title: The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study.
abstract: Replica exchange molecular dynamics simulations in neutral and acidic aqueous solutions were employed to study the intrinsic helical propensities of three helices in both Syrian hamster (syPrP) and human (huPrP) prion proteins. The helical propensities of syPrP HA and huPrP HA are very high under both pH conditions, which implies that HA is barely involved in the helix-to-β transition. The SyPrP HB chain has a strong tendency to adopt an extended conformation, which is possibly involved in the mechanism of infectious prion diseases in Syrian hamster. HuPrP HC has more of a preference for the extended conformation than huPrP HA and huPrP HB do, which leads to the conjecture that it is more likely to be the source of β-rich structure for human prion protein. We also noticed that the presence of salt bridges is not correlated with helical propensity, indicating that salt bridges do not stabilize helices.
authors.affiliation: Center for Laser and Computational Biophysics, State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China.
authors.forename: Xiaoliang
authors.initials: X
authors.lastname: Lu
authors.forename: Juan
authors.initials: J
authors.lastname: Zeng
authors.forename: Ya
authors.initials: Y
authors.lastname: Gao
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.forename: Dawei
authors.initials: D
authors.lastname: Zhang
authors.forename: Ye
authors.initials: Y
authors.lastname: Mei
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006224:Cricetinae; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008647:Mesocricetus; D056004:Molecular Dynamics Simulation; D011328:Prions / Q000737:chemistry*; D011489:Protein Denaturation; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D011328:Prions
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