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ω-Helices in Proteins

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Abstract

A modification of the α-helix, termed the ω-helix, has four residues in one turn of a helix. We searched the ω-helix in proteins by the HELFIT program which determines the helical parameters—pitch, residues per turn, radius, and handedness—and p = rmsd/(N − 1)1/2 estimating helical regularity, where “rmsd” is the root mean square deviation from the best fit helix and “N” is helix length. A total of 1,496 regular α-helices 6–9 residues long with p ≤ 0.10 Å were identified from 866 protein chains. The statistical analysis provides a strong evidence that the frequency distribution of helices versus n indicates the bimodality of typical α-helix and ω-helix. Sixty-two right handed ω-helices identified (7.2% of proteins) show non-planarity of the peptide groups. There is amino acid preference of Asp and Cys. These observations and analyses insist that the ω-helices occur really in proteins.

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Abbreviations

N c :

The first residue of helices

C c :

The last residue of helices

N :

Residues per turn in helices

P :

Helix pitch

r :

Helix radius

∆z :

Helix rise per residue

ϕ, φ:

Backbone dihedral angles

ω:

Torsion angle

rmsd:

The root mean square deviation from the best fit helix

FDH:

Frequency distributions of helices versus residues per turn

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Acknowledgments

We thank Dr. Robert H. Kretsinger of University of Virginia for his valuable suggestion and comments. This work was supported by the program for developing the supporting system for upgrading the education and research from the Ministry Education, Science, Sports and Culture of Japan (to N. M.).

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Authors and Affiliations

  1. Division of Biophysics, Center for Medical Education, Sapporo Medical University Sapporo, Hokkaido, 060-8556, Japan

    Norio Matsushima

  2. Department of Biophysics and Bioinformatics, Faculty of Biology, National University of Mongolia, Ulaanbaatar, 210646/377, Mongolia

    Purevjav Enkhbayar

  3. Department of Ecology, Faculty of Biology, National University of Mongolia, Ulaanbaatar, 210646/377, Mongolia

    Bazartseren Boldgiv

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  1. Purevjav Enkhbayar
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  2. Bazartseren Boldgiv
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  3. Norio Matsushima
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Correspondence to Norio Matsushima.

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Enkhbayar, P., Boldgiv, B. & Matsushima, N. ω-Helices in Proteins. Protein J 29, 242–249 (2010). https://doi.org/10.1007/s10930-010-9245-5

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