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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Enzymatic Modification and Flow Cytometry Assessment of Yeast Surface Displayed Proteins
10:54

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Published on: May 30, 2025

Quantitative residue-level structure-evolution relationships in the yeast membrane proteome.

Eric A Franzosa1, Ran Xue, Yu Xia

  • 1Bioinformatics Program, Boston University, USA.

Genome Biology and Evolution
|March 21, 2013
PubMed
Summary

Membrane protein regions, especially transmembrane (TM) sections, evolve slower due to packing constraints, not just hydrophobicity. Residue evolutionary rate correlates with burial depth, offering insights into protein evolution.

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Area of Science:

  • Biophysics
  • Evolutionary Biology
  • Proteomics

Background:

  • Membrane proteins have unique biophysical properties compared to soluble proteins.
  • Little is known about how these properties influence residue-level evolutionary dynamics.
  • Transmembrane (TM) regions are generally more conserved than extramembrane (EM) regions, but the reasons are unclear.

Purpose of the Study:

  • To quantitatively assess residue-level structure-evolution relationships in yeast membrane proteins.
  • To understand the mechanisms behind the slower evolution of TM regions compared to EM regions.
  • To investigate the role of residue burial and solvent environment in protein evolution.

Main Methods:

  • Utilized homology-based high-resolution 3D protein models.
  • Performed rigorous evolutionary rate calculations.
  • Analyzed the yeast membrane proteome.

Main Results:

  • Residue evolutionary rate increases linearly with decreasing residue burial, irrespective of solvent environment.
  • Packing interactions, not hydrophobicity, directly correlate with selective constraint.
  • For similar burial depths, TM residues evolve significantly slower than EM residues.

Conclusions:

  • The unique membrane environment imposes distinct evolutionary constraints on TM regions.
  • Increased packing constraints in TM regions, coupled with reduced hydrophobic effects, drive slower evolution.
  • Residue burial is a universal predictor of selective constraint across different environments.