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Related Concept Videos

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...
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...
Insertion of Single-pass Transmembrane Proteins in the RER01:26

Insertion of Single-pass Transmembrane Proteins in the RER

Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
Integral transmembrane proteins possess transmembrane and extra membrane domains. The transmembrane domains are primarily made of 20-25 hydrophobic amino acids arranged in a helical secondary confirmation. These...
Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

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...
Insertion of Multi-pass Transmembrane Proteins in the RER01:29

Insertion of Multi-pass Transmembrane Proteins in the RER

The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Alpha helical trans-membrane proteins: Enhanced prediction using a Bayesian approach.

Paul D Taylor1, Christopher P Toseland, Teresa K Attwood

  • 1The Jenner Institute, University of Oxford, Compton,Newbury, Berkshire, RG20 7NN, UK.

Bioinformation
|June 29, 2007
PubMed
Summary

Predicting membrane protein topology is crucial for understanding protein function. A new Bayesian Network method accurately determines alpha-helical membrane protein topology, aiding in computational analysis.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Membrane proteins represent a significant portion of cellular proteomes, yet are challenging for experimental structure determination.
  • Understanding membrane protein topology is vital for elucidating their biological functions and interactions.
  • Computational methods offer a complementary approach to experimental techniques for studying membrane proteins.

Purpose of the Study:

  • To develop and evaluate a novel computational method for predicting the topology of alpha-helical membrane proteins.
  • To assess the accuracy of the proposed method in distinguishing between prokaryotic and eukaryotic membrane proteins.

Main Methods:

  • A method based on Bayesian Networks was employed for statistical inference in topology prediction.
  • The Bayesian Network approach was applied to a dataset of known alpha-helical membrane proteins.

Main Results:

  • The developed Bayesian Network method achieved prediction accuracies of 77.4% for prokaryotic membrane proteins.
  • The method demonstrated accuracies of 61.4% for eukaryotic membrane proteins.

Conclusions:

  • The Bayesian Network-based method represents a significant advancement in the computational prediction of membrane protein topology.
  • This approach provides a valuable and complementary tool for the analysis of membrane proteins across various applications.