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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.
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Membrane Proteins

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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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

Relation between sequence and structure in membrane proteins.

Mireia Olivella1, Angel Gonzalez, Leonardo Pardo

  • 1Grup de Recerca en Bioinformàtica i Estadística Mèdica, Departament de Biologia de Sistemes, Escola Politècnica Superior, Universitat de Vic, 08500 Vic, Barcelona, Catalonia, Spain. Mireia.Olivella@uvic.cat

Bioinformatics (Oxford, England)
|May 17, 2013
PubMed
Summary

Integral membrane proteins, like alpha-helix bundles and beta-barrels, maintain structural integrity even with low sequence identity. This finding is crucial for homology modeling of related membrane proteins.

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Area of Science:

  • Structural biology
  • Biochemistry
  • Bioinformatics

Background:

  • Integral polytopic membrane proteins utilize either alpha-helix bundles or beta-barrels in their transmembrane domains.
  • Advances in crystal structure determination enable analysis of sequence variability's impact on transmembrane domain structure conservation.

Purpose of the Study:

  • To determine the minimum pairwise sequence identity required to preserve transmembrane molecular architectures within the lipid bilayer.
  • To investigate the relationship between sequence identity and structural similarity in transmembrane domains of homologous membrane proteins.

Main Methods:

  • Structural alignment of homologous polytopic membrane protein pairs.
  • Calculation of root-mean-square deviation (rmsd) and sequence identity.
  • Analysis of structural similarity across varying sequence identity thresholds.

Main Results:

  • Transmembrane segments with sequence identity in the 20-35% 'twilight zone' exhibit high structural similarity (rmsd < 1.5 Å).
  • Beta-barrel proteins with less than 20% sequence identity maintain close structural similarity (rmsd < 2.5 Å).

Conclusions:

  • Fold preservation in transmembrane regions necessitates less sequence conservation compared to globular proteins.
  • These findings have significant implications for homology modeling of evolutionary-related membrane proteins.