The following commentary is similar to that found on pages 441-444 in B. J. Gaffney, 1996, Lipoxygenases: structural principles and apectroscopy, Annual Reviews of Biophysics and Biomolecular Structure 25:431-59. Relevant references can be found in the article.
Professor of Biological Science
In the period 1950-1952, there was active discussion of possible stable helical arrangements of polypeptides that did not have an integral number of residues per turn. This discussion had a background of 15 years of papers on the principles of protein structure by Huggins, Bragg, Kendrew, Pauling, Perutz, and others. During the 1950-52 period, Pauling and coworkers proposed the a- and g-helices and evaluated many others. A year later (1952), Low and Baybutt noted that there was another helix that fit the criteria for helices laid out by Pauling, Corey, and Branson, and they named it the p-helix. This postulated helix has 4.4 residues per turn and a pitch of 5 Å. Low and Baybutt cited a personal communication from Pauling criticizing the p-helix on the basis that it would have a hole down the center. The calculated N-N van der Waals contacts across the middle of the helices are 3.0 Å for a p-helix and 3.2 Å for the g-helix, compared to 2.9 Å for a a-helix. Donohue suggested that water molecules could fill the void in a g-helix (5.1 residues per turn), but not in a p-helix.
The energetics of p- and other helices were calculated by Donohue. Compared to the a-helix, the p-helix is less stable by only 0.5 kcal/mole, whereas the 310 helix and the g-helix are 1.0 and 2.0 kcal/mole less stable than the a-helix. Factors included in the calculation are (1) nonplanarity of the peptide groups, (2) deformation of other single bonds, and (3) nonlinearity of hydrogen bonds. These estimates do not include the van der Waals forces or the energies of hydrogen bonds.
Irregularities in the lipoxygenase p-helix may be adjustments to maintain a normal protein packing density. Residues T503, H499, and M497, in the p-helix of the soybean L-1 structure, have phi/psi angles that are abnormal for p-, a-, or 310 helices. Of these, H499 is a ligand to iron and it may be flexible during the catalytic cycle. In addition, S498 and N502 have backbone carbonyls that are bent out and not participating in hydrogen bonding along the helix. The region of apparent p-helix in the lipoxygenase structure might be described, alternatively, as a a-helix with two single-amino-acid insertions. However, it is clearly a region of interesting structure and of critical importance to the enzymatic activity.
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