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

• Published in: Journal of molecular modeling Vol. 25; no. 5; pp. 108 - 9
• Main Author: Zhang, Jiapu
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.05.2019; Springer Nature B.V
• Subjects: Backbone; Carbonyls; Chains; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Crystal structure; Crystallography; Fasteners; Hydrogen bonds; Molecular Medicine; Short Comments; Theoretical and Computational Chemistry; Fibril formation peptides; Mathematical formulas and optimizations; Polar clasps; Hydrogen bonds; PrP structured region
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-019-3981-z

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 β 2- α 2 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 ).