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

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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.

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Acknowledgments

We are grateful for the financial support from the National Natural Science Foundation of China (grant nos. 10974054, 20933002, and 21173082). We also thank Prof. Donghai Lin and Dr. Yi Wen at Xiamen University for helpful discussions. The High Performance Computer Center of East China Normal University is acknowledged for its support in allowing us CPU time.

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Authors and Affiliations

  1. 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

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

  2. Department of Chemistry, New York University, New York, NY, 10003, USA

    John Z. H. Zhang

  3. Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore

    Dawei Zhang

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  1. Xiaoliang Lu
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  2. Juan Zeng
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  4. John Z. H. Zhang
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  5. Dawei Zhang
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Correspondence to Ye Mei.

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Lu, X., Zeng, J., Gao, Y. et al. The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study. J Mol Model 19, 4897–4908 (2013). https://doi.org/10.1007/s00894-013-1985-7

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  • DOI: https://doi.org/10.1007/s00894-013-1985-7

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