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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

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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...
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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Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Translocation of Proteins into the Mitochondria

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Sorting of outer membrane proteins:
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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.
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Related Experiment Video

Updated: May 29, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

Enhanced Inter-helical Residue Contact Prediction in Transmembrane Proteins.

Y Wei1, C A Floudas

  • 1Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544-5263, U.S.A.

Chemical Engineering Science
|September 6, 2011
PubMed
Summary

This study enhances a mathematical model for predicting contacts in transmembrane alpha-helical proteins using a larger dataset and improved constraints. The improved method shows higher accuracy than previous approaches, aiding protein structure prediction.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: November 3, 2011

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biophysics

Background:

  • Predicting contacts in transmembrane alpha-helical proteins is crucial for understanding protein structure and function.
  • Existing mathematical models have limitations due to restricted datasets.

Purpose of the Study:

  • To enhance a mathematical optimization model for predicting residue contacts in transmembrane alpha-helical proteins.
  • To improve prediction accuracy by expanding the training dataset and refining physical constraints.

Main Methods:

  • Constructed a more comprehensive dataset for transmembrane alpha-helical proteins.
  • Modified physical constraints within the mathematical optimization model.
  • Developed and applied a novel blind contact prediction scheme.

Main Results:

  • Achieved an average accuracy of 56% when predicting contacts on proteins from the training set (excluding the target protein).
  • Obtained varying prediction accuracies on six independent membrane proteins, with an average of 60.7%.
  • Demonstrated superior prediction accuracy compared to the TMhit support vector machine method.

Conclusions:

  • The enhanced mathematical model and blind prediction scheme significantly improve contact prediction accuracy for transmembrane alpha-helical proteins.
  • The refined approach offers a more reliable tool for structural bioinformatics and computational biology.
  • Further validation on diverse membrane protein sets is warranted.