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

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 bo...

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Main Authors: Zhang, John Z. H., Lu, Xiaoliang, Zeng, Juan, Gao, Ya, Zhang, Dawei, Mei, Ye
Other Authors: School of Physical and Mathematical Sciences
Format: Article
Language:English
Published: 2013
Online Access:https://hdl.handle.net/10356/99170
http://hdl.handle.net/10220/17372
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-991702020-03-07T12:31:21Z The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions : a replica exchange molecular dynamics study Zhang, John Z. H. Lu, Xiaoliang Zeng, Juan Gao, Ya Zhang, Dawei Mei, Ye School of Physical and Mathematical Sciences 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. 2013-11-07T06:32:39Z 2019-12-06T20:04:06Z 2013-11-07T06:32:39Z 2019-12-06T20:04:06Z 2013 2013 Journal Article Lu, X., Zeng, J., Gao, Y., Zhang, J. Z. H., Zhang, D., & Mei, Y. (2013). The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study. Journal of Molecular Modeling, 19(11), 4897-4908. https://hdl.handle.net/10356/99170 http://hdl.handle.net/10220/17372 10.1007/s00894-013-1985-7 en Journal of molecular modeling
institution Nanyang Technological University
building NTU Library
country Singapore
collection DR-NTU
language English
description 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.
author2 School of Physical and Mathematical Sciences
author_facet School of Physical and Mathematical Sciences
Zhang, John Z. H.
Lu, Xiaoliang
Zeng, Juan
Gao, Ya
Zhang, Dawei
Mei, Ye
format Article
author Zhang, John Z. H.
Lu, Xiaoliang
Zeng, Juan
Gao, Ya
Zhang, Dawei
Mei, Ye
spellingShingle Zhang, John Z. H.
Lu, Xiaoliang
Zeng, Juan
Gao, Ya
Zhang, Dawei
Mei, Ye
The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions : a replica exchange molecular dynamics study
author_sort Zhang, John Z. H.
title The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions : a replica exchange molecular dynamics study
title_short The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions : a replica exchange molecular dynamics study
title_full The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions : a replica exchange molecular dynamics study
title_fullStr The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions : a replica exchange molecular dynamics study
title_full_unstemmed The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions : a replica exchange molecular dynamics study
title_sort intrinsic helical propensities of the helical fragments in prion protein under neutral and low ph conditions : a replica exchange molecular dynamics study
publishDate 2013
url https://hdl.handle.net/10356/99170
http://hdl.handle.net/10220/17372
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