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Related Concept Videos

Introduction to Membrane Proteins01:16

Introduction to Membrane Proteins

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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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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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Tail-anchoring of Proteins in the ER Membrane01:45

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Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
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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
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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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AlignMe--a membrane protein sequence alignment web server.

Marcus Stamm1, René Staritzbichler1, Kamil Khafizov1

  • 1Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main 60438, Germany.

Nucleic Acids Research
|April 23, 2014
PubMed
Summary
This summary is machine-generated.

The AlignMe web server offers tools for comparing membrane protein sequences. It provides two modes for pair-wise sequence alignment and hydropathy profile alignment to aid in analyzing protein structures.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Membrane proteins play crucial roles in cellular functions.
  • Accurate sequence alignment is essential for understanding membrane protein structure and function.
  • Existing tools may not adequately address the complexities of membrane protein sequence analysis.

Purpose of the Study:

  • To introduce the AlignMe web server for analyzing and comparing membrane protein sequences.
  • To provide user-friendly access to advanced alignment tools for membrane proteins.
  • To facilitate the study of transmembrane topologies and potential 3D folds.

Main Methods:

  • Development of a web server implementing the AlignMe program.
  • Two operational modes: sequence-to-sequence alignment (PW mode) and hydropathy profile alignment (HP mode).
  • PW mode utilizes various inputs including substitution matrices, secondary structure, and transmembrane propensities.
  • HP mode aligns family-averaged hydrophobicity profiles derived from multiple sequence alignments.

Main Results:

  • The AlignMe server offers optimized parameter sets for PW mode based on sequence similarity.
  • HP mode enables qualitative comparison of transmembrane topologies for proteins with low sequence similarity.
  • The server integrates information from multiple sources for enhanced sequence analysis.

Conclusions:

  • The AlignMe web server provides accessible and versatile tools for membrane protein sequence analysis.
  • It aids in comparing protein sequences and inferring structural similarities.
  • The server facilitates research into membrane protein function and evolution.