310-helices in proteins are parahelices

The 310‐helix is characterized by having at least two consecutive hydrogen bonds between the main‐chain carbonyl oxygen of residue i and the main‐chain amide hydrogen of residue i + 3. The helical parameters — pitch, residues per turn, radius, and root mean square deviation (rmsd) from the best‐fit helix — were determined by using the HELFIT program. All 310‐helices were classified as regular or irregular based on rmsd/(N − 1)1/2 where N is the helix length. For both there are systematic, position‐specific shifts in the backbone dihedral angles. The average ϕ, ψ shift systematically from ∼ −58°, ∼ −32° to ∼ −90°, ∼ −4° for helices 5, 6, and 7 residues long. The same general pattern is seen for helices, N = 8 and 9; however, in N = 9, the trend is repeated with residues 6, 7, and 8 approximately repeating the ϕ, ψ of residues 2, 3, and 4. The residues per turn and radius of regular 310‐helices decrease with increasing length of helix, while the helix pitch and rise per residue increase. That is, regular 310‐helices become thinner and longer as N increases from 5 to 8. The fraction of regular 310‐helices decreases linearly with helix length. All longer helices, N ≥ 9 are irregular. Energy minimizations show that regular helices become less stable with increasing helix length. These findings indicate that the definition of 310‐helices in terms of average, uniform dihedral angles is not appropriate and that it is inherently unstable for a polypeptide to form an extended, regular 310‐helix. The 310‐helices observed in proteins are better referred to parahelices. Proteins 2006. © 2006 Wiley‐Liss, Inc.