Structure, three-dimensional oligomers

A mechanism for explaining how oligomeric and polymeric forms of a protein or polypeptide can arise by three-dimensional swapping of internal domains in monomers. The basic idea is that a protein s ternary structure is stabilized by the contacts between its domains, and under certain circumstances, the domains of several polypeptide chains may bind in a way that gives rise to nonphysiologic oligomers, polymers, and aggregates. 

Primary structure of a protein is simply amino acids sequence of the peptide chain. The secondary structure is a result of the different conformations that the chain can take. The tertiary structure refers to the three dimensional shape that results from twisting, bending and folding of protein helix. The quaternary structure refers to the way in which these amino acid chains of a complex protein are associated with each other (oligomer, dimers, trimers, etc.). 

Because of its rigid three-dimensional structure, an enzyme forms highly active catalytic site. Short peptide oligomers possess a more mobile structure, but, nevertheless, are also catalytically active. 

Using Ugi-4CR as prototypical reaction, a possible reaction leading to twofold and fourfold cyclic adduct is shown in Scheme 17. The first Ugi adduct 58 could react further with FGi and FG2 to afford the cyclic product 59 ((1), Scheme 17). Alternatively, the adduct 58 can react with a second equivalent of a bifunctional substrate 56, FGj and FG2 to provide twofold linear Ugi adduct 60, which could be further transformed to fourfold Ugi cyclic adduct 62 via intermediate 61. The formation of higher-order ohgomers/cyclic oligomers could be competitive making this reaction quite difficult to control. However, it is expected that the overall reaction outcome could in principle be governed by the three-dimensional structure of the bifunctional inputs 56 and 57. 

This strategy may be realized by the use of reactive oligomers (RO), i.e. low-molecular weight compounds which may be converted to polymers of linear, branched, ladder and three-dimensional network structures. Of special importance are RO s which form cross-linked polymers since in this case materials with optimal values of heat and fire resistance, strength, chemical stability, atmospheric resistance, durability, etc. may be obtained. 

Calixarenes are cyclic oligomers obtained by condensation reactions between para-t-butyl phenol and formaldehyde. By judicious choice of base, reaction temperature, and reaction time, calixarenes having different ring sizes can be prepared in good yield. Calixarenes are like crowns in that they are preorganized complexants, yet, unlike crowns, they can be readily synthesized in large quantities. Unlike porphyrins, calixarenes are not fully conjugated, and the three-dimensional structure leads to cavities. 

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