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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 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.
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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...
Protein Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the translocon complex.
Introduction to Membrane Proteins01:16

Introduction to Membrane Proteins

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 types have...

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Transmembrane Domain Oligomerization Propensity determined by ToxR Assay
06:45

Transmembrane Domain Oligomerization Propensity determined by ToxR Assay

Published on: May 26, 2011

Transmembrane helix: simple or complex.

Wing-Cheong Wong1, Sebastian Maurer-Stroh, Georg Schneider

  • 1Bioinformatics Institute (BII), Agency for Science, Technology and Research (A STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671. wongwc@bii.a-star.edu.sg

Nucleic Acids Research
|May 9, 2012
PubMed
Summary
This summary is machine-generated.

The transmembrane helix: simple or complex (TMSOC) webserver distinguishes simple and complex transmembrane helices. Masking simple transmembrane helices improves sequence similarity searches for membrane proteins.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Transmembrane helices (TMs) are classified as simple or complex based on their roles.
  • Simple TMs act as hydrophobic anchors, often due to convergent evolution.
  • Complex TMs possess ancestral information and have structural/functional roles beyond membrane insertion.

Purpose of the Study:

  • To develop a computational tool for distinguishing simple and complex transmembrane helices.
  • To address limitations in sequence homology searches for membrane proteins.

Main Methods:

  • Development of the Transmembrane Helix: Simple or Complex (TMSOC) webserver.
  • Implementation of a masking strategy for simple TM segments in seed sequences.
  • Evaluation of the tool's impact on sequence similarity search accuracy.

Main Results:

  • The TMSOC webserver accurately identifies simple and complex TMs.
  • Masking simple TMs significantly reduces the false-discovery rate in similarity searches.
  • Sensitivity is maintained while improving the accuracy of identifying evolutionarily related sequences.

Conclusions:

  • TMSOC is a valuable tool for analyzing membrane proteins.
  • It enhances the reliability of sequence similarity searches by accounting for TM complexity.
  • The tool benefits both experimental and computational biologists in the field of membrane protein research.