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Related Concept Videos

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Conservation of Protein Domains Over Different Proteins

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Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...
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The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
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Transmembrane Domain Oligomerization Propensity determined by ToxR Assay
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Structure determination protocol for transmembrane domain oligomers.

Qingshan Fu1, Alessandro Piai1, Wen Chen1

  • 1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

Nature Protocols
|July 5, 2019
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Summary
This summary is machine-generated.

This study presents a robust nuclear magnetic resonance (NMR) protocol for determining the atomic-resolution structures of transmembrane (TM) protein oligomers. The method overcomes challenges in structural biology for hydrophobic TM domains, enabling new insights into cell signaling and viral structures.

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Area of Science:

  • Structural biology
  • Biophysics
  • Molecular biology

Background:

  • Transmembrane (TM) protein anchors are crucial for cell surface receptor signaling and viral stability.
  • Their hydrophobic and dynamic nature presents significant challenges for structural characterization using traditional methods like X-ray crystallography and cryo-electron microscopy (cryo-EM).
  • Understanding the oligomeric states of TM domains is vital for deciphering their functions.

Purpose of the Study:

  • To establish and detail a robust protocol for determining atomic-resolution structures of transmembrane protein oligomers.
  • To overcome existing limitations in structural biology for characterizing hydrophobic TM domains.
  • To provide a broadly applicable method for studying type I/II membrane proteins.

Main Methods:

  • Production of isotopically labeled TM or membrane-proximal (MP) protein fragments via TrpLE fusion, inclusion body expression, and cyanogen bromide (CNBr) cleavage.
  • Nuclear magnetic resonance (NMR) spectroscopy in bicelles to mimic lipid bilayers.
  • Determination of oligomeric state, intermolecular contacts (using NOE experiments), structure determination, and membrane partitioning (using paramagnetic probe titration, PPT).

Main Results:

  • A detailed protocol for atomic-resolution structural determination of TM oligomers has been successfully established.
  • The protocol effectively addresses challenges associated with hydrophobic and dynamic TM domains.
  • Demonstrated applicability to immune receptors and viral membrane proteins.

Conclusions:

  • The developed NMR protocol provides a powerful tool for elucidating the structures of challenging transmembrane protein oligomers.
  • This method significantly advances the field of structural biology by filling structural gaps in membrane protein research.
  • The protocol is broadly applicable to various type I/II membrane proteins, aiding in understanding their functions in health and disease.