2018
DOI: 10.1002/jcc.25380
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Prion protein conversion triggered by acidic condition: a molecular dynamics study through different force fields

Abstract: Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy. The three‐dimensional structure of PrPSc, the altered isoform of the prion protein, has not been fully elucidated yet, and studies on prion conversion mechanisms must rely on hypothetical β‐rich structures. Experimental and computational studies indicate that the use of low pH is capable to produce a gain of β‐structure content in the otherwise unstructured N‐term… Show more

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Cited by 6 publications
(3 citation statements)
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References 94 publications
(178 reference statements)
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“…This was identical to the results using molecular dynamics simulation techniques that elevating temperature could accelerate the unfolding process of prion protein and increase the β ‐sheet structures (Chamachi & Chakrabarty, 2017; Chen et al., 2013). Our data were also in accordance with the molecular dynamics simulation results that the structural conversion of cellular prion protein was triggered by acidic pH (Lu et al., 2013; Thompson et al., 2018).…”
Section: Discussionsupporting
confidence: 92%
See 1 more Smart Citation
“…This was identical to the results using molecular dynamics simulation techniques that elevating temperature could accelerate the unfolding process of prion protein and increase the β ‐sheet structures (Chamachi & Chakrabarty, 2017; Chen et al., 2013). Our data were also in accordance with the molecular dynamics simulation results that the structural conversion of cellular prion protein was triggered by acidic pH (Lu et al., 2013; Thompson et al., 2018).…”
Section: Discussionsupporting
confidence: 92%
“…The surfactants like sarkosyl in solution of pH 9.0 (Khan et al., 2018) and sodium dodecyl benzenesulfonate in solution of pH 7.4 (Khan et al., 2019), and food colouring agent like Allura red in solution of pH 7.0 (Al‐Shabib et al., 2019) can also promote the formation of HEWL fibrils. Like HEWL protein, prion protein can form into amyloid fibrils under acidic pH conditions demonstrated both by experimental studies (Hornemann & Glockshuber, 1998; Singh & Udgaonkar, 2016) and molecular dynamics simulation techniques (Thompson et al., 2018). Elevated temperatures can accelerate the unfolding process and increase the β ‐sheet structures of prion protein using molecular dynamics simulation techniques (Chen et al., 2013; Gu et al., 2003).…”
Section: Introductionmentioning
confidence: 99%
“…Such an elongated structure is a novel indicator of misfolding and drove the conformational conversion of PrP C to PrP Sc , critical information needed for understanding the molecular pathogenesis of prion diseases. Furthermore, Thompson et al 66 performed molecular dynamics simulations using a set of force fields to study the molecular basis of PrP C misfolding followed by conformational conversion and found that only GROMOS96 53a6 and AMBER99SB force fields are capable of capturing the crucial elongated β-sheet structure during refolding. Moreover, another study also found a discrepancy in protein force fields in replicating the experimental state populations.…”
Section: Methodsmentioning
confidence: 99%