Molecular Dynamics Simulation of Synthetic Polymers

Sandoval, Claudia

doi:10.5772/35006

Cited by 3 publications

(3 citation statements)

References 35 publications

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“…It is the average distance between the first and last atoms in the peptide, with respect to time. A lower stable value might indicate a probable, largely folded/compact conformation and while a large value indicates extended conformation 42,43 . From Figure 1D, we can see that initially, all systems had a very high end‐to‐end distance, as initially, proteins are in an unfolded extended confirmation.…”

Section: Resultsmentioning

confidence: 91%

N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

et al. 2022

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Various posttranslational modifications like hyperphosphorylation, O-GlcNAcylation, and acetylation have been attributed to induce the abnormal folding in tau protein.Recent in vitro studies revealed the possible involvement of N-glycosylation of tau protein in the abnormal folding and tau aggregation. Hence, in this study, we performed a microsecond long all atom molecular dynamics simulation to gain insights into the effects of N-glycosylation on Asn-359 residue which forms part of the microtubule binding region. Trajectory analysis of the stimulations coupled with essential dynamics and free energy landscape analysis suggested that tau, in its Nglycosylated form tends to exist in a largely folded conformation having high beta sheet propensity as compared to unmodified tau which exists in a large extended form with very less beta sheet propensity. Residue interaction network analysis of the lowest energy conformations further revealed that Phe378 and Lys353 are the functionally important residues in the peptide which helped in initiating the folding process and Phe378, Lys347, and Lys370 helped to maintain the stability of the protein in the folded state.

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Section: Resultsmentioning

confidence: 91%

N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

et al. 2022

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“…It is the average distance between the first and last atoms in the peptide, with respect to time. A lower stable value might indicate a probable, largely folded / compact conformation and while a large value indicates extended conformation 38,39 . From Figure 1 D we can see that initially, all systems had a very high end to end distance, as initially, proteins are in an unfolded extended confirmation.…”

Section: Radius Of Gyration and End To End Distancementioning

confidence: 99%

N-glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

Mathew

Baidya

Das

et al. 2022

Preprint

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Various post translational modifications like hyper phosphorylation, O-GlycNAcylation, and acetylation have been attributed to induce the abnormal folding in tau protein. Recent in vitro studies revealed the possible involvement of N–glycosylation of tau protein in the abnormal folding and tau aggregation. Hence in this study, we performed microsecond long all atom molecular dynamics simulation to gain insights into the effects of N-glycosylation on Asn-359residue which forms part of the microtubule binding region. Trajectory analysis of the stimulations coupled with essential dynamics and free energy landscape analysis suggested that tau, in its N-glycosylated form tend to exist in a largely folded conformation having high beta sheet propensity as compared to unmodified tau which exists in a large extended form with very less beta sheet propensity. Residue interaction network analysis of the lowest energy conformations further revealed that Phe378 and Lys353 are the functionally important residues in the peptide which helped in initiating the folding process and Phe378, Lys347&Lys370 helped maintaining the stability of the protein in the folded state.

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“…The theoretical–computational study of polymer have been conducted with coarse-grained and mean-field approaches, − and the atomistic molecular dynamics (MD) simulation is now becoming a useful method. − The structure and dynamics of polymer medium have been analyzed at atomic resolution, and the gas permeability and proton conductivity have been studied in connection to the separation membrane and electrolyte fuel cell. In the present work, we develop an atomistic method for the mixing free energy of polymers by combining all-atom MD simulation and the energy-representation method of solvation. − In a previous work, we formulated an approximate approach to the chemical potential of a polymer.…”

Section: Introductionmentioning

confidence: 99%

Chain-Increment Approach to the Mutual Miscibility of Polymers with All-Atom Molecular Simulation

Yamada

Matubayasi

2023

Macromolecules

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The mutual miscibility of polymers was addressed with all-atom molecular dynamics (MD) simulation and the energy-representation theory of solvation. The chain-increment method was extended to polymer mixtures, and the mixing free energy was related to the incremental free energy for the constituent polymer species that is the free-energy change of turning on the interaction of a monomer in the tagged polymer chain with the surrounding molecules. The free energy was then computed for the mixing of polyethylene (PE) and poly(vinylidene difluoride) (PVDF) and of poly(vinyl alcohol) (PVA) and polyvinylpyrrolidone (PVP). It was seen that the incremental free energy is insensitive to the location of the monomer in the inner part of the polymer chain and depends on the mixing ratio of the polymer system in parallel with the average interaction energy of the incremented monomer with the surrounding polymers. The intermolecular interactions of each polymer species were further analyzed at atomic resolution. The PVDF–PVDF interaction was found to become less favorable (more positive) upon addition of PE in the mixture of PE and PVDF, making them immiscible with each other. PVP favors PVA more than PVP, on the other hand, leading to the miscibility of PVA and PVP. The connection of our formulation of the mixing free energy with the Flory–Huggins expression is also described.

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Molecular Dynamics Simulation of Synthetic Polymers

Cited by 3 publications

References 35 publications

N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

N‐glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

N-glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

Chain-Increment Approach to the Mutual Miscibility of Polymers with All-Atom Molecular Simulation

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