Molecular modeling of lipid probes and their influence on the membrane

Abstract

In this review a number of Molecular Dynamics simulation studies are discussed which focus on the understanding of the behavior of lipid probes in biomembranes. Experiments often use specialized probe moieties or molecules to report on the behavior of a membrane and try to gain information on the membrane as a whole from the probe lipids as these probes are the only things an experiment sees. Probes can be used to make NMR, EPR and fluorescence accessible to the membrane and use fluorescent or spin-active moieties for this purpose. Clearly membranes with and without probes are not identical which makes it worthwhile to elucidate the differences between them with detailed atomistic simulations. In almost all cases these differences are confined to the local neighborhood of the probe molecules which are sparsely used and generally present as single molecules. In general, the behavior of the bulk membrane lipids can be qualitatively understood from the probes but in most cases their properties cannot be directly quantitatively deduced from the probe behavior.

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

“…In recent years, molecular dynamics (MD) simulations have emerged as such a tool to help characterize the behavior of fluorescent membrane probes, able to fill in the gaps left by the incomplete and indirect fluorescence measurements and also provide new insights, with atomic-level detailed information [18][19][20]. Probably due to its importance, DPH was the first probe to be studied in this way.…”

Aptamer‐Engineered Natural Killer Cells for Cell‐Specific Adaptive Immunotherapy

“…To render NK cells target‐specificity, the ApEn‐NK were generated by simply engineering synthetic aptamer‐anchor structures on the cell surfaces via biophysical intercalation into the cell membrane ( Figure A). Lipophilic linkers have been widely used to anchor functional molecules on the membranes of living cells for different purposes, with no adverse impact on cell viability . In this study, a CD30‐specific single‐stranded DNA (ssDNA) aptamer sequence was synthesized to different lipophilic anchors, including single‐ or double‐C18 hydrocarbon chains, cholesterol, or vitamin E, to produce the aptamer‐anchor structures Apt‐C18, Apt‐2xC18, Apt‐Chol, and Apt‐VitE, respectively (Figure B).…”

“…Cholesterol is an essential component of the membrane and is dispersed between phospholipids to maintain membrane integrity and flexibility . Notably, phospholipid and cholesterol derivatives have the capacity to intercalate between cell membranes via hydrophobic interactions and thus have been used as linkers for fluorescence labeling of membranes . In this study, different phospholipid and cholesterol derivatives were tested in the production of amphiphilic aptamer‐anchor structures (Figure B).…”

Lipid membranes: Theory and simulations bridged to experiments

“…In this context, Bunker et al [7] discuss how PEGylated lipids can be used as drug delivery carriers. Meanwhile, Faller [8] presents a survey of lipid probes' applications and their effects on lipid bilayer properties. Examples of synthetic lipids and their pharmacological applications are discussed in the article by Kepczynski and Róg [9], and gold nanoparticles interacting with lipid bilayers and their numerous biomedical applications are discussed in the article by Rossi and Monticelli [10].…”