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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...
Bacterial Translocation and Protein Secretion01:26

Bacterial Translocation and Protein Secretion

Bacterial protein secretion involves translocation systems to ensure proteins reach their designated locations, including the plasma membrane, periplasm, outer membrane, or the external environment. These translocation systems are vital for bacterial physiology, supporting processes like membrane assembly, enzymatic activity in the periplasm, and interactions with the external environment. The division of labor between Sec and Tat pathways ensures efficiency in handling proteins with diverse...
Cotranslational Protein Translocation01:20

Cotranslational Protein Translocation

Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
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.
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

TMBB-DB: a transmembrane β-barrel proteome database.

Thomas C Freeman1, William C Wimley

  • 1Department of Biochemistry, Tulane University, New Orleans, LA 70112, USA.

Bioinformatics (Oxford, England)
|July 31, 2012
PubMed
Summary
This summary is machine-generated.

This study presents a comprehensive database of transmembrane beta-barrels (TMBBs) in Gram-negative bacteria. The database aids in identifying novel TMBBs and understanding their functions.

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Area of Science:

  • Genomics
  • Proteomics
  • Structural Biology

Background:

  • Transmembrane beta-barrels (TMBBs) are crucial outer membrane proteins in Gram-negative bacteria.
  • Previous work developed a statistical algorithm for TMBB identification from genomic data.
  • A comprehensive database of TMBBs from over 600 Gram-negative bacterial genomes has been constructed.

Purpose of the Study:

  • To create a publicly accessible, searchable database of all proteins within Gram-negative bacterial genomes.
  • To identify and catalog transmembrane beta-barrels (TMBBs) using a refined statistical algorithm.
  • To provide detailed information for each protein to facilitate accurate TMBB identification and structural prediction.

Main Methods:

  • Application of a previously developed statistical algorithm to identify TMBBs in genomic sequences.
  • Construction of a searchable, up-to-date database of proteins from over 600 Gram-negative bacterial genomes.
  • Inclusion of specific predictive data for each protein: TMBB probability, strand/hairpin propensity, signal sequence score, and transmembrane alpha-helix predictions.

Main Results:

  • The database contains nearly 50,000 predicted TMBBs out of 1.9 million total proteins.
  • Over 15,000 predicted TMBBs are identified as 'hypothetical' or 'putative' proteins, representing novel discoveries.
  • Detailed protein information supports accurate identification and structural analysis of TMBBs.

Conclusions:

  • The TMBB genomic database offers a unique and valuable resource for researchers.
  • This resource facilitates the discovery and characterization of transmembrane beta-barrels in Gram-negative bacteria.
  • The database provides essential data for advancing our understanding of bacterial outer membrane protein structures and functions.