Self-Assembly of Synthetic and Biological Polymeric Systems of ...

acids whose lateral side chains change in size, form, charge, hydrophobic character and
chemical reactivity.
5.1.2.- Secondary structure of the proteins.
The secondary structure of proteins depends on four factors: i) bond length and angles of
peptidic bonds; ii) the coplanar arrangement of the substituted atoms in amide groups; iii) the
hydrogen bonding between functional –NH and C=O groups in order to maintain structural
stability; iv) the distance of the hydrogen bonds that can be formed (3). For instance, segments
of polypeptide chains are in a coiled conformation due to intramolecular interaction, i.e. the
atoms involved in amide groups must remain coplanar, and for maximal stability, each N-H
group must be hydrogen bonded to a –CO and each -CO to a –NH. Under ideal conditions,
functional groups (carboxylic and amine groups) of amino acids can form hydrogen bonds, with
an energy of 5 kcal/mol. The polypeptide chains tend to adopt up to three different
configurations that enable the formation of a maximum number of hydrogen bonds: alpha
helix, beta sheet, turns or loops (Figure 5.2).
The alpha helix (α-helix) displays a cylindrical structure (Figure 5.2a) where the polypeptidic
backbone possesses a helical conformation strongly folded into the internal cylindrical core.
The side lateral chains are extended out of the helical distribution. The α-helix is stabilised by
the hydrogen bonding along the principal backbone chain. Within this, the separation between
the amino acids is close to 1.5 Å, and each complete helical turn has 3.6 amino acids
(4)(91)(92). Alanine and leucine are strong helix favouring residues, while proline is rarely
found in helices, because in its backbone nitrogen is not to available for the hydrogen bonding
required for helix formation. The aromatic side chain of phenylalanine can sometimes
participate in weakly polar interactions (4).
The beta sheet fold (β-sheet) differs markedly from the α-helix. A polypeptide chain, called a β-
strand, in a β-sheet is almost fully extended rather than being tightly coiled as in the α-helix.
(Figure 5.2b). The distance between adjacent amino acids along the β-strands is approximately
3.5 Å, in contrast with the distance of 1.5 Å along the α-helix. A β-sheet is formed by linking
two or more β-strands by hydrogen bonds. Adjacent chains in β-sheets can run in opposite
direction (antiparallel β-sheet) or in the same direction (parallel β-sheet). In the antiparallel
arrangement, the –NH and the –CO groups of each amino acid are, respectively, hydrogen
bonded to the –CO and the –NH groups of a partner on the adjacent chain. In the parallel
arrangement, the –NH group is hydrogen bonded to the –CO group of one amino acid on the
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