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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...
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...
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 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...
Porin Insertion in the Outer Mitochondrial Membrane01:12

Porin Insertion in the Outer Mitochondrial Membrane

Porins are beta-barrel proteins translocated to the mitochondrial outer membrane through the TOM complex into the intermembrane space. Porin precursors bind TIM chaperones within the intermembrane space and are guided to the Sorting and Assembly Machinery complex or SAM complex on the outer mitochondrial membrane.
Three models describe the assembly of porins by the SAM complex and their insertion into the outer membrane. Model 1 suggests that porins are assembled outside the SAM channel as the...
Structure of Porins01:21

Structure of Porins

Mitochondria, chloroplasts, and gram-negative bacteria have transmembrane, beta-barrel proteins called porins to mediate the free diffusion of ions and metabolites across the membrane. Mitochondrial porin precursors contain conserved amino acid sequences called beta signals at their C-terminal. Beta signals have a  motif of PoXGXXHyXHy (Po-Polar, X-Any amino acid, G-Glycine, Hy-LargeHydrophobic), which are crucial for precursor recognition to initiate precursor assembly. Beta-barrel precursors...

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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

Beta barrel 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

This study introduces a Bayesian Network method for predicting beta-barrel transmembrane protein topology. The new computational approach achieves 88.6% accuracy for individual strand predictions, advancing membrane protein analysis.

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Area of Science:

  • Biochemistry and Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Membrane proteins are crucial cellular components, representing about 20% of genomic content.
  • They exist in two primary structural classes: alpha helical and beta barrel transmembrane proteins.
  • Accurate prediction of transmembrane protein topology is vital for understanding protein function and cellular processes.

Purpose of the Study:

  • To develop and evaluate a novel computational method for predicting the topology of beta-barrel transmembrane proteins.
  • To improve the accuracy of beta-barrel protein topology prediction using statistical inference techniques.

Main Methods:

  • Utilized Bayesian Networks, a robust statistical inference framework.
  • Applied the developed Bayesian Network model to the problem of beta-barrel topology prediction.
  • Evaluated the predictor's performance based on individual strand accuracies.

Main Results:

  • The beta-barrel topology predictor achieved an individual strand accuracy of 88.6%.
  • Demonstrated the effectiveness of Bayesian Networks for predicting transmembrane protein topology.
  • The proposed method shows significant promise in computational membrane protein analysis.

Conclusions:

  • The Bayesian Network-based method represents a significant advancement in the computational determination of membrane protein topology.
  • This approach offers a powerful tool for researchers studying beta-barrel proteins.
  • Further development could enhance the prediction of complex membrane protein structures.