Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

Protein Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

Protein Folding Quality Check in the RER

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...

You might also read

Related Articles

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

Sort by

Same author

Corrigendum to "<sup>19</sup>F NMR Strategy for Probing Site-specific RNA Dynamics in Large RNA-protein Complexes: Application to the Hfq RNA Chaperone" [J. Mol. Biol. 438 (2026) 169797].

Journal of molecular biology·2026

Same author

<sup>19</sup>F NMR Strategy for Probing Site-specific RNA Dynamics in Large RNA-protein Complexes: Application to the Hfq RNA Chaperone.

Journal of molecular biology·2026

Same author

Amide <sup>1</sup>H and <sup>15</sup>N NMR signal assignments of all naturally-occurring di-ubiquitins.

Biomolecular NMR assignments·2026

Same author

Selective control of ligand binding through a distal mutation that alters the protein native ensemble.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

NMR screening of low molecular weight inhibitors targeting the papain-like protease (PLPro) of SARS-CoV-2.

FEBS open bio·2025

Same author

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.

PLoS computational biology·2024

Search research articles

Related Experiment Video

Updated: May 6, 2026

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.

Konstantin Berlin¹, Andrew Longhini, T Kwaku Dayie

¹Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.

Journal of Biomolecular NMR

|October 31, 2013

Summary

The enhanced ROTDIF program accurately analyzes molecular dynamics in proteins, DNA, and RNA using nuclear magnetic resonance data. Its new features improve usability and speed, enabling deeper insights into biomolecular conformational changes.

More Related Videos

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Related Experiment Videos

Last Updated: May 6, 2026

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Area of Science:

Biophysics
Structural Biology
Computational Chemistry

Background:

Nuclear Magnetic Resonance (NMR) relaxation data provides insights into molecular motions.
Accurate determination of the rotational diffusion tensor is crucial for understanding biomolecular dynamics.
Previous computational tools had limitations in versatility and accuracy.

Purpose of the Study:

To introduce a new, versatile, and user-friendly version of the ROTDIF program.
To improve the accuracy and speed of analyzing NMR relaxation data for molecular motion studies.
To enable the characterization of complex biomolecular systems, including multi-domain proteins and nucleic acids.

Main Methods:

Analysis of (13)C and (15)N NMR relaxation data at single or multiple magnetic fields.
Improved computation of the rotational diffusion tensor, accounting for biased errors like conformational exchange.
Integration of domain alignment and docking for multi-domain system analysis.
Development of a Java-based graphical user interface (GUI) for enhanced accessibility.
Implementation of a faster deterministic minimization algorithm.

Main Results:

The new ROTDIF program demonstrates improved accuracy in analyzing (13)C and (15)N relaxation data.
Significant speedup (order of magnitude) compared to the previous version.
Successful characterization of subtle conformational changes in RNA dynamics as a function of temperature.
Demonstrated versatility across proteins, DNA, and RNA systems.

Conclusions:

The enhanced ROTDIF program offers a powerful and accessible tool for rigorous analysis of biomolecular dynamics.
The improvements facilitate more accurate and efficient determination of rotational diffusion tensors.
The program enables the discovery of previously hidden conformational dynamics in complex biological molecules.