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Related Concept Videos

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...
Types of Membrane Protrusions01:28

Types of Membrane Protrusions

The protrusion of the cell surface is an initial step for several cellular processes, including cell migration, phagocytosis, and neurite outgrowth. These membrane protrusions are a result of cytoskeletal rearrangement. The most  widely observed cell protrusions include lamellipodia, pseudopodia, filopodia, microvilli, invadopodia, and podosomes. These protrusions can be of two types — static or dynamic.
The microvilli, an example of stable protrusions, are finger-like projections with a...
Multi-pass Transmembrane Proteins and β-barrels01:09

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
Multi-pass transmembrane proteins such as G-protein-linked receptors (GPCRs) and...
Membrane Proteins01:30

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...
Membrane Proteins01:30

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...
Membrane Asymmetry Regulating Transporters01:19

Membrane Asymmetry Regulating Transporters

Enzymes like flippase, floppase, and scramblase transfer phospholipids from one layer to another in the membrane, thereby affecting membrane asymmetry.
Flippase
Eukaryotic flippases are type-IV P-type ATPases or P4-ATPases belonging to P-type ATPase family proteins that are membrane-bound pumps involved in the ATP-mediated transport of ions and molecules across the membrane. Flippases flip specific phospholipids from the outer to the inner leaflet of a membrane. All P4-ATPases have one...

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Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
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Published on: April 20, 2015

Predicting membrane protein types with bragging learner.

Bing Niu1, Yu-Huan Jin, Kai-Yan Feng

  • 1School of Materials Science and Engineering, Shanghai University, Shanghai, People's Republic of China.

Protein and Peptide Letters
|August 6, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a novel bootstrap aggregating (bragging learner) method for predicting membrane protein types using amino acid composition. The new approach achieved over 84% accuracy, showing potential for protein attribute prediction.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Membrane protein type is crucial for understanding protein folding and function.
  • Accurate prediction of membrane protein types is an ongoing challenge in bioinformatics.
  • Existing methods require significant computational resources or specialized data.

Purpose of the Study:

  • To develop a novel and efficient computational method for predicting membrane protein types.
  • To evaluate the performance of the proposed method using a benchmark dataset.
  • To explore potential improvements for future prediction models.

Main Methods:

  • Utilized the bootstrap aggregating (bragging learner) ensemble method.
  • Employed protein amino acid composition as the primary feature for prediction.
  • Validated the method using jackknife cross-validation on a benchmark dataset.

Main Results:

  • The bragging learner achieved an overall success rate exceeding 84% in predicting membrane protein types.
  • The method demonstrates high potential as a complementary tool to existing protein prediction algorithms.
  • The study highlights the effectiveness of amino acid composition for this prediction task.

Conclusions:

  • The proposed bragging learner offers a promising approach for membrane protein type prediction.
  • Further enhancements are expected with the incorporation of pseudo amino acid composition.
  • An online web server is available for practical application of the developed predictor.