title: Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in transmissible spongiform encephalopathies.
abstract: In this study, a new beta-helical model is proposed that explains the species barrier and strain variation in transmissible spongiform encephalopathies. The left-handed beta-helix serves as a structural model that can explain the seeded growth characteristics of beta-sheet structure in PrP(Sc) fibrils. Molecular dynamics simulations demonstrate that the left-handed beta-helix is structurally more stable than the right-handed beta-helix, with a higher beta-sheet content during the simulation and a better distributed network of inter-strand backbone-backbone hydrogen bonds between parallel beta-strands of different rungs. Multiple sequence alignments and homology modelling of prion sequences with different rungs of left-handed beta-helices illustrate that the PrP region with the highest beta-helical propensity (residues 105-143) can fold in just two rungs of a left-handed beta-helix. Even if no other flanking sequence participates in the beta-helix, the two rungs of a beta-helix can give the growing fibril enough elevation to accommodate the rest of the PrP protein in a tight packing at the periphery of a trimeric beta-helix. The folding of beta-helices is driven by backbone-backbone hydrogen bonding and stacking of side-chains in adjacent rungs. The sequence and structure of the last rung at the fibril end with unprotected beta-sheet edges selects the sequence of a complementary rung and dictates the folding of the new rung with optimal backbone hydrogen bonding and side-chain stacking. An important side-chain stack that facilitates the beta-helical folding is between methionine residues 109 and 129, which explains their importance in the species barrier of prions. Because the PrP sequence is not evolutionarily optimised to fold in a beta-helix, and because the beta-helical fold shows very little sequence preference, alternative alignments are possible that result in a different rung able to select for an alternative complementary rung. A different top rung results in a new strain with different growth characteristics. Hence, in the present model, sequence variation and alternative alignments clarify the basis of the species barrier and strain specificity in PrP-based diseases.
authors.affiliation: Pepscan Systems B.V., Lelystad, The Netherlands. j.p.m.langedijk@pepscan.nl
authors.forename: J P M
authors.initials: JP
authors.lastname: Langedijk
authors.forename: G
authors.initials: G
authors.lastname: Fuentes
authors.forename: R
authors.initials: R
authors.lastname: Boshuizen
authors.forename: A M J J
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D000595:Amino Acid Sequence; D000682:Amyloid / Q000737:chemistry; D000818:Animals; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D018620:PrPSc Proteins / Q000737:chemistry* / Q000378:metabolism*; D017096:Prion Diseases / Q000378:metabolism*; D017433:Protein Structure, Secondary; D013045:Species Specificity; D013816:Thermodynamics
chemical_list: D000682:Amyloid; D018620:PrPSc Proteins