The polar clasps of a bank vole PrP(168–176) prion protofibril revisiting

  • Jiapu ZhangEmail author
Short Comments


On 2018-01-17 two electron crystallography structures (with PDB entries 6AXZ, 6BTK) on a prion protofibril of bank vole PrP(168-176) (a segment in the PrP β2-α2 loop) were released into the PDB Bank. The paper published by Gallagher-Jones et al. (Nat Struct Mol Biol 25(2):131–134, 2018) reports some polar clasps for these two crystal structures, and “an intersheet hydrogen bond between Tyr169 and the backbone carbonyl of Asn171 on an opposing strand.”—this hydrogen bond is not directly between the neighboring chain B and chain A. In addition, by revisiting the polar clasps, we found another two hydrogen bonds (B.Asn171@H–A.Gln172@OE1, B.Tyr169@OH–A.Gln172@N) between the strand A of one sheet and the opposing strand B of the mating sheet. For the neighboring two single beta-sheets AB, the two new hydrogen bonds are completely different from the experimental one (an intersheet hydrogen bond between Tyr169 and the backbone carbonyl of Asn171 on an opposing strand) in (Nat Struct Mol Biol 25(2):131–134, 2018).


PrP structured region Fibril formation peptides Polar clasps Mathematical formulas and optimizations Hydrogen bonds 



This research (with project no. pb04) was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government. The author thanks Rodriguez JA (University of California Los Angeles) for his help in understanding their paper [2] deeply. The author is also grateful to comments from reviewers, which have improved this paper greatly.


  1. 1.
    Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJ, McFarlane HT, Madsen A, Riekel C, Eisenberg D (2007) Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 447(7143):453–457CrossRefGoogle Scholar
  2. 2.
    Gallagher-Jones M, Glynn C, Boyer DR, Martynowycz MW, Hernandez E, Miao J, Zee C T, Novikova IV, Goldschmidt L, McFarlane HT, Helguera GF, Evans JE, Sawaya MR, Cascio D, Eisenberg DS, Gonen T, Rodriguez JA (2018) Sub-ngstrm cryo-EM structure of a prion protofibril reveals a polar clasp. Nat Struct Mol Biol 25(2):131–134CrossRefGoogle Scholar
  3. 3.
    Zhang JP (2016) Mathematical formulas for prion all cross-β structures listed in the Protein Data Bank. Med Chem 6(3): 179–188Google Scholar
  4. 4.
    Yu L, Lee SJ, Yee VC (2015) Crystal structures of polymorphic prion protein β1 peptides reveal variable steric zipper conformations. Biochemistry 54(23):3640–3648CrossRefGoogle Scholar
  5. 5.
    Kozin SA, Bertho G, Mazur AK, Rabesona H, Girault JP, Haertl T, Takahashi M, Debey P, Hoa G H (2001) Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution. J Biol Chem 276(49):46364–46370CrossRefGoogle Scholar
  6. 6.
    Apostol MI, Perry K, Surewicz WK (2013) Crystal structure of a human prion protein fragment reveals a motif for oligomer formation. J Am Chem Soc 135(28):10202–10205CrossRefGoogle Scholar
  7. 7.
    Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38CrossRefGoogle Scholar
  8. 8.
    Guex N, Peitsch MC, Schwede T (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis 30 Suppl 1:S162–173CrossRefGoogle Scholar
  9. 9.
    Guex N, Peitsch MC (1997) SWISS-MODEL And the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714–2723CrossRefGoogle Scholar
  10. 10.
    Zhang JP (2011) Derivative-free Hybrid Methods in Global Optimization and Applications in December 2010. LAMBERT Academic Publishing, Germany. ISBN 978–3–8454–3580–0 (Available online Scholar
  11. 11.
    Zhang JP (2015) Molecular Structures and Structural Dynamics of Prion Proteins and Prions: Mechanism Underlying the Resistance to Prion Diseases. Springer, Dordrecht. ISBN:978–94–017–7317–1CrossRefGoogle Scholar
  12. 12.
    Zhang JP (2018) Molecular Dynamics Analyses of Prion Protein Structures (1st edn. 2018 Edition): The Resistance to Prion Diseases Down Under. Springer, Singapore. ISBN 978–981–10–8814–8CrossRefGoogle Scholar

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© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Centre of Informatics and Applied OptimisationThe Federation University AustraliaBallaratAustralia

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