Side-chains, oligomers

Peptoids are an archetypal and relatively conservative example of a peptidomimetic oligomer (Tab. 1.1). In fact, the sequence of atoms along the peptoid backbone is identical to that of peptides. However, peptoids differ from peptides in the marmer of side chain appendage. Specifically, the side chains of peptoid oligo-... 

The second step introduces the side chain group by nucleophilic displacement of the bromide (as a resin-bound a-bromoacetamide) with an excess of primary amine. Because there is such diversity in reactivity among candidate amine submonomers, high concentrations of the amine are typically used ( l-2 M) in a polar aprotic solvent (e.g. DMSO, NMP or DMF). This 8 2 reaction is really a mono-alkylation of a primary amine, a reaction that is typically complicated by over-alkylation when amines are alkylated with halides in solution. However, since the reactive bromoacetamide is immobilized to the solid support, any over-alkyla-tion side-products would be the result of a cross-reaction with another immobilized oligomer (slow) in preference to reaction with an amine in solution at high concentration (fast). Thus, in the sub-monomer method, the solid phase serves not only to enable a rapid reaction work-up, but also to isolate reactive sites from... 

If the individual residues of a peptide are transformed into the corresponding peptoid monomers to make hybrid oligomers, there will be a perturbation in the distance between side chains at the boundary between oligomer types. That is, spacing of side chains at a peptoid-peptide linkage will be different from that between either two peptide or peptoid residues. 

Burkoth, T. S., Faearman, A.T., Char-YCH, D. H., Connolly, M.D., and Zuckermann, R.N. Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis. J. Am. Chem. Soc. 2003 125, 8841-8845. 

Wu, C.W., Sanborn, T.J., Zuckermann, R.N., and Barron, A. E. Peptoid oligomers with alpha-chiral, aromatic side chains Effects of chain length on secondary structure. /. Am. Chem. Soc. 2001, 723, 2958-2963. 

Next to the subunit from which these oligomers were released, two other subunits were recognized a highly methyl esterified xylogalacturonan segment and residual stubs of the backbone rich in branched arabinose side chains. 

Milieu conditions in gastrointestinal tract can influence the pectin structure and properties. Under the acid conditions of the stomach (pH 2-4) extraction of pectin from plant cell walls and hydrolysis of side chains can occur. In small intestine (pH 5-6) -elimination of main chains or de-esterification seems to be possible. In caecum and colon (pH 6-8) a strong fermentation of pectin takes place causing depolymerization to oligomers and leading to formation of short chain fatty acids and gases. The presence of OligoGalA is not yet clarified. 

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