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Related Concept Videos

Membrane Proteins01:30

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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...
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Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
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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.
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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...
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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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Determining Membrane Protein Topology Using Fluorescence Protease Protection FPP
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De novo membrane protein structure prediction.

Timothy Nugent1

  • 1Bioinformatics Group, Department of Computer Science, University College London, Office: 8.11, Desk: 206, Gower Street, London, WC1E 6BT, UK, t.nugent@cs.ucl.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|October 22, 2014
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Summary

Recent advances in predicting protein structures, particularly alpha-helical transmembrane proteins, are detailed. New methods allow accurate 3D modeling of receptors from sequence data alone.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Protein structure prediction has significantly advanced due to improved methods for identifying residue-residue contacts.
  • Large multiple sequence alignments are crucial for these predictive advancements.

Purpose of the Study:

  • To discuss recent advances in protein structure prediction.
  • To provide a guide for de novo modeling of alpha-helical transmembrane proteins.
  • To demonstrate accurate 3D modeling of G protein-coupled receptors using primary sequence.

Main Methods:

  • Utilizing residue-residue contact predictions from multiple sequence alignments.
  • Applying de novo modeling techniques for transmembrane proteins.
  • Employing computational tools for 3D structure generation.

Main Results:

  • Demonstrated accurate 3D model construction of a G protein-coupled receptor.
  • Successfully oriented the predicted receptor model within a membrane environment.
  • Showcased the feasibility of modeling complex proteins from primary sequence data.

Conclusions:

  • Recent advances enable accurate de novo modeling of alpha-helical transmembrane proteins.
  • Primary protein sequence is sufficient for building detailed 3D models of receptors.
  • Computational approaches are powerful tools for structural biology research.