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3.0 Types of Secondary Structure

3.2 Sheets

Besides the alpha helix, beta sheets are another other major structural element in globular proteins containing 20-28% of all residues (Kabsch & Sander, 1983; Creighton, 1993). The extended conformation of the polypeptide strands composing a beta sheet was already proposed in the 1930's from diffraction data (1.0) but researchers had to wait until the X-ray crystal structure of lysozyme was solved before getting a look at one in a globular protein. The basic unit of a beta sheet is a beta strand (which can be thought of as a helix with n = 2 residues/turn) with approximate backbone dihedral angles phi = -120 and psi = +120 producing a translation of 3.2 to 3.4 Angstroms/residue for residues in antiparallel and parallel strands, respectively. The beta strand is then like the alpha helix, a repeating secondary structure. However, since there are no intrasegment hydrogen bonds and van der Waals interactions between atoms of neighboring residues are not significant due to the extended nature of the chain, this extended conformation is only stable as part of a beta sheet where contributions from hydrogen bonds and van der Waals interactions between aligned strands exert a stabilizing influence. The beta sheet is sometimes called the beta "pleated" sheet since sequentially neighboring CA atoms are alternately above and below the plane of the sheet giving a "pleated" appearance.

Beta sheets are found in two forms designated as "Antiparallel" or "Parallel" based on the relative directions of two interacting beta strands. The average length of a beta sheet is about 6 residues and most beta sheets contain less than 6 strands. Side chains from adjacent residues of a strand in a beta sheet are found on opposite sides of the sheet and do not interact with one another. Therefore, like alpha-helices, beta-sheets have the potential for amphiphilicity with one face polar and the other apolar. However, unlike alpha-helices which are comprised of residues from a continuous polypeptide segment (i.e., hydrogen bonds between CO of residue i and NH of residue i+3), beta sheets are formed from strands that are very often from distant portions of the polypeptide sequence. Hydrogen bonds in beta sheets are on average 0.1 Angstrom shorter than those found in alpha helices (Baker & Hubbard, 1984).

Figure 8. The protein thioredoxin (2TRX.PDB) contains a five-stranded beta sheet comprised of three parallel strands and three antiparallel strands. The entire protein is shown as a cartoon with the beta strands (three parallel strands and three antiparallel strands) colored red and alpha helices colored yellow.

download 2TRX.PDB

Half of the backbone hydrogen bond donors and acceptors in strands at the edges of a beta sheets are uninvolved in the sheet interactions. Unlike the situation with alpha helices ("helix capping""), capping residues in beta sheets have not yet been characterized (interesting project??). Proline is sometimes found in antiparallel beta sheets and in all cases I am aware of, the imide nitrogen points away from the strand interior. A good example of this is found in dendrotoxin K (1DTK; Berndt et al., 1993), a BPTI homologue which has a proline in each strand of the beta hairpin. Sheets can fold onto themselves forming a barrel or cylinder, thus eliminating the non-hydrogen bonded "ends" (see the tim barrel in Figure 1 ).

Figure 9. Hydrogen bond patterns in beta sheets. Here a four-stranded beta sheet is drawn schematically which contains three antiparallel and one parallel strand. Hydrogen bonds are indicated with red lines (antiparallel strands) and green lines (parallel strands) connecting the hydrogen and receptor oxygen.

3.2.1 - Antiparallel
3.2.2 - Parallel
3.2.3 - Twists
3.2.4 - Bulges
3.2.5 - Strand connections

No Title - 31 MAY 96
written by Kurt D. Berndt

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