Investigation of the conformation of human prion protein in ethanol solution using molecular dynamics simulations

Xia, Kui; Shen, Haolei; Wang, Peng; Tan, Rongri; Xun, D. M.

doi:10.1080/07391102.2022.2099466

Cited by 2 publications

(2 citation statements)

References 53 publications

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“…Soto et al suggested that no significant free energy barrier separates the different conformations available [15]. Xia et al showed that the extension of a β-sheet occurs more easily and the α-helix is more easily disrupted at high temperatures [16]. Man et al showed that the β-strand content is important for controlling the aggregation rate [17].…”

Section: Introductionmentioning

confidence: 99%

The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations

Feng,

Xia,

Jiang

2024

Molecules

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The effect of β-sheet ratio and chain length on all-β proteins was investigated by MD simulations. Protein samples composed of different repeating units with various β-sheet ratios or a different number of repeating units were simulated under a broad temperature range. The simulation results show that the smaller radius of gyration was achieved by the protein with the higher proportion of β-sheet secondary structure, which had the lower nonbonded energy with more HBs within the protein. The root mean square deviation (RMSD) and the root mean square fluctuation (RMSF) both increased with temperature, especially in the case of a longer chain. The visible period was also shown according to the repeated secondary structure. Several minimum values of RMSF were located on the skeleton of Cα atoms participating in the β-sheet, indicating that it is a kind of stable secondary structure. We also concluded that proteins with a short chain or a lower ratio of β-sheet could easily transform their oriented and compact structures to other ones, such as random coils, turns, and even α-helices. These results clarified the relationship from the primary level to the 3D structure of proteins and potentially predicted protein folding.

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Section: Introductionmentioning

confidence: 99%

The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations

Feng,

Xia,

Jiang

2024

Molecules

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“…Previously, atomistic MD simulations have been used to study the effect of alcohol on various proteins. − The effect of alcohol can differ depending on the initial secondary and tertiary structures of the protein. Alcohol can denature a globular protein and disturb intraprotein hydrogen bond network due to hydrophobic interaction with ethanol .…”

Section: Introductionmentioning

confidence: 99%

Spidroins under the Influence of Alcohol: Effect of Ethanol on Secondary Structure and Molecular Level Solvation of Silk-Like Proteins

Tolmachev,

Malkamäki,

Linder

et al. 2023

Biomacromolecules

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Future sustainable materials based on designer biomolecules require control of the solution assembly, but also interfacial interactions. Alcohol treatments of protein materials are an accessible means to this, making understanding of the process at the molecular level of seminal importance. We focus here on the influence of ethanol on spidroins, the main proteins of silk. By large-scale atomistically detailed molecular dynamics (MD) simulations and interconnected experiments, we characterize the protein aggregation, secondary structure changes, molecular level origins of them, and solvation environment changes for the proteins, as induced by ethanol as a solvation additive. The MD and circular dichoroism (CD) findings jointly show that ethanol promotes ordered structure in the protein molecules, leading to an increase of helix content and turns but also increased aggregation, as revealed by dynamic light scattering (DLS) and light microscopy. The structural changes correlate at the molecular level with increased intramolecular hydrogen bonding. The simulations reveal that polar amino acids, such as glutamine and serine, are most influenced by ethanol, whereas glycine residues are most prone to be involved in the ethanol-induced secondary structure changes. Furthermore, ethanol engages in interactions with the hydrophobic alanine-rich regions of the spidroin, significantly decreasing the hydrophobic interactions of the protein with itself and its surroundings. The protein solutes also change the microstructure of water/ethanol mixtures, essentially decreasing the level of larger local clustering. Overall, the work presents a systematic characterization of ethanol effects on a widely used, common protein type, spidroins, and generalizes the findings to other intrinsically disordered proteins by pinpointing the general features of the response. The results can aid in designing effective alcohol treatments for proteins, but also enable design and tuning of protein material properties by a relatively controllable solvation handle, the addition of ethanol.

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Investigation of the conformation of human prion protein in ethanol solution using molecular dynamics simulations

Cited by 2 publications

References 53 publications

The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations

The Effect of β-Sheet Secondary Structure on All-β Proteins by Molecular Dynamics Simulations

Spidroins under the Influence of Alcohol: Effect of Ethanol on Secondary Structure and Molecular Level Solvation of Silk-Like Proteins

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