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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.Fatty acids tails of phospholipids can be either saturated or...
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Multi-pass Transmembrane Proteins and β-barrels

In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
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Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...
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...
Detergent Purification of Membrane Proteins01:18

Detergent Purification of Membrane Proteins

Detergents are used to purify the integral proteins of the membrane. The hydrophobic portion of the detergent can replace membrane phospholipids while solubilizing the membrane proteins. When detergent monomers reach a specific concentration in a solution called critical micelle concentration (CMC), they form micelles. Above CMC, the concentration of the detergent monomers remains in equilibrium with the micelle. The number of detergent monomers present in the CMC varies for each detergent, and...

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Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
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A unified hydrophobicity scale for multispan membrane proteins.

Julia Koehler1, Nils Woetzel, René Staritzbichler

  • 1Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-8725, USA.

Proteins
|December 18, 2008
PubMed
Summary

This study introduces a new unified hydrophobicity scale (UHS) for membrane proteins (MPs), integrating alpha-helical and beta-barrel structures. The knowledge-based UHS accurately predicts trans-membrane spans and aids in computational protein structure elucidation.

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Assembly of Cell Mimicking Supported and Suspended Lipid Bilayer Models for the Study of Molecular Interactions

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Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology and Bioinformatics

Background:

  • Hydrophobicity is crucial for membrane protein (MP) folding, structure, and function.
  • Existing hydrophobicity scales are derived using experimental or statistical methods, often optimized for specific phenomena.
  • A unified approach for diverse MP types is needed to enhance predictive accuracy.

Purpose of the Study:

  • To develop the first knowledge-based hydrophobicity scale unifying alpha-helical and beta-barrel multispan MPs.
  • To introduce a knowledge-based scale specifically for mammalian alpha-helical MPs.
  • To provide a tool for computational protein structure elucidation and design.

Main Methods:

  • Developed a unified hydrophobicity scale (UHS) based on amino acid preferences in solution, transition, and trans-membrane states.
  • Created a knowledge-based hydrophobicity scale for mammalian alpha-helical MPs (MHS).
  • Validated the UHS by analyzing diverse MPs and comparing its performance against nine established scales for trans-membrane span prediction.

Main Results:

  • The unified hydrophobicity scale (UHS) integrates characteristics of both alpha-helical and beta-barrel MPs.
  • The UHS demonstrates a striking similarity to a recent experimental scale, consolidating findings from different approaches.
  • The UHS outperforms nine established scales in predicting trans-membrane spans and serves as an accurate free energy measure for folded MPs.

Conclusions:

  • The developed knowledge-based hydrophobicity scales (UHS and MHS) enhance the understanding of MP structure and function.
  • The UHS provides a valuable tool for computational protein structure prediction, machine learning applications, and protein design.
  • The UHS significantly improves the accuracy of trans-membrane span prediction, benefiting from recent PDB data expansion.