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Related Concept Videos

Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

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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...
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Structure of Porins01:21

Structure of Porins

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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...
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Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

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

Insertion of Single-pass Transmembrane Proteins in the RER

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

Insertion of Multi-pass Transmembrane Proteins in the RER

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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...
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Introduction to Membrane Proteins01:16

Introduction to Membrane Proteins

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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...
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Related Experiment Video

Updated: Jul 23, 2025

From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins
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From Constructs to Crystals – Towards Structure Determination of β-barrel Outer Membrane Proteins

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General features of transmembrane beta barrels from a large database.

Daniel Montezano1, Rebecca Bernstein1, Matthew M Copeland1

  • 1Computational Biology Program, University of Kansas, Lawrence, KS 66045.

Proceedings of the National Academy of Sciences of the United States of America
|July 11, 2023
PubMed
Summary

Researchers developed IsItABarrel, a new method for identifying transmembrane β-barrels (TMBB) with 95.88% accuracy. This tool utilizes a large, high-quality TMBB database, significantly outperforming previous algorithms and offering a valuable resource for biological research.

Keywords:
contact mapdatabaseouter membrane proteintransmembrane β-barrelβ-signal

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Transmembrane β-barrels (TMBBs) are crucial membrane proteins, but their study has been limited by data availability.
  • Previous methods for TMBB identification often suffer from high false positive rates.

Purpose of the Study:

  • To create a large, high-quality database of bacterial transmembrane β-barrels (TMBBs).
  • To develop and validate a novel computational method for accurate TMBB identification.
  • To analyze the diversity and characteristics of TMBBs.

Main Methods:

  • Coevolution data analysis to construct a comprehensive TMBB database.
  • Feature detection on evolutionary contact maps using the IsItABarrel algorithm.
  • Comparative analysis against existing TMBB datasets and algorithms.

Main Results:

  • The IsItABarrel method achieved 95.88% balanced accuracy in discriminating protein classes.
  • The new TMBB database is significantly larger (1,938,936 proteins) and more accurate than previous resources (TMBB-DB, OMPdb).
  • Identified 11 TMBB types, including three novel ones, and observed significant variation in proteome usage and TMBB length distributions.

Conclusions:

  • The developed TMBB database and IsItABarrel method represent a significant advancement in the field.
  • The findings provide a valuable resource for researchers requiring high-quality TMBB sequence data.
  • New insights into TMBB diversity, evolutionary patterns, and potential signaling motifs were uncovered.