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Related Concept Videos

Membrane Fluidity01:26

Membrane Fluidity

Membrane fluidity is explained by the fluid mosaic model of the cell membrane, which describes the plasma membrane structure as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character.
Mosaic nature of the membrane
The mosaic characteristic of the membrane helps the plasma membrane remain fluid. The integral proteins and lipids exist as separate but loosely-attached molecules in the membrane. The membrane is a relatively...
Membrane Fluidity01:23

Membrane Fluidity

Cell membranes are composed of phospholipids, proteins, and carbohydrates loosely attached to one another through chemical interactions. Molecules are generally able to move about in the plane of the membrane, giving the membrane its flexible nature called fluidity. Two other features of the membrane contribute to membrane fluidity: the chemical structure of the phospholipids and the presence of cholesterol in the membrane.
Lipids as Anchors01:32

Lipids as Anchors

In the plasma membrane, the lipids forming the bilayer can also act as an anchor to tether proteins to the membrane. The three main types of lipid anchors found in eukaryotes are – prenyl groups, fatty acyl groups, and glycosylphosphatidylinositol or GPI groups. Prenyl and fatty acyl groups act as anchors on the cytosolic surface of the membrane, whereas GPI anchors proteins on the extracellular side.
The carboxy-terminal of most of the prenylated proteins, such as Ras proteins, contains the...

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Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
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Improving the CHARMM force field for polyunsaturated fatty acid chains.

Jeffery B Klauda1, Viviana Monje, Taehoon Kim

  • 1Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA. jbklauda@umd.edu

The Journal of Physical Chemistry. B
|June 16, 2012
PubMed
Summary

The CHARMM36 force field was improved for polyunsaturated fatty acids (PUFAs) using quantum mechanics. The new C36p model accurately simulates PUFA bilayers, enhancing molecular dynamics simulations.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Materials Science

Background:

  • The CHARMM36 (C36) force field accurately models saturated and monounsaturated lipid bilayers.
  • However, C36 exhibits inaccuracies in molecular dynamics (MD) simulations of bilayers containing polyunsaturated fatty acids (PUFAs).
  • Specifically, surface area per lipid (SA) and deuterium order parameters (S(CD)) for 1-stearoyl-2-docosahexaenoyl-sn-glycerco-3-phosphocholine (SDPC) bilayers are misrepresented.

Purpose of the Study:

  • To improve the accuracy of the C36 force field for simulating polyunsaturated fatty acid (PUFA) containing lipid bilayers.
  • To develop an enhanced force field, termed C36p, by refining dihedral potentials.
  • To validate the C36p force field through molecular dynamics simulations and comparison with experimental data.

Main Methods:

  • High-level quantum mechanical calculations were employed to refine the dihedral potential of neighboring double bonds in PUFAs.
  • The modified force field, C36p, was used for molecular dynamics (MD) simulations of 1-stearoyl-2-docosahexaenoyl-sn-glycerco-3-phosphocholine (SDPC) bilayers.
  • Simulations were also performed on 1,2-diarachidonyl-phosphatidylcholine (DAPC) bilayers to further validate the C36p parameters.

Main Results:

  • The C36p force field significantly improved the surface area per lipid (SA) for SDPC bilayers, increasing it from 63.2 to 70.8 Å(2) at 303 K, aligning with X-ray diffraction data.
  • Deuterium order parameters (S(CD)) calculated using C36p showed excellent agreement with experimental values for both sn-1 and sn-2 chains.
  • NMR (13)C relaxation times and X-ray form factors from C36p simulations also matched experimental results.
  • Simulations of DAPC bilayers confirmed the force field's ability to capture expected changes in bilayer thickness and SA for lipids with multiple PUFA chains.

Conclusions:

  • The C36p force field provides a significant improvement for accurately simulating polyunsaturated fatty acid (PUFA) containing lipid bilayers.
  • This enhanced force field enables more reliable molecular dynamics (MD) simulations of complex lipid systems.
  • The validated C36p model is expected to advance research in areas involving PUFA-rich biological membranes.