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Related Concept Videos

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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Introduction to Membrane Proteins01:16

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

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

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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.
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Multi-pass Transmembrane Proteins and β-barrels01:09

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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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Protein-protein Interfaces02:04

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method.

Han Wang1,2, Jingru Wang1,2, Li Zhang3

  • 1School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.

International Journal of Biological Sciences
|July 11, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces TMSA, a new method for aligning alpha-helical transmembrane proteins (αTMPs). TMSA improves alignment accuracy and aids in recognizing αTMP folds, crucial for predicting their structures.

Keywords:
Segment AlignmentTopologyTransmembrane Protein

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Alpha-helical transmembrane proteins (αTMPs) are vital in eukaryotic cells, participating in numerous biological processes.
  • Their unique properties make experimental structure determination challenging.
  • Accurate sequence alignment is essential for predicting αTMP conformations and structures.

Purpose of the Study:

  • To develop a novel method for segment alignment of αTMPs.
  • To enhance the accuracy of αTMP structure prediction through improved alignment.

Main Methods:

  • Developed the Alpha-helical Transmembrane Protein Segment Alignment (TMSA) method.
  • Utilized segment information from topology structures and evolutionary data as features.
  • Trained and tested TMSA on distinct non-redundant datasets.

Main Results:

  • TMSA demonstrated higher alignment accuracy compared to the general alignment method HHalign.
  • The TMSA method facilitates easier recognition of αTMP folds.
  • Improved alignment accuracy contributes to better structure prediction.

Conclusions:

  • TMSA is an effective tool for aligning αTMP sequences.
  • This method advances the prediction of αTMP structures.
  • TMSA offers a significant improvement over general alignment approaches for this protein class.