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Related Concept Videos

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...
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...
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...
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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...
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Membrane Proteins

Plasma membranes have integral transmembrane proteins involved in facilitated transport. These proteins are collectively referred to as transport proteins, and they function as either channels for the material or as carriers themselves. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids and a hydrophilic channel through their core that provides a hydrated opening for solutes to pass through the membrane layers. Passage through the channel allows...

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Rapid Assessment of Membrane Protein Quality by Fluorescent Size Exclusion Chromatography
06:26

Rapid Assessment of Membrane Protein Quality by Fluorescent Size Exclusion Chromatography

Published on: January 6, 2023

Model quality assessment for membrane proteins.

Arjun Ray1, Erik Lindahl, Björn Wallner

  • 1Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.

Bioinformatics (Oxford, England)
|October 16, 2010
PubMed
Summary
This summary is machine-generated.

A new method, ProQM, improves protein structure quality assessment by focusing on membrane proteins. This approach enhances accuracy for critical regions like binding sites, aiding pharmaceutical research.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Drug discovery

Background:

  • Learning-based model quality assessment (MQA) methods effectively distinguish protein structure quality.
  • Focusing MQA on specific contexts, like membrane proteins, can significantly enhance performance.
  • Membrane proteins are crucial targets in pharmaceutical research, necessitating accurate local quality assessment, especially for binding sites.

Purpose of the Study:

  • To develop an improved MQA method tailored for membrane proteins.
  • To enhance the prediction of local model quality in functionally important regions of membrane proteins.
  • To provide a tool that aids in selecting near-native structural models for pharmaceutical applications.

Main Methods:

  • Development of the ProQM method, utilizing a support vector machine.
  • Integration of general and membrane protein-specific features into the ProQM model.
  • Combination of ProQM with the Rosetta low-resolution energy function.

Main Results:

  • ProQM significantly outperforms generic MQA methods for transmembrane regions while maintaining performance for extra-membrane domains.
  • ProQM accurately predicts both global and local quality for G protein-coupled receptor (GPCR) models, surpassing consensus-based scoring.
  • The synergy of ProQM and Rosetta's energy function yields a 7-fold enrichment in selecting near-native structural models with minimal computational overhead.

Conclusions:

  • ProQM offers a specialized and highly effective approach to MQA for membrane proteins.
  • The method provides accurate local and global quality predictions, valuable for drug discovery targeting membrane proteins.
  • ProQM, when combined with other tools, substantially improves the efficiency of identifying high-quality protein structural models.