Oligomers, helical structure

The well-defined helical structure associated with appropriately substituted peptoid oligomers (Section 1.6) can be employed to fashion compounds that closely mimic the stracture and function of certain bioactive peptides. There are many examples of small helical peptides (<100 residues) whose mimicry by non-natural ohgomers could potentially yield valuable therapeutic and bioactive compounds. This section describes peptoids that have been rationaUy designed as mimics of antibacterial peptides, lung surfactant proteins, and coUagen proteins. Mimics of HIV-Tat protein, although relevant to this discussion, were described previously in this chapter (Sections 1.3.2 and 1.4.1). 

Fig. 2.3 Model of the 2i- and 3i-helical structures proposed for PHB chains with ideal torsion angle values. The 2i-helix was determined by fiber X-ray diffraction of PHB [49-51] while the 3i-helical fold was constructed by using preferred dihedral angles found along the backbone in crystal structures of cyclic oligomers 9 ( oligolides ) [37, 43, 45]...

The zinc complex of 1,1,1,5,5,5-hexafluoroacetylacetonate forms coordination polymers in reaction with either 2,5-bis(4-ethynylpyridyl)furan or l,2-bis(4-ethynylpyridyl)benzene. The X-ray crystal structures demonstrate an isotactic helical structure for the former and a syndio-tactic structure for the latter in the solid state. Low-temperature 1H and 19F NMR studies gave information on the solution structures of oligomers. Chiral polymers were prepared from L2Zn where L = 3-((trifluoromethyl)hydroxymethylene)-(+)-camphorate. Reaction with 2,5-bis(4-ethy-nylpyridyl)furan gave a linear zigzag structure and reaction with tris(4-pyridyl)methanol a homo-chiral helical polymer.479... 

The consistent solvent- and chain-length-dependent phenomena suggest that a helical structure is being formed however, double-helical, knotlike or alternatively folded structures could not be ruled out (Fig. 4). Double-helical structures are not believed to be present since there is no concentration dependence below 10 pmol for the 12-mer in acetonitrile at room temperature. To rule out misfolded knotlike structures, a series of oligomers were designed with a methyl group in the internal position of the helix (19-27) [28]. The... 

Incorporation of an imine unit into a mPE began with a Monte Carlo search of dodecamer (58e), which indicated that the oligomer adopted a six-turn helical structure [86]. To verify these results solvent denaturation studies were performed on 58e which showed a helix coil transition with a AG(CH3CN) very similar to that of the native oligomers (3.0 0.2 for 58e vs 3.2 0.1 for 15). The small difference in the AG(CH3CN) indicates that the imine bond has a negligible effect on the stability of the folded state of the oligomer. With this... 

The other major type of symmetry found in oligomers, helical symmetry, also occurs in capsids. Tobacco mosaic virus is a right-handed helical filament made up of 2,130 identical subunits (Fig. 4-25b). This cylindrical structure encloses the viral RNA. Proteins with subunits arranged in helical filaments can also form long, fibrous structures such as the actin filaments of muscle (see Fig. 5-30). 

The surprising discovery that small oligo-P-peptides exhibit extraordinary tendencies to form stable secondary structures has led to rapid developments in the chemistry of these peptides. The earliest work in the field revolved around the synthesis of P-peptide polymers (the so-called nylon-3 derivatives). 2 Polymerization of P-amino acids led to polymers of undefined length. It was noted they could form stable structures but it proved impossible to gain any concrete information about the nature of those structures at that time. The developments in the synthesis of P-peptide oligomers of predefined length and advances in methods (i.e., NMR spectroscopy and X-ray crystallography) for the 3D characterization of such compounds has led to the discovery of new helical structures found to be adopted by a variety of P-peptides. I1,3-7 ... 

The discovery of these base pairs, which imply the double helical structure of DNA, stimulated a series of crystal structural studies not only of complexes of purines and pyrimidines, but of other complexes involving related molecules and their derivatives. Although we can formulate a large number of possible heterocombinations in matrix form, as shown below these complexes are reluctant to crystallize even when there is spectroscopic evidence of hetero-complex formation in solution. This is presumably because self-(homo)-association is energetically more favorable and only in rare cases were crystals of hetero complexes actually formed. Because of their three hydrogen bonds, G-C complexes form and crystallize more readily. There have been many attempts to crystallize the Watson-Crick A-U base pair, but none was successful and it only formed when the dinucleoside phosphate adenylyl-3,5,-uridine (ApU [536]) or higher oligomers were crystallized (see Part III, Chapter 20). 

The helical structure of polychloral was proposed by Vogl in 198028 and was demonstrated by Ute, Hatada, and Vogl via a detailed conformational analysis of chloral oligomers.29 As an example of a helical polymer with an inorganic backbone, polysilanes bearing a chiral side chain were synthesized and their conformational aspects were studied. A helical conformation with an excess screw sense for this class of polymers in solution was found in 1994 independently by Fujiki30a and by Moller.300 Matyjaszewski had pointed out such a conformation for chiral polysilanes in the solid state in 1992.30c... 

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