Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

Conservation of Protein Domains Over Different Proteins

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Disruption of Pik3r1 promotes muscle hyperplasia and lipolysis in grass carp (Ctenopharyngodon idella).

Comparative biochemistry and physiology. Part A, Molecular & integrative physiology·2026

Same author

Structural insights into predicted protein-protein interactions and protein complexes in the human proteome.

Scientific reports·2026

Same author

Universal and Lineage-Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms.

Proteins·2026

Same author

Family-level specialization in protein domain insertion architectures.

Protein science : a publication of the Protein Society·2026

Same author

Reciprocal best matching: a new pipeline for scoring models with unknown stoichiometry in CASP experiments.

BMC bioinformatics·2026

Same author

A taxonomic overview of the <i>Apodemia mormo</i> complex from a genomic perspective.

The taxonomic report of the International Lepidoptera Survey·2026

Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026

Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026

Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026

Same journal

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026

Same journal

Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.

PLoS computational biology·2026

Same journal

Neuronal excitability and parameter variability in the Hodgkin-Huxley model.

PLoS computational biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 9, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Using evolutionary context to classify difficult protein folds.

Jimin Pei^1,2,3, R Dustin Schaeffer², Qian Cong^1,2,3

¹Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

Plos Computational Biology

|December 1, 2025

Summary

This summary is machine-generated.

Advances in protein structure prediction reveal novel protein domains. Integrating structural and evolutionary methods like DPAM helps classify these domains and uncover distant evolutionary links.

More Related Videos

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jan 9, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural biology
Bioinformatics
Evolutionary biology

Background:

Recent protein structure prediction tools, like AlphaFold2, have identified numerous novel protein domains with unique structures.
The Encyclopedia of Domains (TED) project cataloged over 7400 candidate novel-fold (CNF) domains based on structural classification.

Purpose of the Study:

To analyze the evolutionary and structural context of TED CNF domains using a new method.
To compare domain parsing results from TED and DPAM to understand their relationship and refine protein domain classification.

Main Methods:

Applied DPAM (Domain Parser for AlphaFold Models), which integrates AlphaFold confidence scores with sequence and structure similarity searches.
Parsed domains in AlphaFold models containing TED CNF domains.
Compared domain boundaries and classifications between TED and DPAM.

Main Results:

Identified 8044 DPAM domains overlapping with TED CNF domains; 2490 were confidently classified within the ECOD hierarchy.
A significant portion of TED CNF domains are distant homologs of known ECOD domains.
Observed varied domain boundary patterns between TED and DPAM, with TED domains often embedded within DPAM domains, indicating insertions or extensions.

Conclusions:

Structural and evolutionary approaches are complementary for protein domain annotation.
Integrative methods like DPAM are powerful for refining classification of complex protein folds and identifying remote evolutionary relationships.
The study refines our understanding of novel protein folds and their evolutionary connections.