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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.
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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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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-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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The living membranes are flexible due to their fluid mosaic nature; however, their bending into different shapes is an active process regulated by specific lipids and proteins. The membrane bending can be transient as seen in vesicles or stable for a long time as in microvilli. Cells regulate the size, location, and duration of the membrane curvature.
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Detergents are used to purify the integral proteins of the membrane. The hydrophobic portion of the detergent can replace membrane phospholipids while solubilizing the membrane proteins. When detergent monomers reach a specific concentration in a solution called critical micelle concentration (CMC), they form micelles. Above CMC, the concentration of the detergent monomers remains in equilibrium with the micelle. The number of detergent monomers present in the CMC varies for each detergent, and...
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Computational design of membrane proteins using RosettaMembrane.

Amanda M Duran1,2, Jens Meiler1,2

  • 1Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37235.

Protein Science : a Publication of the Protein Society
|November 2, 2017
PubMed
Summary

Computational design of membrane proteins is advancing. RosettaMembrane shows promise, recovering native-like sequences and properties, making it the best option for designing membrane proteins with Rosetta.

Keywords:
RosettaRosettaMembranecomputational designmembrane protein designmembrane protein engineeringmembrane proteins

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Membrane protein structure elucidation is challenging due to limited high-resolution structures and conformational states.
  • Advances in structural determination and soluble protein design enable tackling membrane protein design.
  • High-throughput biophysical assays for monitoring membrane protein function are limited.

Purpose of the Study:

  • Benchmark the Rosetta software for computational membrane protein design.
  • Evaluate strategies for handling reduced quality experimental membrane protein structures.
  • Assess the utility of symmetry in design protocols for homo-oligomeric membrane proteins.
  • Compare Rosetta's soluble scoring function against RosettaMembrane for membrane protein design.

Main Methods:

  • Benchmarking Rosetta for membrane protein design.
  • Evaluating strategies for reduced quality experimental structures.
  • Testing symmetry in design protocols.
  • Comparing soluble scoring function with RosettaMembrane.

Main Results:

  • Both scoring functions recovered approximately 50% of the native sequence in complete redesigns.
  • RosettaMembrane recovered the most native-like amino acid property composition.
  • RosettaMembrane designs exhibited native-like surface hydrophobicity, despite leucine overrepresentation in hydrophobic regions.

Conclusions:

  • RosettaMembrane is currently the optimal choice for computational membrane protein design using Rosetta.
  • The software demonstrates potential for designing functional membrane proteins, addressing previous limitations.