Coarse-grained simulation of transmembrane peptides in the gel phase

Al-Lehyani, Ibrahim; Grime, John M. A.; Bano, M.; McKelvey, Kim; Allen, Michael

doi:10.1016/j.jcp.2012.12.014

Cited by 2 publications

(1 citation statement)

References 34 publications

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“… 37 It calculates the dynamic behavior of the system based on molecular dynamics. Compared to molecular dynamics simulations, DPD can take longer time steps and is more suitable for simulating solution systems with complex components, such as polymer, 40 surfactant, 41 gels, 42 and microemulsions. 39 In a study conducted by Li 43 et al, the interfacial behavior of sodium dodecylbenzenesulfonate [surfactant sodium dodecyl benzenesulfonate (SDBS)] and sodium oleate (OAS) surfactants in oil–water emulsification was investigated using DPD and the study revealed that the stacking behavior on the interfacial film is influenced by the surfactant concentration and the structure of the hydrophobic tail in the oil phase.…”

Section: Introductionmentioning

confidence: 99%

Surfactant Synergistic Effect and Interfacial Properties of Microemulsions Compounded with Anionic and Nonionic Surfactants Using Dissipative Particle Dynamics

Zhang,

Guan,

Tao

et al. 2024

ACS Omega

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Microemulsions are one of the most promising directions in enhanced oil recovery, but conventional screening methods are time-consuming and labor-intensive and lack the means to analyze them at the microscopic level. In this paper, we used the Clint model to predict the changes in the synergistic effect of the mixed system of anionic surfactant sodium dodecyl benzenesulfonate and nonionic surfactant polyethoxylated fatty alcohols (C12E6), generated microemulsions using surfactant systems with different mole fractions, and used particle size to analyze the performance and stability of microemulsions, analyze the properties and stability of microemulsions using particle size, and analyze the interfacial behaviors and changes of microemulsions when different systems constitute microemulsions from the point of view of mesoscopic microemulsion self-assembly behaviors by combining with dissipative particle dynamics. It has been shown that microemulsion systems generated from anionic and nonanionic surfactants with a synergistic effect, based on the Clint model, exhibit excellent performance and stability at the microscopic level. The method proposed in this paper can dramatically improve the screening efficiency of microemulsions of anionic and nonanionic surfactants and accurately analyze the properties of microemulsions, so as to provide a theoretical basis for the subsequent research on microemulsions.

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Section: Introductionmentioning

confidence: 99%

Surfactant Synergistic Effect and Interfacial Properties of Microemulsions Compounded with Anionic and Nonionic Surfactants Using Dissipative Particle Dynamics

Zhang,

Guan,

Tao

et al. 2024

ACS Omega

View full text Add to dashboard Cite

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Construction of a linker library with widely controllable flexibility for fusion protein design

Huang

Zhang

et al. 2015

Appl Microbiol Biotechnol

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Flexibility or rigidity of the linker between two fused proteins is an important parameter that affects the function of fusion proteins. In this study, we constructed a linker library with five elementary units based on the combination of the flexible (GGGGS) and the rigid (EAAAK) units. Molecular dynamics (MD) simulation showed that more rigid units in the linkers lead to more helical conformation and hydrogen bonds, and less distance fluctuation between the N- and C-termini of the linker. The diversity of linker flexibility of the linker library was then studied by fluorescence resonance energy transfer (FRET) of cyan fluorescent protein (CFP)-yellow fluorescent protein (YFP) fusion proteins, which showed that there is a wide range of distribution of the FRET efficiency. Dissipative particle dynamics (DPD) simulation of CFP-YFP with different linkers also gave identical results with that of FRET efficiency analysis, and we further found that the combination manner of the linker peptide had a remarkable effect on the orientation of CFP and YFP domains. Our studies demonstrated that the construction of the linker library with the widely controllable flexibility could provide appropriate linkers with the desirable characteristics to engineer the fusion proteins with the expected functions.

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Coarse-grained simulation of transmembrane peptides in the gel phase

Cited by 2 publications

References 34 publications

Surfactant Synergistic Effect and Interfacial Properties of Microemulsions Compounded with Anionic and Nonionic Surfactants Using Dissipative Particle Dynamics

Surfactant Synergistic Effect and Interfacial Properties of Microemulsions Compounded with Anionic and Nonionic Surfactants Using Dissipative Particle Dynamics

Construction of a linker library with widely controllable flexibility for fusion protein design

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