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Related Concept Videos

Membrane Proteins01:30

Membrane Proteins

Plasma membranes have integral transmembrane proteins involved in facilitated transport. These proteins are collectively referred to as transport proteins, and they function as either channels for the material or as carriers themselves. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids and a hydrophilic channel through their core that provides a hydrated opening for solutes to pass through the membrane layers. Passage through the channel allows...
Membrane Proteins01:30

Membrane Proteins

Plasma membranes have integral transmembrane proteins involved in facilitated transport. These proteins are collectively referred to as transport proteins, and they function as either channels for the material or as carriers themselves. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids and a hydrophilic channel through their core that provides a hydrated opening for solutes to pass through the membrane layers. Passage through the channel allows...
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...
Membrane Domains01:18

Membrane Domains

The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the anterior...
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...

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Related Experiment Video

Updated: Jul 9, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Co-evolving residues in membrane proteins.

Angelika Fuchs1, Antonio J Martin-Galiano, Matan Kalman

  • 1Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

Bioinformatics (Oxford, England)
|December 11, 2007
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method for predicting contacts in alpha-helical membrane proteins using correlated mutations. The consensus prediction approach significantly improves the accuracy of identifying helix-helix contacts, aiding structural model construction.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Co-evolving residue analysis is established for soluble proteins but limited for membrane proteins.
  • Existing methods for predicting intramolecular contacts lack sufficient accuracy for reliable structural modeling.
  • Membrane proteins, crucial for biological functions, remain understudied in contact prediction.

Purpose of the Study:

  • To present the first general study of correlated mutations in alpha-helical membrane proteins.
  • To develop and evaluate a consensus prediction method for identifying residue contacts.
  • To improve the prediction accuracy of helix-helix contacts in membrane proteins.

Main Methods:

  • Applied seven different prediction algorithms to identify co-evolving residues in 14 membrane proteins with solved 3D structures.
  • Calculated distances between correlated residue pairs across transmembrane segments.
  • Developed a consensus prediction by combining results from multiple algorithms and removing false positives.

Main Results:

  • Correlated residue pairs in membrane proteins were significantly closer than random predictions.
  • Covariation often occurred near helix-helix contacts.
  • Consensus prediction identified 53% of residue pairs within one helix turn of observed contacts.
  • Predicting interacting helices achieved 83% specificity and 42% sensitivity.

Conclusions:

  • Correlated mutation analysis is applicable to alpha-helical membrane proteins.
  • The developed consensus prediction method enhances the accuracy of contact prediction.
  • This approach facilitates the structural modeling of membrane proteins.