Backmapping triangulated surfaces to coarse-grained membrane models
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Backmapping triangulated surfaces to coarse-grained membrane models. / Pezeshkian, Weria; Konig, Melanie; Wassenaar, Tsjerk A.; Marrink, Siewert J.
I: Nature Communications, Bind 11, Nr. 1, 2296, 08.05.2020.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Backmapping triangulated surfaces to coarse-grained membrane models
AU - Pezeshkian, Weria
AU - Konig, Melanie
AU - Wassenaar, Tsjerk A.
AU - Marrink, Siewert J.
PY - 2020/5/8
Y1 - 2020/5/8
N2 - Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide range of spatiotemporal scales that cannot be investigated in full by any single current simulation technique. A potential solution is to combine different levels of resolution through a multiscale scheme. Here, we present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface (DTS) to its corresponding molecular model based on the coarse-grained (CG) Martini force field. Thus, we can use DTS simulations to equilibrate slow large-scale membrane conformational changes and then explore the local properties at CG resolution. We demonstrate the power of our method by backmapping a vesicular bud induced by binding of Shiga toxin and by transforming the membranes of an entire mitochondrion to near-atomic resolution. Our approach opens the way to whole cell simulations at molecular detail. Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field.
AB - Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide range of spatiotemporal scales that cannot be investigated in full by any single current simulation technique. A potential solution is to combine different levels of resolution through a multiscale scheme. Here, we present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface (DTS) to its corresponding molecular model based on the coarse-grained (CG) Martini force field. Thus, we can use DTS simulations to equilibrate slow large-scale membrane conformational changes and then explore the local properties at CG resolution. We demonstrate the power of our method by backmapping a vesicular bud induced by binding of Shiga toxin and by transforming the membranes of an entire mitochondrion to near-atomic resolution. Our approach opens the way to whole cell simulations at molecular detail. Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field.
KW - SPONTANEOUS-CURVATURE
KW - MOLECULAR-DYNAMICS
KW - FORCE-FIELD
KW - MECHANISM
KW - PROTEINS
KW - GROMACS
KW - MARTINI
KW - TOOL
U2 - 10.1038/s41467-020-16094-y
DO - 10.1038/s41467-020-16094-y
M3 - Journal article
VL - 11
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 2296
ER -
ID: 316752526