310‐helices in proteins are parahelices

Abstract The 3 10 ‐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 3 10 ‐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 3 10 ‐helices decrease with increasing length of helix, while the helix pitch and rise per residue increase. That is, regular 3 10 ‐helices become thinner and longer as N increases from 5 to 8. The fraction of regular 3 10 ‐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 3 10 ‐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 3 10 ‐helix. The 3 10 ‐helices observed in proteins are better referred to parahelices. Proteins 2006. © 2006 Wiley‐Liss, Inc.