Secondary Structure (Terms)

In describing a polypeptide secondary structure, there are several terms to understand.

Figure 6.2 illustrates the rotation that can take place about the N-C and C-C(O)– bonds in a polypeptide chain. The angles of rotation about these bonds are defined as and , respectively. The closer and approach 180 or -180, the more extended (like a sheet) the overall structure is. The closer and approach zero (like an -helix), the more compact (and coiled) the overall structure is.

Helices are repeating coiled structures commonly found in polypeptides. A helix can be described using the following important terms (Figure 4B.2).

> Axis - a helix has an axis that is a central line of symmetry running through it.

> Pitch (p) - the spacing distance between individual adjacent coils of the helix. For an -helix, p=0.54 nm/turn

> Repeat (c) - the distance along the axis it takes for a helix to exactly repeat itself. For an -helix, the helix repeats itself after 5 turns, so c=2.7 nm. For the helix in Figure 4B.2, the term 'm' is defined as the integral number of polymer residues it takes for the helix to repeat. In that example, m=4. For an -helix, m = 18 (5 turns times 3.6 residues per turn).

> Rise (h) - the distance the helix "rises" between adjacent polymer units. For an -helix, h=0.15 nm/residue.

Helices can be coiled in two different ways, and are referred to as right- or left-handed. In Figure 6.5, compare the n=3 helix (right-handed) with the n = -3 helix (left-handed).

If a helix is "flattened", the resulting structure is a sheet .

Hydrogen bonds stabilize secondary structures. These can be within a chain (as in an -helix) or between different chains (as in a -pleated sheet). Figure 6.6 illustrates how hydrogen bonds stabilize four different helical structures. When hydrogen bonds stabilize adjacent polypeptide chains in -sheet structures, the adjacent chains can be oriented parallel or antiparallel to each other. When both chains are parallel, they have the same amino to carboxyl orientation. When they are antiparallel, the two chains have opposite amino to carboxyl orientations.

Figure 6.6 helps illustrate another important naming convention which describes helices. Recall from Table 6.1 that a 3 10 helix has 3 residues per turn and a 10 member loop. The "loop" can be seen in Figure 6.6 by the numbered atoms. Thus, for a 3 10 helix, atom #1 is the oxygen and atom #10 is the unnumbered hydrogen below nitrogen #9. Notice, furthermore, that an -helix is also a 3.6 13 helix, because it has 3.6 residues per turn and a loop of 13.

See also: Secondary Structure (General), Secondary Structures (Specific examples), Ramachandran Plots, Hydrogen Bonds (from Chapter 2), -Helix, -Sheet, Factors Determining Secondary and Tertiary Structure