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Related Concept Videos

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...
Asymmetric Lipid Bilayer01:35

Asymmetric Lipid Bilayer

Biological membranes show uneven distribution of different types of lipids in the inner and outer layers, resulting in transverse asymmetric membranes. The treatment of the erythrocyte membrane with the enzyme phospholipase confirmed the asymmetric nature of the lipid bilayer. The enzyme hydrolyzes lipids into fatty acids and hydrophilic groups. The phospholipase acts only on the outer layer of the membrane, while the inner layer remains intact. The phospholipase treatment resulted in 80%...
Structure of Lipids03:38

Structure of Lipids

Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and...
Structure of Lipids03:38

Structure of Lipids

Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and...
Structure of Lipids03:38

Structure of Lipids

Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and...
Biosynthesis of Lipids01:29

Biosynthesis of Lipids

Microbial membranes exhibit remarkable diversity in lipid composition, reflecting evolutionary adaptations to various environmental conditions. The three domains of life—Bacteria, Archaea, and Eukarya—synthesize membrane lipids through distinct biosynthetic pathways, leading to fundamental structural differences that impact membrane stability, function, and adaptability.Fatty Acid-Based Lipids in Bacteria and EukaryaBacteria and eukaryotes share a common fatty acid biosynthesis pathway, which...

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Related Experiment Video

Updated: May 19, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
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Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

LIPID11: a modular framework for lipid simulations using amber.

Åge A Skjevik1, Benjamin D Madej, Ross C Walker

  • 1Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway.

The Journal of Physical Chemistry. B
|August 25, 2012
PubMed
Summary
This summary is machine-generated.

Researchers developed LIPID11, a new computational framework for simulating lipid bilayers in molecular dynamics. This flexible tool enhances the study of membrane proteins by providing compatible lipid force fields within the Amber software.

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Last Updated: May 19, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
05:57

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Published on: April 26, 2024

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics simulations

Background:

  • Accurate simulation of complex lipid bilayers is crucial for understanding membrane protein structure and function.
  • Experimental methods for studying membrane proteins are often challenging.
  • Existing Amber force fields have limited focus on lipid simulations.

Purpose of the Study:

  • To introduce LIPID11, a novel, modular framework for lipid simulations within the Amber molecular dynamics environment.
  • To establish a new charge derivation strategy and nomenclature for lipids compatible with Amber's RESP approach.
  • To provide a foundation for developing comprehensive Amber-compatible lipid force fields.

Main Methods:

  • Developed a new charge derivation strategy for lipids consistent with the Amber RESP approach.
  • Implemented a new atom and residue naming and type convention.
  • Combined the new strategy with General Amber Force Field (GAFF) parameters to create the LIPID11 framework.

Main Results:

  • LIPID11 offers a flexible and modular framework for simulating lipids.
  • The framework is fully compatible with existing Amber force fields.
  • Preliminary simulation results demonstrate the feasibility of LIPID11 for phospholipids.

Conclusions:

  • LIPID11 represents a significant advancement for lipid simulations in Amber.
  • It serves as a flexible starting point for developing a comprehensive Amber-compatible lipid force field.
  • This framework will facilitate more accurate studies of membrane protein behavior.