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

19.6K
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...
19.6K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

2.9K
2.9K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

11.0K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
11.0K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

4.1K
4.1K
Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

27.2K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
27.2K
Extrinsic and Intrinsic Pathways of Hemostasis01:20

Extrinsic and Intrinsic Pathways of Hemostasis

13.1K
Blood clotting or coagulation involves extrinsic and intrinsic pathways, which ultimately merge into the common pathway, forming a fibrin clot.
The Extrinsic Pathway
The extrinsic pathway of coagulation is typically initiated by tissue damage that exposes blood to tissue factor (TF), a protein released by the damaged tissue cells outside the blood vessels—this interaction with TF triggers biochemical reactions involving specific clotting factors. The key player here is Factor VII, which...
13.1K

You might also read

Related Articles

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

Sort by
Same author

Identification of Moonlighting Proteins from Published Literature Using Natural Language Processing and AI.

The protein journal·2026
Same author

Classification of driver and passenger mutations in different cancer types using deep neural networks.

Bioinformatics advances·2026
Same author

Protein-DNA interactions in disease and drug discovery.

Chemical communications (Cambridge, England)·2026
Same author

Discovery of Tetrahydroisoquinoline-Based SARS-CoV-2 Helicase Inhibitors with Iterative, Deep Learning-Enhanced Virtual Screening.

Journal of chemical information and modeling·2025
Same author

Herpes Simplex Virus Glycoprotein D Associated with Aβ<sub>1-42</sub> Tetramers Mediates Neurotoxicity by Perturbing Neuronal Membrane Integrity: A Molecular Dynamics Simulation.

ACS chemical neuroscience·2025
Same author

Computational design of protein complexes: influence of binding affinity.

Chemical communications (Cambridge, England)·2025

Related Experiment Video

Updated: Feb 9, 2026

Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins
07:24

Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins

Published on: September 23, 2021

2.3K

Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins.

Ambuj Srivastava1, Shandar Ahmad2, M Michael Gromiha3

  • 1Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India. ambuj.88.in@gmail.com.

International Journal of Molecular Sciences
|May 31, 2018
PubMed
Summary

Protein regions that transition from disordered to ordered upon RNA binding are small and rich in charged, hydrophobic, and aromatic residues. These intrinsically disordered regions (IDRs) show unique interaction patterns with RNA, offering insights into protein-RNA binding.

Keywords:
disorder-to-order regionsintrinsically disorder proteinsprotein–RNA interactionsunstructured proteins

More Related Videos

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection
06:44

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection

Published on: January 26, 2019

8.4K
Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis
08:46

Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis

Published on: September 16, 2014

8.2K

Related Experiment Videos

Last Updated: Feb 9, 2026

Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins
07:24

Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins

Published on: September 23, 2021

2.3K
Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection
06:44

Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection

Published on: January 26, 2019

8.4K
Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis
08:46

Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis

Published on: September 16, 2014

8.2K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Intrinsically disordered regions (IDRs) and proteins (IDPs) lack stable structures, conferring high flexibility.
  • A subset of IDPs binds substrates like RNA, often adopting ordered structures upon complex formation.
  • Understanding these disorder-to-order transitions (DOT) is crucial for deciphering protein-RNA interactions.

Purpose of the Study:

  • To analyze protein-RNA complexes exhibiting a disorder-to-order transition (DOT) upon binding.
  • To characterize the properties and interaction patterns of DOT regions in RNA-binding proteins.

Main Methods:

  • Analysis of a dataset of protein-RNA complexes.
  • Characterization of DOT region size, residue composition, and solvent exposure.
  • Comparison of interaction frequencies between DOT regions and structured regions.
  • Calculation of amino acid-nucleotide interaction energies.

Main Results:

  • DOT regions in RNA-binding proteins are typically small (less than 3 residues).
  • Positively charged, hydrophobic, and aromatic residues are prevalent in DOT regions, engaging in electrostatic, cation-π, and hydrophobic interactions.
  • DOT regions exhibit higher water exposure compared to structured regions.
  • RNA binding in DOT regions promotes sheet formation with minimal changes to helix content.
  • Specific amino acid-nucleotide preferences were identified (His-G, Asn-U, Ser-U).

Conclusions:

  • DOT regions possess distinct characteristics and interaction preferences compared to structured protein interfaces.
  • These findings enhance the understanding of protein-RNA interactions and the role of disorder-to-order transitions.
  • The study's results can inform the development of tools for identifying DOT regions in RNA-binding proteins.