Hexapeptides, structure

Structurally unique, potent, and selective oxytocin antagonistic agents characterized by a cyclic hexapeptide structure have recently been isolated from the broth filtrate of a novel Streptomyces silvensis strain [434,435]. As shown in formula (106), these compounds contain two hexahydro-3-pyrid-azinecarboxylic acid moieties. A study has been made of their structural modifications (including oxidation of the reduced pyridazine nuclei) [436]. 

These computations, with a hard-sphere potential, were extended to helical pentapeptide and hexapeptide structures of the type gly-X4 and gly-X5 in order to determine the additional steric restrictions which arise... 

A peptidolipid exhibiting antibiotic properties against mycobacteria and viruses produced by Pseudomonas viscosa was obtained as a crystalline compound of m.p. 270-273 °C, [a]o — 168° (ethanol). The N-3d-hydroxydecanoyl-hexapeptide structure (49) proposed originally (118) was later shown to be incorrect because the synthetic product was different from natural viscosin (119). 

Structure of GFP and its chromophore. To study the chro-mophore of GFP, a sample of GFP was denatured by heating it at 90°C. It was digested with papain, and then a peptide containing the fluorophore was isolated and purified from the digested mixture. The structural study of the peptide has indicated that the chromophore of GFP is an imidazolone derivative shown below (Shimomura, 1979). This chromophore structure was confirmed later by Cody etal. (1993) in a hexapeptide isolated from GFP. It is intriguing that the structure of the GFP chromophore is a part of the structure of coelenterazine. 

Branchini, B. R., Lusins, J. O., and Zimmer, M. (1997). A molecular mechanics and database analysis of the structural preorganization and activation of the chromophore-containing hexapeptide fragment in green fluorescent protein. /. Biomol. Struct. Dyn. 14 441-448. 

Cody, C. W., et al. (1993). Chemical structure of the hexapeptide chro-mophore of the Aequorea green-fluorescent protein. Biochemistry 32 1212-1218. 

Tab. 2.8 Comparison of selected backbone torsion angles characteristic of the y-peptide 2.5-heli-cal backbone extracted from NMR solution structure of y -hexapeptide 141 and solid-state structure of y -tetrapeptide 146 [200, 205, 207]...

Surprisingly, in contrast to a- and y9-peptides, CD spectra of y-peptides gave only a very hmited amount of stmctural information. Experiments conducted on heh-cal y" -hexapeptides did not reveal any characteristic CD signature (no Cotton effect) [200, 201]. Similarly, y -peptides built from 2,4-disubstituted y-amino acids of like configuration and shown to adopt a more stable 2.6-helical structure, do not display typical CD curves either [201]. However, CD spectra of the 2.6-helical -peptide 147 and its Boc-protected derivative recorded in MeOH and CD3CN present an intense maximum around 215 nm with a shoulder at ca. 200 nm [207]. 

Saaby S, Knudsen KR, Ladlow M, Ley SV (2005) The Use of a Continuous Flow-Reactor Employing a Mixed Flydrogen-Liquid Flow Stream for the Efficient Reduction of Imines to Amines. Chem Commun 23 2909-2911 Seebach D, Overhand M, Kilhnle FNM, Martinoni D, Oberer L, Hommel U, Widmer H (1996) Beta-Peptides Synthesis by Arndt-Eistert Homologation with Concomitant Peptide Coupling. Structure Determination by NMR and CD Spectroscopy and by X-ray Crystallography. Helical Secondary Structure of a Beta-Hexapeptide in Solution and its Stability Towards Pepsin. Helv Chim Acta 79 913-941... 

From a structural point of view the OPLS results for liquids have also shown to be in accord with available experimental data, including vibrational spectroscopy and diffraction data on, for Instance, formamide, dimethylformamide, methanol, ethanol, 1-propanol, 2-methyl-2-propanol, methane, ethane and neopentane. The hydrogen bonding in alcohols, thiols and amides is well represented by the OPLS potential functions. The average root-mean-square deviation from the X-ray structures of the crystals for four cyclic hexapeptides and a cyclic pentapeptide optimized with the OPLS/AMBER model, was only 0.17 A for the atomic positions and 3% for the unit cell volumes. 

The trisaccharide-hexapeptide partial structure (151) of aleukemia-virus envelope glycoprotein, which was obtained from 46 (see Section 11,2) via saccharide and carboxyl deprotection, has also been coupled to BSA to furnish a synthetic glycoprotein 152 containing 12% of carbohydrate in the form of the trisaccharide (19). 

Menziani, M.C., Cocchi, M., Fanelli, F. and De Benedetti, P.G. (1995) Quantitative structure-affinity/ selectivity relationship analysis on three-dimensional models of the complexes between the ETA and ETB receptors and C-terminal endothelin hexapeptide antagonists. Journal of Molecular Structure (Theochem), 333, 243—248. 

The tripeptides in Fig. 6.17 underwent a few breakdown reactions (N-ter-minus elimination, Qm formation, peptide bond hydrolysis), some of which will be considered later in this section. Of relevance here was that, of the two amidated tripeptides, the amide at the C-terminus underwent deamidation predominantly (Fig. 6.17, Reaction a), which, perhaps, explains the somewhat lesser stability compared to the free carboxylic acid forms. While the hexapeptide (6.52, Fig. 6.17) followed a different pattern of decomposition [76b], deamidation was also a predominant hydrolytic reaction at all pH values. Thus, the procedure to extrapolate results from small model peptides to larger medicinal peptides appears to be an uncertain one, since small modifications in structure can cause large differences in reactivity. 

The structurally related myxochromides Aj.j are cyclic hexapeptides produced by several Myxococcus species. These examples contain a proline residue, which is not present in myxochromides Si 3, as the fourth amino acid in their peptide core. The NRPSs responsible for myxochromides A and S biosynthesis have exacdy the same module and domain organization thus, the fourth module of the myxochromide S synthetase must be skipped to account for the natural product. Biochemical experiments revealed that the A domain of this module activates L-proline, but the adjacent PCP domain cannot be phosphopantetheinylated by a PPTase. These results suggest that the C domain of module 5 reacts directly with the tripeptide intermediate bound to the PCP domain of module 3 in myxochromide S biosynthesis. A similar example of domain skipping has been noted in the biosynthesis of the mannopeptimycins. ... 

Fig. 8 Bound conformations of the hexapeptide DRPVPY. Superposition of structures was performed within Insight II and is based on the backbone atoms of residues 4-6. A Family of 27 structures calculated using trNOE-derived restraints only. B Average of the 27 structures in panel A. Reproduced with permission from [125]. 2002 American Chemical Society...

Cyclic hexapeptides can be considered as the classical and the most prominent representatives among cyclic peptides. Natural products are numerous and widespread (see Scheme 11), e.g. segetalin A,[278] bouvardin/279280 RA-IIlJ281-283 or pneumocandin B0,[284 286] and this type of ring structure has frequently been used to stabilize conformational preferences of bioactive portions of larger peptides or even proteins. 

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