The polar clasps of a bank vole PrP(168–176) prion protofibril revisiting
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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).
KeywordsPrP 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  deeply. The author is also grateful to comments from reviewers, which have improved this paper greatly.
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