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 phi, psi shift systematically from approximately -58 degrees, approximately -32 degrees to approximately -90 degrees, approximately -4 degrees 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 phi, psi 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 > or = 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.

Helix compactness and stability: Electron structure calculations of conformer dependent thermodynamic functions

“…Molecular structure I: torsion angles and twisting Molecular structures of both the β-stranded and helical structures of Ala 10 ( Figure 1) are very similar to those calculated previously [1], [16], [17], [18], [19] and [28]. The backbone folds of helices in membrane proteins [φ −60°, ψ −45° [29] and [30] and in water soluble globular proteins [φ −65°, ψ −40° [31] and [32] are close to each other, and are somewhat different from those of 3 10 -helices [φ −68°, ψ −18° [31] and [33]. As expected, the dihedral angles of the QM optimized structures ( Figure S1 Internal -CO) i (HN) i+3 -hydrogen bonds are indicated by dashed lines.…”

“…Thus, for shorter polypetides, in the 'build up phase' of a 3 10 -helix (n < 5) cooperativity is conspicuous, as when the backbone folds into a helix its complexity increases. The shortest 3 10 -helix is characterized by at least two consecutive hydrogen bonds formed between the main-chain CO of residue i and NH of residue (i + 3) [33]. However, passing beyond this length cooperativity drops, entropy and complexity changes quasi linearly.…”

Structural determinants stabilizing helical distortions related to proline

“…The phi/psi angles of residue X1 (position PÀ3) are located at the bottom of the a2 area (À68°± 8°/À13°± 7°), whereas the phi/psi angles of X2 (position PÀ2) are located between the a and a2 regions (À91°± 9°/ À10°± 10°). This shift in phi/psi values is similar to that described previously in short 3 10 helices (Enkhbayar et al, 2006;Pal et al, 2003). Most of these motifs possess a bend angle in the 30-50°r ange, as observed in P2_a2 motifs, but the wobbling motion is significantly larger with an average value of 130 ± 20° (Table 2).…”

Differentially Instructive Extracellular Protein Micro-nets

“…28 In marked contrast, no periodicities were detected for D2 and D1+D2 (Figure 3e). The results in combination with the spectroscopy and microscopy data confirm near-crystalline periodicity for SaNet at the observed length scales.…”