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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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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...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Related Experiment Video

Updated: Mar 31, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

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Evolutionary reprograming of protein-protein interaction specificity.

Eyal Akiva1, Patricia C Babbitt2

  • 1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.

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|October 27, 2015
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Summary
This summary is machine-generated.

Researchers studied protein-protein interaction evolution using a toxin-antitoxin model. They found that intermediate, promiscuous proteins likely facilitate evolutionary trajectories, avoiding non-interactive states.

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Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Biochemistry

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Understanding the evolutionary pathways of PPIs is essential for comprehending biological complexity.

Purpose of the Study:

  • To investigate the evolutionary trajectories of protein-protein interactions.
  • To identify potential mechanisms that facilitate the evolution of new or modified PPIs.

Main Methods:

  • Construction and deep sequencing of mutation libraries.
  • Utilizing a toxin-antitoxin system as a model for studying PPI evolution.

Main Results:

  • Identified probable evolutionary pathways for PPIs.
  • Evidence suggests that promiscuous intermediate proteins facilitate transitions between interaction states.
  • Observed avoidance of non-interactive states during evolution.

Conclusions:

  • The evolution of protein-protein interactions may follow general principles applicable across various biological systems.
  • Promiscuous intermediates play a significant role in mediating evolutionary transitions.
  • Findings contribute to understanding enzyme evolution and the broader principles of biological interaction evolution.