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 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 Folding01:22

Protein Folding

Overview
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...
Protein Folding01:22

Protein Folding

Overview
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...
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

Trustworthy Compound-Protein Interaction Prediction with Interpretable and Conformalized Cross-Attention Transformers.

Journal of chemical information and modeling·2026
Same author

Factors regarding blood donation willingness and preferences toward feedback between first-time donors and repeat donors in China: a cross-sectional survey.

Frontiers in medicine·2026
Same author

Development and validation of a LASSO-based predictive model for inadvertent hypothermia in ICU patients.

Frontiers in medicine·2025
Same author

A structure-based tool to interpret the significance of kinase mutations in clinical next generation sequencing in cancer.

Frontiers in oncology·2025
Same author

A role for pH dynamics regulating transcription factor DNA-binding selectivity.

Nucleic acids research·2025
Same author

InSty: A ProDy Module for Evaluating Protein Interactions and Stability.

Journal of molecular biology·2025
Same journal

Complementing Onsager's Conductivity Theory by Grotthuss Mechanism Mitigation via Ion-Induced Depletion of Hydrogen-Bond-Donating Water.

Journal of chemical theory and computation·2026
Same journal

Microscopic Stress in Biomembranes: A Perspective on Key Concepts, Methods, and Applications.

Journal of chemical theory and computation·2026
Same journal

Analytic Nuclear Gradients Including Oriented External Electric Fields in a Molecule-Fixed Frame.

Journal of chemical theory and computation·2026
Same journal

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.

Journal of chemical theory and computation·2026
Same journal

Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins.

Journal of chemical theory and computation·2026
Same journal

Improving PCM in Protic Media: Markov State Models for TD-DFT Calculations.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: May 31, 2026

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

Assessing protein loop flexibility by hierarchical Monte Carlo sampling.

Jerome Nilmeier1, Lan Hua, Evangelos A Coutsias

  • 1Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, California 94158-2517.

Journal of Chemical Theory and Computation
|July 12, 2011
PubMed
Summary
This summary is machine-generated.

We developed a new Monte Carlo method to generate protein loop conformations. This computational approach accurately models protein flexibility, crucial for biological function.

More Related Videos

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 15, 2010

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Related Experiment Videos

Last Updated: May 31, 2026

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

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 15, 2010

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein loop flexibility is essential for biological function in solution.
  • Understanding protein dynamics requires accurate modeling of conformational ensembles.

Purpose of the Study:

  • To introduce a novel Monte Carlo method for generating conformational ensembles of protein loops and cyclic peptides.
  • To validate the method's ability to model protein loop flexibility and distinguish between flexible and rigid loops.

Main Methods:

  • A new Monte Carlo method incorporating triaxial loop closure for backbone sampling.
  • Hierarchical sampling of sidechains with the backbone to overcome energy barriers.
  • Application to triosephosphate isomerase active site loop and three additional test cases.

Main Results:

  • The method successfully generates conformational ensembles for protein loops.
  • Ensembles for the triosephosphate isomerase active site loop align with existing structural data.
  • The method can differentiate between flexible and rigid loops within the same protein.

Conclusions:

  • The developed Monte Carlo method provides a robust approach for modeling protein loop dynamics.
  • This tool aids in understanding the relationship between protein structure, flexibility, and function.
  • Accurate modeling of loop flexibility is key for advancing protein structure-based drug design and biological studies.