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Related Concept Videos

Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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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...
Fluid Mosaic Model01:19

Fluid Mosaic Model

Scientists identified the plasma membrane in the 1890s and its principal chemical components (lipids and proteins) by 1915. The model for plasma membrane structure, proposed in 1935 by Hugh Davson and James Danielli, was the first model to be widely accepted in the scientific community. The model was based on the plasma membrane's "railroad track" appearance in early electron micrographs. Davson and Danielli theorized that the plasma membrane's structure resembled a sandwich with the analogy of...
Introduction to Membrane Proteins01:16

Introduction to Membrane Proteins

The cell membrane, or plasma membrane, is an ever-changing landscape. It is described as a fluid mosaic where various macromolecules are embedded in the phospholipid bilayer. Among the macromolecules are proteins. The protein content varies across cell types. For example, mitochondrial inner membranes contain ~76% protein content, while myelin contains ~18% protein content. Individual cells contain many types of membrane proteins—red blood cells contain over 50—and different cell types have...
Tail-anchoring of Proteins in the ER Membrane01:45

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Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
Mechanisms of Membrane Domain Formation00:59

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Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
Another mechanism for membrane domain formation involves membrane proteins interacting with cytoskeletal...

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SAHBNET, an accessible surface-based elastic network: an application to membrane protein.

Nicolas Dony1, Jean Marc Crowet, Bernard Joris

  • 1Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium. l.lins@ulg.ac.be.

International Journal of Molecular Sciences
|June 1, 2013
PubMed
Summary

We developed SAHBNET, a new elastic network model for coarse-grained molecular dynamics simulations. SAHBNET maintains protein structure in simulations, offering a physics-based approach for membrane protein studies.

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Area of Science:

  • Computational biology
  • Biophysics
  • Molecular modeling

Background:

  • Molecular Dynamics (MD) is crucial for membrane simulations.
  • Coarse-grained forcefields enable longer simulations by reducing computational cost.
  • Existing elastic network models may lack sufficient physical basis.

Purpose of the Study:

  • Introduce SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), a novel physics-based elastic network model.
  • Enhance the structural stability of proteins in coarse-grained simulations.
  • Improve the simulation of membrane proteins within complex lipid bilayers.

Main Methods:

  • Developed SAHBNET based on hydrogen bonds and buried residue proximity from atomistic structures.
  • Applied SAHBNET to coarse-grained beads using the MARTINI model.
  • Evaluated SAHBNET against atomistic simulations and compared it with ELNEDYN models.
  • Simulated membrane proteins in complex lipid bilayers using a modified GROMACS tool.

Main Results:

  • SAHBNET successfully maintains protein structures close to atomistic simulations.
  • The model demonstrates effectiveness in simulating membrane proteins within complex lipid bilayers.
  • SAHBNET provides a more physics-based approach compared to simpler elastic networks.

Conclusions:

  • SAHBNET is a robust and effective method for maintaining protein structural integrity in coarse-grained molecular dynamics.
  • The model facilitates accurate simulations of membrane proteins in realistic lipid bilayer environments.
  • SAHBNET represents an advancement in coarse-grained simulation methodologies for structural biology.