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Related Concept Videos

Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Fluid Mosaic Model01:19

Fluid Mosaic Model

Scientists identified the plasma membrane in the 1890s and its principal chemical components (lipids and proteins) by 1915. The model for plasma membrane structure, proposed in 1935 by Hugh Davson and James Danielli, was the first model to be widely accepted in the scientific community. The model was based on the plasma membrane's "railroad track" appearance in early electron micrographs. Davson and Danielli theorized that the plasma membrane's structure resembled a sandwich with the analogy of...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
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...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Current status of membrane protein structure classification.

Sindy Neumann1, Angelika Fuchs, Armen Mulkidjanian

  • 1Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, D-85354 Freising, Germany.

Proteins
|February 27, 2010
PubMed
Summary
This summary is machine-generated.

Classifying alpha-helical membrane proteins is challenging due to limited structural data and the lipid bilayer

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Membrane protein research

Background:

  • Protein structure classification efforts have been ongoing for over two decades.
  • Discrepancies exist in classifying soluble proteins, but membrane protein classification remains understudied due to limited structural data.
  • Alpha-helical membrane proteins present unique classification challenges within structural databases.

Purpose of the Study:

  • To comparatively analyze the classification of alpha-helical membrane proteins in the SCOP and CATH databases.
  • To identify discrepancies in domain and fold assignments for membrane proteins.
  • To investigate the impact of transmembrane helices on classification consistency.

Main Methods:

  • Analysis of 63 alpha-helical membrane protein chains with 1-13 transmembrane helices.
  • Comparative study of protein classification in the Structural Classification of Proteins (SCOP) and Common Architecture Tool (CATH) databases.
  • Examination of domain and fold assignments across different numbers of transmembrane helices.

Main Results:

  • Significant discrepancies were observed in the classification of alpha-helical membrane proteins between SCOP and CATH.
  • Discrepancies predominantly affect proteins with few transmembrane helices (1-4 helices).
  • Proteins with more than five helices show consistent classification, suggesting structural constraints of the lipid bilayer impact smaller bundles.

Conclusions:

  • The lipid bilayer's structural constraints complicate the classification of membrane proteins with few transmembrane regions.
  • Small membrane helix bundles exhibit high structural continuity, making them sensitive to classification method variations.
  • Accurate classification of small, structurally diverse membrane proteins requires refined fold definitions incorporating fine-grained features like helix interactions.