3-D Structure of Proteins 2

Secondary Structure

Alpha helix: (text Figure 4-4a, Model) The most frequent secondary structure is the right-handed -helix.

• In this cylinder-like structure the amino acid residues curl around in a spring/rod-like structure. (text Figure 4-4a)
• There is a rise/residue (movement along the axis) of 0.15 nm and a pitch (rise/turn) of 0.54 nm. (text Figure 4-4a)
• There are 3.6 residues per turn and 13 atoms/H-bonded "ring" - this makes it a 3.6₁₃ helix.
• Very importantly, the H-bonds are nearly linear and therefore of near maximum strength. The side chains of the helix stick out from the sides.
  • The stability of the helix is determined in part by the side chains. Thus glycine allows too much rotational freedom to favor this structure, while very large or like charged side chains can also destabilize it. (text Table 4-1)
  • Note that the polarities of the H-bonds add up since they are all aligned with the helix axis. (text Figure 4-5)
• As you might expect a proline residue stops a helix abruptly since proline's angles are not accommodated in the helix.
• Aside: Fibrous proteins 1: alpha-keratin (hair etc., -helix based) (text Figure 4-10a & b). Stretched -keratin (parallel -pleated sheet). Permanent wave, text Box 4-2.

Beta Strand: The next secondary structural element is the -strand, which is seen in the supersecondary structures called parallel (text Figure 4-6b) and anti-parallel (text Figure 4-6a) beta sheets.

• The beta strand is in a sense an abstract structure, since, unlike the -helix, a -strand does not exist alone, there is always another strand to make a sheet.
• In the older literature -sheets are considered secondary structures, but they are more consistently considered super secondary with the current nomenclature.
• Beta strands are nearly fully extended, thus they have very little extensibility (stretch).
• Beta strands are stabilized by hydrogen bonding to adjacent beta-strands. Thus they are stabilized by inter-strand H-bonds whereas -helices are stabilized by intra-strand H-bonds.

Aside: Fibrous proteins 2: silk, antiparallel -pleated sheet (text Figure 4-13 a & b) .

Non-repetitive secondary elements: Proteins can also have non-repetitive secondary structures which consist of a few residues in a turn or loop. Among these are:

• -turns:
  • Type I turns: (text Figure 4-7a) four amino acid residues in a 180° turn, usually H-bonded between the carbonyl O of the first residue and the amide N of the fourth. Proline is often the second residue.
  • Type II turns: (text Figure 4-7a) four amino acid residues in a 180° turn, usually H-bonded between the carbonyl O of the first residue and the amide N of the fourth. Glycine is most frequently the third residue and proline is often the second residue. The cis-conformation of proline (about 6% of all prolines) is frequently found in these turns.
• A partial turn of a 3₁₀ helix. Short sections of this helix often occur at the ends of alpha-helixes as transitional elements.

Collagen strand: This is a specialized structure occurring in only a particular family of fibrous proteins. It does not occur in globular proteins that I am aware of.

• Collagen triple helix. Note repeating sequence of -(gly-x-y)- where x is usually proline and y is usually hydroxyproline. (text Figures 4-12, Model)

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Last modified 19 September 2008