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 Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

Overview
Molecular Chaperones and Protein Folding03:00

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...
Protein Folding Quality Check in the RER01:29

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...
Protein Folding01:25

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...
Molecular Chaperones and Protein Folding03:00

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...

You might also read

Related Articles

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

Sort by
Same author

Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.

Journal of chemical theory and computation·2024
Same author

Static mechanical strain induces capillary endothelial cell cycle re-entry and sprouting.

Physical biology·2016
Same author

Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field.

Journal of chemical theory and computation·2015
Same author

Deltorphin analogs restricted via a urea bridge: structure and opioid activity.

Advances in experimental medicine and biology·2009
Same author

The occurrence and the type of germline mutations in the RET gene in patients with medullary thyroid carcinoma and their unaffected kindred's from Central Poland.

Cancer investigation·2007
Same author

Recombination and positive selection contribute to evolution of Listeria monocytogenes inlA.

Microbiology (Reading, England)·2007

Related Experiment Video

Updated: Jul 13, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 16, 2010

The protein folding problem: global optimization of the force fields.

H A Scheraga1, A Liwo, S Oldziej

  • 1Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853, USA. has5@cornell.edu

Frontiers in Bioscience : a Journal and Virtual Library
|September 9, 2004
PubMed
Summary

Researchers developed a theoretical approach for protein folding, combining all-atom and hierarchical methods. This computational strategy aids in predicting protein structures, especially for larger proteins, and exploring folding pathways.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy
08:34

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy

Published on: February 5, 2020

Related Experiment Videos

Last Updated: Jul 13, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 16, 2010

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy
08:34

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy

Published on: February 5, 2020

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • The protein folding problem remains a significant challenge in biology.
  • Accurate prediction of protein three-dimensional structures is crucial for understanding function.
  • Existing methods face limitations with larger protein molecules.

Purpose of the Study:

  • To trace the evolutionary development of a theoretical approach for protein folding.
  • To present a hierarchical strategy for predicting protein structures.
  • To evaluate the performance of physics-based ab initio methods in protein structure prediction.

Main Methods:

  • Development of an empirical all-atom potential energy function.
  • Implementation of global optimization search algorithms.
  • Creation of a hierarchical approach using a united residue (UNRES) description for larger proteins.
  • Validation through CASP (Critical Assessment of protein Structure Prediction) blind tests.

Main Results:

  • The all-atom approach is effective for small molecules and alpha-helical proteins up to 46 residues.
  • The hierarchical UNRES-based approach successfully predicts structures for larger proteins.
  • The method demonstrated performance in successive CASP challenges.
  • Recent efforts focus on computing protein folding pathways.

Conclusions:

  • A robust theoretical framework for protein structure prediction has been established.
  • The hierarchical approach significantly advances the ability to model larger proteins.
  • Physics-based ab initio methods show promise for accurate protein structure prediction and folding pathway analysis.