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Related Concept Videos

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 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...
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...
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...
Translocation of Proteins into the Mitochondria01:19

Translocation of Proteins into the Mitochondria

Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
Mitochondrial Protein Sorting01:39

Mitochondrial Protein Sorting

Mitochondria are double-membrane organelles of the eukaryotes involved in cellular metabolism, signaling, ATP synthesis, and programmed cell death.  Each of these processes requires specific proteins and enzymes that must be correctly sorted to the right mitochondrial subcompartment for the proper functioning of the organelle.
Most of these mitochondrial proteins are encoded by the nucleus and imported to the mitochondria as unfolded or loosely folded precursors. Mitochondrial precursors...

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Related Experiment Video

Updated: Jun 22, 2026

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
08:14

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)

Published on: April 20, 2015

Transmembrane protein topology prediction using support vector machines.

Timothy Nugent1, David T Jones

  • 1Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK. t.nugent@cs.ucl.ac.uk

BMC Bioinformatics
|May 28, 2009
PubMed
Summary
This summary is machine-generated.

We developed a new computational tool to predict the topology of alpha-helical transmembrane proteins, achieving high accuracy in identifying protein structures and crucial elements like signal peptides. This method aids in understanding protein function and drug development.

More Related Videos

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

Related Experiment Videos

Last Updated: Jun 22, 2026

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)
08:14

Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)

Published on: April 20, 2015

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

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Alpha-helical transmembrane (TM) proteins are crucial for cellular functions including signaling and transport.
  • These proteins are significant drug targets, yet structural data is limited due to crystallization challenges.
  • Sequence-based methods are vital for investigating TM protein topology in the absence of structural data.

Purpose of the Study:

  • To develop and validate a computational method for predicting alpha-helical TM protein topology.
  • To integrate signal peptide and re-entrant helix prediction into a unified TM protein topology predictor.
  • To create a tool capable of discriminating between TM and globular proteins for accurate genome annotation.

Main Methods:

  • Utilized a support vector machine (SVM) based approach for TM protein topology prediction.
  • Integrated prediction of signal peptides and re-entrant helices.
  • Benchmarked the method using full cross-validation on a dataset of 131 sequences with known crystal structures.
  • Developed an additional SVM to differentiate between globular and TM proteins.

Main Results:

  • Achieved 89% accuracy for TM protein topology prediction.
  • Signal peptides and re-entrant helices were predicted with 93% and 44% accuracy, respectively.
  • The globular vs. TM protein discriminator showed zero false positives and a 0.4% false negative rate.
  • The tools were applied to complete genomes, with code and data made publicly available.

Conclusions:

  • The developed method offers high accuracy in predicting TM protein topology, including signal peptides and re-entrant helices.
  • The tool effectively distinguishes TM from globular proteins, facilitating whole-genome annotation.
  • This computational approach is well-suited for annotating alpha-helical TM proteins across various genomes.