The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: A replica exchange molecular dynamics study

Xiaoliang Lu, Juan Zeng, Ya Gao, John Z.H. Zhang, Dawei Zhang, Ye Mei

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)4897-4908
Number of pages12
JournalJournal of Molecular Modeling
Volume19
Issue number11
DOIs
StatePublished - Nov 1 2013

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Keywords

  • Helical propensity
  • Prion
  • Replica exchange molecular dynamics
  • pH condition

ASJC Scopus subject areas

  • Catalysis
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Computational Theory and Mathematics
  • Inorganic Chemistry

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