2021
DOI: 10.1021/acs.langmuir.1c02084
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All-Atom Modeling of Complex Cellular Membranes

Abstract: Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane’s lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key exam… Show more

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Cited by 8 publications
(6 citation statements)
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“…Models with diverse types of headgroups and fatty acyl tails can provide more realistic biophysical and biochemical properties, and the work here falls within correspondingly more complex molecular models that have been constructed for other kinds of bacteria or cells . For example, 5 different phospholipids and cholesterol molecules were initially used to model a yeastlike membrane .…”
Section: Introductionmentioning
confidence: 99%
“…Models with diverse types of headgroups and fatty acyl tails can provide more realistic biophysical and biochemical properties, and the work here falls within correspondingly more complex molecular models that have been constructed for other kinds of bacteria or cells . For example, 5 different phospholipids and cholesterol molecules were initially used to model a yeastlike membrane .…”
Section: Introductionmentioning
confidence: 99%
“…Invariably there is a need for large scale membrane components, as the number of different membranes in a single cell include nuclear, golgi, phagosomes, proteasomes, lysosomes, excretory vesicles and a number of specialized elements for specific cell types. Some of these have already begun to be simulated, apparent from reviews of complex membrane systems, now including a number of intercellular membranes and bacterial cell membranes [ 180 , 181 , 182 ]. Additionally, each of these has localized membrane differences, such as lipid rafts and charge, or drastic pH and other solvent extremes on either side.…”
Section: Future Perspectives For Membrane Based Molecular Dynamicsmentioning
confidence: 99%
“…However, the hope that, with a continuing increase in capacity, all processes could be captured with such detailed models turned out to be idle. Even today, with access to exascale computing power, all‐atom simulations are still limited to spatiotemporal scales less than 100 nm and typically covering few microseconds 3–5 . Considering the gap with processes in real life, the need for a CG description is still as urgent as in the early days 5–11 .…”
Section: Introductionmentioning
confidence: 99%
“…Even today, with access to exascale computing power, all-atom simulations are still limited to spatiotemporal scales less than 100 nm and typically covering few microseconds. [3][4][5] Considering the gap with processes in real life, the need for a CG description is still as urgent as in the early days. [5][6][7][8][9][10][11] The requirement of more sampling speed became (re)apparent in the late 90s, and caused a surge in the development of numerous enhanced sampling methods as well as the re-valuation of the principle of coarsegraining.…”
mentioning
confidence: 99%