swirling of 400 ml. of acetone. The salt was collected, washed with 300 ml. of acetone, and dried overnight at 25° under reduced pressure (< 1 min.) to give a fluffy product, m.p. 206-208° (decomp.). An isomeric salt, A-ethyl-5-phenylisoxazolium-4 -sulfonate, which may be obtained by the usual synthetic procedure,2 is also useful in peptide synthesis. 

In this case, we point to the fact that a fast (r < 5 s) and a slow phase have been observed in temperature-jump experiments also with the peptide Col 1-3. The slow phase - as already mentioned - has been associated with the cis-trans isomerism of peptide bonds in the direct neighborhood of the helical part. Only peptide bonds to which proline or hydroxyproline contribute their secondary nitrogen are able to assume a cry-configuration at equilibrium (cis to trans ratios of 1 40 to 1 l)l45). Therefore, the fast... 

One may conclude that the rate-determining step of the renaturation is at least partly influenced by the cis-trans isomerization of the peptide bond the secondary nitrogen atom of which arises from proline. Otherwise, only the entropy-controlled slow nuclea-tion should be observed kinetically. The covalent bridging through Lys-Lys, therefore, gives rise not only to thermodynamic stabilization of the triple helix but also to kinetic properties which have hitherto been observed in the case of type III procollagen146) and its aminoterminal fragment Col 1-3144). 

If peptide residues are converted to peptoid residues, the conformational heterogeneity of the polymer backbone is likely to increase due to cis/trans isomerization at amide bonds. This will lead to an enhanced loss of conformational entropy upon peptoid/protein association, which could adversely affect binding thermodynamics. A potential solution is the judicious placement of bulky peptoid side chains that constrain backbone dihedral angles. 

All X-Pro peptide bonds—where X represents any residue—are synthesized in the trans configuration. However, of the X-Pro bonds of mature proteins, approximately 6% are cis. The cis configuration is particularly common in P-turns. Isomerization from trans to cis is catalyzed by the enzyme proline-CM,tr(2 r-iso-merase (Figure 5-9). 

Figure 5-9. Isomerization of the N-a, prolyl peptide bond from a cis to a trans configuration relative to the backbone of the polypeptide.

Reversed micelles have also shown to be useful not only in bioconversions, but also in organic synthesis. Shield et al. (1986) have reviewed this subject and brought out its advantages in peptide synthesis, oxidation or reduction of steroids, selective oxidation of isomeric mixtures of aromatics, etc. In the oxidation of aromatic aldehydes to carboxylic acids with enzymes hosted in reverse micelles, the ortho substituted substrates react much more slowly than other isomers. 

T. Geiger and S. Clarke, Deamidation, isomerization and racemization at asparaginyl and aspartyl residues in peptides, J. Biol. Chem, 262, 785 (1987). 

Fig. 3 Protonation states, isomerism and mesomerism of the HBI chromophore (p-hydroxybenzi-lidene-imidazolinone). The chromophore is shown in its most stable Z ( cw ) conformation, conventionally associated to a 0° value of the dihedral angle t, while the E ( trans ) conformation corresponds to t = 180°. For model compound HBDI (4 -hydroxy-benzylidene-2,3-dimethyl-imidazolinone), Ri = R2 = CH3, for chromophore in GFP, Ri, and R2 stand for the peptidic main chains toward N-terminus and C-terminus, respectively, (a) Possible protonation states of HBI (a) neutral, (b) anionic, (c) enolic, (d) cationic, and (e) zwitterionic. (b) Two resonance structures of the anionic form of HBI...

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