Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

Moradi, Sajad; Nowroozi, Amin; Shahlaei, Mohsen

doi:10.1039/c8ra08441f

Cited by 78 publications

(96 citation statements)

References 95 publications

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“…The average of such local APL values found to be significantly larger than that of the conventional APL (more than 8% growth), namely 70. and have an upper tail (shown in black in Figure 5) which can be well described using lognormal distribution. However, assumption of normal distribution and arithmetic mean as expected value results within 2 Å 2 of the expected values of APL obtained from the proper lognormal fit ( Figure 5) making a reasonable trade-off of APL widely used in the literature 102,113,30 .…”

Section: Area Per Lipidsupporting

confidence: 63%

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

et al. 2019

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1,4-dioxane is a cytotoxic B2 type human carcinogen, a serious water pollutant produced solely by industrial activity. The effect of 1,4-dioxane on phospholipid membrane models composed by DPPC and its branched isomer (IPPC) was investigated using MD simulations. Clear and polluted membranes were compared by membrane parameters such as APL, VPL, compressibility modulus, membrane thickness and orderliness of lipid tails. While neat systems significantly differ from each other, the presence of the pollutant has the same effect on both types of lipid membranes: high density of dioxane appears at the vicinity of ester groups which pushes away lipid headgroups from each other, leading to an overall change in lipid structure: APL and VPL grows, while the orderliness of lipid tails, membrane thickness and compressibility modulus decreases. Orientational preferences of water and dioxane molecules were also investigated and different membrane regions have been specified according to the stance of water molecules. Free energy profile for 1,4-dioxane penetration mechanism into DPPC membranes was carried out using metadynamics for two different concentrations of the pollutant (c 1 =7.51 g/dm 3 , c 2 =75.10 g/dm 3), which showed that the higher the concentration is, the lower the free energy of penetration gets. Only a small free energy barrier was found in the headgroup region and accumulation of dioxane is thermodynamically unfavored in the middle of the bilayer. The penetration mechanism has been described in detail based on the orientational preference of 1,4-dioxane molecules and the free energy profiles.

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Section: Area Per Lipidsupporting

confidence: 63%

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

et al. 2019

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“…3 B shows a cross-section with the higher-density protein crown (opaque blue) encased within a lower-density threshold image (transparent white), in which the major additional volume is derived from the membrane neck of the replication vesicle invaginated from the flanking OMM. Of note, the polar head groups on each side of the lipid bilayer are more electron dense than the intervening fatty acyl chains, causing the membrane to appear as two parallel layers ∼3 nm apart ( 35 ). Interestingly, in the region between the two membrane contacts of the crown, these two headgroup layers appear to approach each other more closely or be bridged by an unknown density ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication

Unchwaniwala

Zhan

Pennington

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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For positive-strand RNA [(+)RNA] viruses, the major target for antiviral therapies is genomic RNA replication, which occurs at poorly understood membrane-bound viral RNA replication complexes. Recent cryoelectron microscopy (cryo-EM) of nodavirus RNA replication complexes revealed that the viral double-stranded RNA replication template is coiled inside a 30- to 90-nm invagination of the outer mitochondrial membrane, whose necked aperture to the cytoplasm is gated by a 12-fold symmetric, 35-nm diameter “crown” complex that contains multifunctional viral RNA replication protein A. Here we report optimizing cryo-EM tomography and image processing to improve crown resolution from 33 to 8.5 Å. This resolves the crown into 12 distinct vertical segments, each with 3 major subdomains: A membrane-connected basal lobe and an apical lobe that together comprise the ∼19-nm-diameter central turret, and a leg emerging from the basal lobe that connects to the membrane at ∼35-nm diameter. Despite widely varying replication vesicle diameters, the resulting two rings of membrane interaction sites constrain the vesicle neck to a highly uniform shape. Labeling protein A with a His-tag that binds 5-nm Ni-nanogold allowed cryo-EM tomography mapping of the C terminus of protein A to the apical lobe, which correlates well with the predicted structure of the C-proximal polymerase domain of protein A. These and other results indicate that the crown contains 12 copies of protein A arranged basally to apically in an N-to-C orientation. Moreover, the apical polymerase localization has significant mechanistic implications for template RNA recruitment and (−) and (+)RNA synthesis.

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“…6. For more details on membrane properties used for the validation of FFs, we recommend the reviews by Poger et al, 96 Leonard et al, 97 and Moradi et al 98…”

Section: Experimental Observables For the Validation Of Lipid Force Fmentioning

confidence: 99%

“…In this ensemble, the number of molecules N, the pressure p, and the temperature T are constant, which is a more realistic ensemble than the NVT ensemble (where the volume V is kept constant) for comparison to experiments. 98 A higher value of A L corresponds to a more disordered state, whereas low A L values reflect highly packed lipids in the membrane. The probability distribution p(A L ) for the area per lipid molecule can also be calculated (see Fig.…”

Section: Area Per Lipidmentioning

confidence: 99%

“…In the case of mixed membranes involving cholesterol, the peaks of the phosphate groups are slightly shifted depending on the cholesterol concentration, whereas the rest of the profile exhibits no significant changes. 98 The electron density profile is symmetric if the two leaflets have the same composition and when the bilayer is in its equilibrium state. The main aspects of an electron density profile are required to be reproduced by a FF, like the overall profile shape and the position of the peaks corresponding to specific groups of atoms (e.g., head groups, glycerols, carbonyls, methylenes in the hydrocarbon chains).…”

Section: Membrane Thickness and Electron Density Profilementioning

confidence: 99%

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Computer simulations of protein–membrane systems

Loschwitz

Olubiyi

Hub

et al. 2020

Progress in Molecular Biology and Translational Science

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Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

Abstract: This review gives an overview about the some of the most important possible analyzes, technical challenges, and existing protocols that can be performed on the biological membrane by the molecular dynamics simulation.

Cited by 78 publications

References 95 publications

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication

Computer simulations of protein–membrane systems

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