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

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

2.0K
2.0K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

15.0K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
15.0K
Protein Folding01:25

Protein Folding

8.8K
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...
8.8K
Protein Folding01:22

Protein Folding

112.3K
Overview
112.3K
Protein Folding01:22

Protein Folding

29.7K
29.7K
Protein Organization01:24

Protein Organization

7.2K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
7.2K

You might also read

Related Articles

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

Sort by
Same author

Targeting Lcn2 to Inhibit Myocardial Cell Ferroptosis is a Potential Therapy for Alleviating Septic Cardiomyopathy.

Inflammation·2025
Same author

Development and validation of a screening tool for sepsis without laboratory results in the emergency department: a machine learning study.

EClinicalMedicine·2025
Same author

UPLC-MS metabolite profiling and antioxidant activity of <i>Sanghuangporus sanghuang</i> extract.

PeerJ·2025
Same author

Mechanical properties and mechanisms of soda residue and fly ash stabilized soil.

Scientific reports·2025
Same author

Angelica gigas Nakai (Korean Dang-gui) Root Alcoholic Extracts in Health Promotion and Disease Therapy - active Phytochemicals and In Vivo Molecular Targets.

Pharmaceutical research·2025
Same author

Extension of an ICU-based noninvasive model to predict latent shock in the emergency department: an exploratory study.

Frontiers in cardiovascular medicine·2025

Related Experiment Video

Updated: May 2, 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

16.2K

New force field on modeling intrinsically disordered proteins.

Wei Wang1, Wei Ye, Cheng Jiang

  • 1State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.

Chemical Biology & Drug Design
|March 5, 2014
PubMed
Summary
This summary is machine-generated.

A new Amber ff99IDPs force field parameter set accurately models intrinsically disordered proteins (IDPs) and their complexes. This advancement is crucial for understanding IDPs in diseases like cancer.

Keywords:
CMAPIDPs force fieldMD simulationff99IDPsφ/ψ dihedrals

More Related Videos

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.2K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.3K

Related Experiment Videos

Last Updated: May 2, 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

16.2K
Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.2K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.3K

Area of Science:

  • Biochemistry and Molecular Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) constitute a significant fraction of eukaryotic proteomes (35-51%) and are implicated in various diseases, including cancer.
  • Existing additive force field parameter sets inadequately capture the structural characteristics of IDPs, limiting their study in molecular simulations.

Purpose of the Study:

  • To systematically correct biases in standard Amber force field parameters for improved simulation of intrinsically disordered proteins.
  • To develop and validate a new force field parameter set, ff99IDPs, suitable for modeling IDPs.

Main Methods:

  • Correction of φ/ψ distributions for disorder-promoting residues using the CMAP method on the Amber ff99SBildn parameter set.
  • Validation through comparison of simulation results with benchmark data for IDP structures, NMR chemical shifts, and residue dipolar couplings.

Main Results:

  • The ff99IDPs parameter set significantly improves φ/ψ distributions of disorder-promoting residues (RMS%D < 0.15%).
  • Simulations using ff99IDPs show quantitative agreement with experimental NMR chemical shifts and high correlation with residue dipolar couplings for tested IDPs.
  • ff99IDPs successfully models both disordered and ordered states of proteins in complex, unlike the original ff99SBildn.

Conclusions:

  • The Amber ff99IDPs parameter set is a reliable tool for studying intrinsically disordered protein structures and their roles in disease.
  • The study highlights the necessity of incorporating IDP structural considerations into general-purpose force field development for both additive and non-additive models.