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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...
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...
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...
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...
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...

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Related Experiment Video

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Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
10:49

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Published on: March 5, 2017

Detecting pore-lining regions in transmembrane protein sequences.

Timothy Nugent1, David T Jones

  • 1Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK.

BMC Bioinformatics
|July 19, 2012
PubMed
Summary

This study introduces a computational method to identify pore-lining regions in transmembrane proteins using only sequence data. This approach aids in understanding protein structure and function for potential therapeutic applications.

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Last Updated: May 20, 2026

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Alpha-helical transmembrane proteins are crucial for biological processes, facilitating ion and molecule transport.
  • Limited crystal structures hinder the study of these vital proteins.
  • Computational methods are essential for predicting structural features from sequence data.

Purpose of the Study:

  • To develop a computational method for identifying pore-lining regions in transmembrane proteins from sequence alone.
  • To predict the pore stoichiometry of transmembrane protein channels.
  • To provide a tool for characterizing transmembrane protein pores.

Main Methods:

  • Developed a support vector machine (SVM) classifier trained on geometric criteria from crystal structures.
  • Utilized sequence information to predict transmembrane helices involved in pore formation.
  • Employed support vector regression (SVR) to predict pore subunit stoichiometry.

Main Results:

  • Achieved 72% accuracy in predicting pore-lining transmembrane helices.
  • Reached 62% accuracy in predicting the number of subunits forming the protein pore.
  • Demonstrated the method's effectiveness on sequences with available crystal structures.

Conclusions:

  • This is the first tool capable of identifying pore-lining regions in transmembrane proteins using sequence data.
  • The method offers insights into transmembrane protein pore characterization.
  • Potential applications include identifying therapeutic targets for various diseases.