2-6 Secondary structure is the local geometry of the protein

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• The chain of amino acids dictates how a proteins folds.
• The major determinant of protein folding is hydrophobic interactions.
• The local geometry of a protein is its secondary structure.
• Two common secondary structures are the α helix and the β sheet.

Peptides and proteins are formed when a ribosome and the rest of the translation machinery link amino acids together in polymers that range from 10 to 10,000 residues in length. During and after protein synthesis, the residues of the primary sequence dictate how the protein folds. The simplest aspect of protein folding is termed its secondary structure, which refers to the geometry of the local polypeptide chain with respect to their immediate neighbors. How a protein folds is dictated by the primary sequence of amino acids, but predicting the overall structure from the primary sequence remains one of the most important unsolved problems in biology. Nevertheless, it is clear that the major determinants of this final structure are hydrophobic interactions. During protein folding, hydrophobic amino acids must be hidden from the water interface by being buried in the interior of the protein. This burying defines the protein core which then influences the immediate structure around it and greatly affects the protein's overall structure.

Common Secondary Structures

Peptide bonds between adjacent amino acids can rotate and twist to allow a large number of interactions, but two local organization schemes, the α helix and the β sheet, are found in many proteins. Their prevalence is certainly because they happen to form particularly energetically favorable structures. Formation of these structures is driven by favorable hydrogen bonding and hydrophobic interactions between nearby amino acids in the protein. The α helix resembles a ribbon of adjacent amino acids wrapped around a tube to form a staircase-like structure. Figure 2-11 [7] shows different representations of an α helix. This structure is very stable, yet cn be flexible in specific cases and is sometimes seen in parts of a protein that may need to bend or move.

In the β sheet, two protein chains (perhaps different segments of the same protein) align themselves in a planar structure such that hydrogen bonds can form between facing amino acids in each sheet. Figure 2-12 [8] shows different representations of this structure. The β sheet is different from the α helix in that it can involve amino acids from different sections of the protein, which come together to form this structure. Also, the structure tends to be rigid and less flexible than the α helix.

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