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Related Concept Videos

Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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.
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Regulation of the Unfolded Protein Response01:31

Regulation of the Unfolded Protein Response

Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...
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...
Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...

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Related Experiment Video

Updated: May 10, 2026

Functional Characterization of RING-Type E3 Ubiquitin Ligases In Vitro and In Planta
10:27

Functional Characterization of RING-Type E3 Ubiquitin Ligases In Vitro and In Planta

Published on: December 5, 2019

SPRY domains encode ubiquitin ligase specificity for ZAP and RIG-I.

Ibrahim Syed1, Sheng Chen1, David J Peeler1,2

  • 1Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom.

Plos Pathogens
|May 8, 2026
PubMed
Summary
This summary is machine-generated.

SPRY domains dictate ubiquitin ligase specificity for antiviral responses. AlphaFold predicts novel interactions, revealing how TRIM25 and Riplet surveil RNA vaccines, impacting expression.

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Related Experiment Videos

Last Updated: May 10, 2026

Functional Characterization of RING-Type E3 Ubiquitin Ligases In Vitro and In Planta
10:27

Functional Characterization of RING-Type E3 Ubiquitin Ligases In Vitro and In Planta

Published on: December 5, 2019

In Vitro Analysis of E3 Ubiquitin Ligase Function
06:06

In Vitro Analysis of E3 Ubiquitin Ligase Function

Published on: May 14, 2021

In-vitro Reconstitution of Bacterial Ubiquitination and VCP/p97-mediated Elimination
07:58

In-vitro Reconstitution of Bacterial Ubiquitination and VCP/p97-mediated Elimination

Published on: January 2, 2026

Area of Science:

  • Immunology
  • Structural Biology
  • Computational Biology

Background:

  • Ubiquitin ligases are crucial for innate immune responses against viruses.
  • The substrate recognition mechanisms of SPRY-containing ubiquitin ligases are not well understood.

Purpose of the Study:

  • To systematically predict interactions between human nucleic acid sensors and SPRY-containing proteins using a structure-based screening pipeline.
  • To elucidate the role of SPRY domains in dictating ligase substrate specificity and antiviral activity.
  • To investigate the implications of these interactions for RNA-based vaccine technologies.

Main Methods:

  • Large-scale structure-based screening pipeline utilizing AlphaFold for interaction prediction.
  • Identification of transient and degradation-sensitive protein complexes.
  • Domain-swapping experiments to assess SPRY domain function.
  • Phylogenetic and structural analyses of ligase evolution.
  • Residue-level modeling and targeted mutagenesis for interface validation.

Main Results:

  • Novel transient interactions, including a TRIM58-OAS1 complex, were discovered.
  • SPRY domains determine substrate specificity: TRIM25 targets ZAP, and Riplet targets RIG-I.
  • Domain swapping confirmed SPRY domains reprogram ligase specificity and antiviral function.
  • Evolutionary analysis revealed conserved substrate preferences despite divergence in TRIM25 and Riplet.
  • Hypervariable SPRY loops were identified as key recognition determinants.
  • Distinct SPRY ligases surveil self-amplifying RNA (saRNA) vaccines differently based on delivery method (lipofection vs. lipid nanoparticle), affecting vaccine expression.

Conclusions:

  • SPRY domains encode the recognition logic for ubiquitin ligases.
  • AlphaFold is a powerful tool for discovering previously hidden protein interactions.
  • Understanding these principles is critical for the development of effective RNA-based therapeutics and vaccines.