Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Folding01:25

Protein Folding

12.7K
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...
12.7K
Protein Folding01:22

Protein Folding

131.1K
Overview
131.1K
Protein Folding01:22

Protein Folding

36.6K
36.6K
The Unfolded Protein Response01:37

The Unfolded Protein Response

7.1K
The ER is the hub of protein synthesis in a cell. It has robust systems to quality control protein folding and also for degradation of terminally misfolded proteins. Under normal conditions, a small proportion of misfolded proteins that cannot be salvaged need to be transported to the cytoplasm by the ER-associated degradation or ERAD pathways. However, if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding...
7.1K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

5.7K
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...
5.7K
Proteins: From Genes to Degradation02:11

Proteins: From Genes to Degradation

15.0K
Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
Transcription is the synthesis of RNA...
15.0K

You might also read

Related Articles

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

Sort by
Same author

Assessment of scoring functions for computational models of protein-protein interfaces.

Physical review. E·2026
Same author

SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators.

Bioinformatics (Oxford, England)·2026
Same author

Droplet breakup against an isolated obstacle.

Soft matter·2026
Same author

Assessment of scoring functions for computational models of protein-protein interfaces.

ArXiv·2026
Same author

Mechanical plasticity of cell membranes enhances epithelial wound closure.

Physical review research·2025
Same author

Particle-scale origin of quadrupolar nonaffine displacement fields in granular solids.

Physical review. E·2025

Related Experiment Video

Updated: Apr 11, 2026

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
10:31

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

3.6K

Residue burial encodes a protein's fold.

Alex T Grigas1, Jacob Sumner2,3, Corey S O'Hern4,2,3,5,6,7

  • 1Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA.

Biorxiv : the Preprint Server for Biology
|April 10, 2026
PubMed
Summary

Residue core identity, a simple binary encoding, efficiently predicts protein structure. This method is more effective than existing approaches for understanding protein folding and conformation.

More Related Videos

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System
11:47

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

16.5K
Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain
14:25

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

19.1K

Related Experiment Videos

Last Updated: Apr 11, 2026

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
10:31

Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability

Published on: February 3, 2022

3.6K
Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System
11:47

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

16.5K
Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain
14:25

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

19.1K

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Protein structure determination is complex, governed by high-dimensional energy landscapes.
  • Accurate low-dimensional representations of these landscapes are sought for efficient prediction.
  • Existing methods for protein fold prediction have limitations in efficiency and accuracy.

Purpose of the Study:

  • To investigate if residue core identity can serve as an efficient low-dimensional representation of protein structure.
  • To compare the predictive efficiency of residue core identity against other established representations.
  • To re-frame protein folding prediction as a problem of predicting residue core identity.

Main Methods:

  • Developed a binary encoding for residue core identity (buried or not buried).
  • Tested the efficiency of this representation in predicting protein backbone conformation.
  • Compared core identity predictions with Cα contact maps and FoldSeek's 3Di embeddings.
  • Evaluated fold quality prediction using sequence information alone.

Main Results:

  • Residue core identity predicts protein backbone conformation more efficiently than tested representations.
  • Core identity is 4x more efficient than previous bit-per-residue estimates for native fold encoding.
  • It is 2x more efficient than Cα contact maps and 1.5x more efficient than FoldSeek's 3Di embeddings.
  • Predicting residue burial from sequence alone provides a more accurate fold quality estimate than predicting pairwise contacts.

Conclusions:

  • Residue core identity offers a highly efficient low-dimensional representation for protein structure.
  • This finding simplifies and reframes the protein folding problem.
  • The study highlights the potential of core identity for accurate and efficient protein structure prediction.