Modeling Lipid Membranes

Khakbaz, Pouyan; Monje-Galvan, Viviana; Zhuang, Xiaohong; Klauda, Jeffery B.

doi:10.1007/978-3-319-43676-0_52-1

Cited by 2 publications

(4 citation statements)

References 90 publications

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“…However, natural membranes are far more complex. Lipid–lipid interactions and lipid interactions with transmembrane and peripheral proteins greatly influence membrane properties. ,, …”

Section: Modeling Cellular Membrane Complexitymentioning

confidence: 99%

“…Lipid−lipid interactions and lipid interactions with transmembrane and peripheral proteins greatly influence membrane properties. 86,173,372 A key lipid species in membrane modeling is Chol in mammalian cells or its homologue ergosterol in fungal cells among others. 373−375 Sterol content is critical for a membrane's health and proper function, so MD simulations have advanced to reproduce accurate sterol−lipid and sterol− sterol interactions.…”

Section: Modeling Cellular Membrane Complexitymentioning

confidence: 99%

“…Moreover, with the development of more accurate lipid FFs, reviews and comparisons on global membrane properties relevant to cells, e.g., mechanical properties, have provided details in the accuracy of measures not typically targeted in FF optimization. There have been some recent reviews on lipid diversity incorporated into MD simulations , providing background and insight into where the field of in vivo cell membrane modeling is progressing. Reviews have also encompassed multiscale modeling of membranes and membrane-associated proteins such as those by Pluhackova and Böckmann .…”

Section: Introductionmentioning

confidence: 99%

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Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

et al. 2019

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The amphipathic nature of the lipid molecule (hydrophilic head and hydrophobic tails) enables it to act as a barrier between fluids with various properties and to sustain an environment where the processes critical to life may proceed. While computer simulations of biomolecules primarily investigate protein conformation and binding to drug-like molecules, these interactions often occur in the context of a lipid membrane. Chemical specificity of lipid models is essential to accurately represent the complex environment of the lipid membrane. This review discusses the development and performance of currently used chemically specific lipid force fields (FF) such as the CHARMM, AMBER, GROMOS, OPLS, and MARTINI families. Considerations in lipid FF development including lipid diversity, temperature dependence, phase behavior, and effects of atomic polarizability are considered, as well as methods and goals of parametrization. Applications of these FFs to complex and diverse models for cellular membranes are summarized. Lastly, areas for future development, such as efficient inclusion of long-range Lennard–Jones interactions (significant in transitions from polar to apolar media), accurate transmembrane dipole potential, and diffusion under periodic boundary conditions are considered.

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“…However, natural membranes are far more complex. Lipid–lipid interactions and lipid interactions with transmembrane and peripheral proteins greatly influence membrane properties. ,, …”

Section: Modeling Cellular Membrane Complexitymentioning

confidence: 99%

Section: Modeling Cellular Membrane Complexitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

et al. 2019

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“…Experimental techniques such as NMR spectroscopy and neutron/X-ray scattering are essential to the accurate study of CER-containing membranes, but these techniques are resource-demanding and do not provide access to atomic-level detail. A complementary approach is the use of molecular dynamics (MD) simulations, which has enjoyed a strong increase in accessibility in recent years as computational power has rapidly expanded. − Molecular dynamics studies of pure CER bilayers have noticed the effects of headgroup size, force field parameters, and hydroxylation on membrane properties. Small headgroup size is extremely influential and produces weaker peaks in electron density profiles compared to SM, whereas varying force-field parameters provide consistent results with some discrepancies in hydrogen bonding.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulations of Ceramide and Ceramide-Phosphatidylcholine Bilayers

Wang

Klauda

2017

J. Phys. Chem. B

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Recent studies in lipid raft formation and stratum corneum permeability have focused on the role of ceramides (CER). In this study, we use the all-atom CHARMM36 (C36) force field to simulate bilayers using N-palmitoylsphingosine (CER16) or α-hydroxy-N-stearoyl phytosphingosine (CER[AP]) in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) or 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), which serve as general membrane models. Conditions are replicated from experimental studies for comparison purposes, and concentration (X) is varied to probe the effect of CER on these systems. Comparisons with experiment based on deuterium order parameters and bilayer thickness demonstrate good agreement, thus supporting further use of the C36 force field. CER concentration is shown to have a profound effect on nearly all membrane properties including surface area per lipid, chain order and tilt, area compressibility moduli, bilayer thickness, hydrogen bonding, and lipid clustering. Hydrogen bonding in particular can significantly affect other membrane properties and can even encourage transition to a gel phase. Despite CER's tendency to condense the membrane, an expansion of CER lipids with increasing X is possible depending on how the balance between various hydrogen-bond pairs and lipid clustering is perturbed. Based on gel phase transitions, support is given for phytosphingosine's role as a hydrogen-bond bridge between sphingosine ordered domains in the stratum corneum.

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Modeling Lipid Membranes

Cited by 2 publications

References 90 publications

Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes

Molecular Dynamics Simulations of Ceramide and Ceramide-Phosphatidylcholine Bilayers

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