Literature DB >> 30259387

Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics.

P Siani1, H Khandelia2, M Orsi3, L G Dias4.   

Abstract

We present a new coarse-grained (CG) model of cholesterol (CHOL) for the electrostatic-based ELBA force field. A distinguishing feature of our CHOL model is that the electrostatics is modeled by an explicit point dipole which interacts through an ideal vacuum permittivity. The CHOL model parameters were optimized in a systematic fashion, reproducing the electrostatic and nonpolar partitioning free energies of CHOL in lipid/water mixtures predicted by full-detailed atomistic molecular dynamics simulations. The CHOL model has been validated by comparison to structural, dynamic and thermodynamic properties with experimental and atomistic simulation reference data. The simulation of binary DPPC/cholesterol mixtures covering the relevant biological content of CHOL in mammalian membranes is shown to correctly predict the main lipid behavior as observed experimentally.

Entities:  

Keywords:  Cholesterol; Coarse-grained; DPPC; Diffusion; Lipid bilayers; Molecular dynamics

Mesh:

Substances:

Year:  2018        PMID: 30259387     DOI: 10.1007/s10822-018-0164-4

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  134 in total

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Authors:  Siewert J Marrink; D Peter Tieleman
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2.  VORO++: a three-dimensional voronoi cell library in C++.

Authors:  Chris H Rycroft
Journal:  Chaos       Date:  2009-12       Impact factor: 3.642

3.  Structure of phospholipid-cholesterol membranes: an x-ray diffraction study.

Authors:  Sanat Karmakar; V A Raghunathan
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-06-29

4.  A deuterium nuclear magnetic resonance study of the condensing effect of cholesterol on egg phosphatidylcholine bilayer membranes. I. Perdeuterated fatty acid probes.

Authors:  G W Stockton; I C Smith
Journal:  Chem Phys Lipids       Date:  1976-10       Impact factor: 3.329

5.  Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.

Authors:  Philipp S Schmalhorst; Felix Deluweit; Roger Scherrers; Carl-Philipp Heisenberg; Mateusz Sikora
Journal:  J Chem Theory Comput       Date:  2017-09-08       Impact factor: 6.006

6.  Interactions of cholesterol with lipid bilayers: the preferred configuration and fluctuations.

Authors:  A Kessel; N Ben-Tal; S May
Journal:  Biophys J       Date:  2001-08       Impact factor: 4.033

7.  Variations in the condensing effect of cholesterol on saturated versus unsaturated phosphatidylcholines at low and high sterol concentration.

Authors:  Paweł Wydro; Sabina Knapczyk; Marta Lapczyńska
Journal:  Langmuir       Date:  2011-03-31       Impact factor: 3.882

8.  Molecular view of cholesterol flip-flop and chemical potential in different membrane environments.

Authors:  W F Drew Bennett; Justin L MacCallum; Marlon J Hinner; Siewert J Marrink; D Peter Tieleman
Journal:  J Am Chem Soc       Date:  2009-09-09       Impact factor: 15.419

9.  Lipid dynamics and domain formation in model membranes composed of ternary mixtures of unsaturated and saturated phosphatidylcholines and cholesterol.

Authors:  Dag Scherfeld; Nicoletta Kahya; Petra Schwille
Journal:  Biophys J       Date:  2003-12       Impact factor: 4.033

10.  Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers.

Authors:  Michael D Daily; Brett N Olsen; Paul H Schlesinger; Daniel S Ory; Nathan A Baker
Journal:  J Chem Theory Comput       Date:  2014-05-13       Impact factor: 6.006

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  1 in total

Review 1.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

  1 in total

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