Improved reweighting protocols for variationally enhanced sampling simulations with multiple walkers

Stevensson, Baltzar; Edén, Mattias

doi:10.1039/d2cp04009c

Phys. Chem. Chem. Phys.

2023

DOI: 10.1039/d2cp04009c

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Improved reweighting protocols for variationally enhanced sampling simulations with multiple walkers

Baltzar Stevensson¹,

Mattias Edén²

Abstract: In molecular dynamics simulations utilizing enhanced-sampling techniques, reweighting is a central component for recovering the targeted ensemble averages of the "unbiased" system by calculating and applying a bias-correction function c(t)....

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Probing the Conformational Ensemble of the Amyloid Beta 16–22 Fragment with Parallel-Bias Metadynamics

Magsumov,

Ibraev,

Sedov

2024

J. Phys. Chem. B

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is a segment of the Alzheimer's-related β-amyloid peptide that plays a crucial role in its aggregation. This study applies well-tempered parallel-bias metadynamics to investigate the impact of several denaturants and osmolytes on the conformational ensembles of both termini-capped and uncapped Aβ(16−22) monomers. Comparison of the different sets of collective variables in the metadynamics bias shows that using the set of backbone torsional angles results in better and faster convergence of simulations than employing more general structural characteristics of the short peptide. The equilibrium conformational ensembles of the peptides are characterized in pure water and in the presence of TMAO, urea, guanidinium chloride, and trifluoroethanol. In particular, trifluoroethanol and TMAO are found to increase the population of compact peptide conformations, whereas urea and guanidinium chloride favor extended structures. The analysis of the free energy surfaces in the presence of various substances with a comparison of the behavior of the capped and uncapped peptide forms reveals the role of different types of intrapeptide interactions such as salt bridges, hydrophobic contacts, and hydrogen bonds in stabilization of the compact or extended structures. As compounds reducing the abundance of the compact states of Aβ(16−22) and other disordered peptides are likely to suppress their amyloid fibril formation, simulations in the systems with this short peptide may be useful for the virtual screening of such compounds.

show abstract

Probing the Conformational Ensemble of the Amyloid Beta 16–22 Fragment with Parallel-Bias Metadynamics

Magsumov,

Ibraev,

Sedov

2024

J. Phys. Chem. B

View full text Add to dashboard Cite

show abstract

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Improved reweighting protocols for variationally enhanced sampling simulations with multiple walkers

Abstract: In molecular dynamics simulations utilizing enhanced-sampling techniques, reweighting is a central component for recovering the targeted ensemble averages of the "unbiased" system by calculating and applying a bias-correction function c(t)....

Cited by 1 publication

References 67 publications

Probing the Conformational Ensemble of the Amyloid Beta 16–22 Fragment with Parallel-Bias Metadynamics

Probing the Conformational Ensemble of the Amyloid Beta 16–22 Fragment with Parallel-Bias Metadynamics

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