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

adjacent segments of an antiparallel β-sheet. The structure is a 180 0 turn involving four amino
acid residues, with a carbonyl oxygen of the first residue forming a hydrogen bond with the
amino-group hydrogen of the fourth. The peptide groups of the central two residues do not
participate in any inter-residue hydrogen bonding (Gly and Pro residues often occur in β-turn,
the former because it is small and flexible, the later because peptide bounds involving the
amino nitrogen of proline readily assume cis configuration). Generally, β-turns are often
localized near the surface of a protein, where the peptide groups of the central two amino acid
residues in the turn can hydrogen-bonded with water. Hence, the secondary structures of
proteins make reference to highly organized regular geometries. Turns and loops invariably lie
on the surfaces of proteins and thus participate in interactions between proteins and other
molecules (91)(92).
5.1.3.- Tertiary Structure of the proteins
The overall three-dimensional arrangement of atoms in a protein is referred to as the protein
tertiary structure. Whereas the secondary structure refers to the spatial arrangement of amino
acid residues that are adjacent in a segment of a polypeptide, tertiary structure includes
longer-range aspects of the amino acid sequence. Amino acids that are far apart in the
polypeptide sequence and are in different types of secondary structure may interact within the
completely folded structure of a protein. In other words, tertiary structure emerges from the
distribution of side chains of amino acid residues. Instead, the buried parts of proteins consist
almost entirely of non-polar residues. On the other hand, charged residues usually are absent
from the inside of proteins. However, both polar and non-polar residues can be found on the
protein surface. In aqueous environment, protein folding is driven by the strong tendency of
hydrophobic residues to be excluded from water (the system is thermodynamically stable
when hydrophobic groups are clustered rather than extended into the aqueous surroundings).
The polypeptide chain therefore folds so that its hydrophobic side chains are buried and its
polar, charged chains are on the surface. Recall that many α-helix and β-strands are
amphipatic since both secondary structures have a hydrophobic face, which points into the
protein interior, and a more polar face, which points into solution. The buried domains in a
hydrophobic environment are stabilized by hydrogen bonding, pairing all the amino and
carboxylic groups. This pairing is neatly accomplished in an α-helix and β-sheet structures. Van
der Waals interactions between tightly packed hydrocarbon side chains also contribute to the
stability of the tertiary protein structure (4).
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