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

Nucleic Acid Structure01:25

Nucleic Acid Structure

10.3K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
10.3K

You might also read

Related Articles

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

Sort by
Same author

PTSD malingering detection in damage claim cases: Diagnostic accuracy in cases of personal injury as a result of motor vehicle accidents.

International journal of law and psychiatry·2023
Same author

In vitro and in silico studies of interaction of synthetic 2,6,9-trisubstituted purine kinase inhibitors BPA-302, BP-21 and BP-117 with liver drug-metabolizing cytochromes P450

Physiological research·2021
Same author

On the rapid in situ oxidation of two-dimensional V<sub>2</sub>CT<sub>z</sub> MXene in culture cell media and their cytotoxicity.

Materials science & engineering. C, Materials for biological applications·2020
Same author

beta-caryophyllene oxide and trans-nerolidol affect enzyme activity of CYP3A4 - in vitro and in silico studies.

Physiological research·2019
Same author

Olomoucine II, New Effective CDK Inhibitor with Strong Cytotoxic Properties.

TheScientificWorldJournal·2018
Same author

Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms.

Pharmacological research·2018

Related Experiment Video

Updated: Mar 30, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.6K

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

M Krepl1, M Havrila1, P Stadlbauer1

  • 1Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.

Journal of Chemical Theory and Computation
|November 19, 2015
PubMed
Summary

Molecular dynamics simulations reveal protein-RNA complex stability varies greatly. Shape-specific recognition leads to more stable complexes than sequence-specific recognition, highlighting individual system challenges.

More Related Videos

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.6K
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

3.4K

Related Experiment Videos

Last Updated: Mar 30, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.6K
Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

2.6K
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

3.4K

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Protein-RNA complexes are crucial for cellular function.
  • Accurate simulation of these complexes is vital for understanding their dynamics and interactions.
  • Existing computational models face challenges in capturing the stability and behavior of diverse protein-RNA systems.

Purpose of the Study:

  • To investigate the stability and behavior of six protein-RNA complexes using extensive molecular dynamics (MD) simulations.
  • To evaluate the performance of different molecular mechanics force fields (AMBER ff99bsc0χ(OL3) for RNA and ff99SB/ff12SB for proteins) in simulating these systems.
  • To identify factors influencing the stability of simulated protein-RNA complexes.

Main Methods:

  • Conducted over 30 microseconds of unrestrained molecular dynamics simulations in explicit solvent.
  • Employed the AMBER ff99bsc0χ(OL3) RNA force field and the ff99SB and ff12SB protein force fields.
  • Analyzed simulation trajectories for structural stability, deviations from experimental structures, and factors affecting behavior.

Main Results:

  • Simulations exhibited variable stability, with some systems deviating significantly from experimental structures.
  • Microsecond-scale simulations were necessary for stabilization after initial structural perturbations.
  • Structural stability did not correlate with buried surface area or binding affinity but was linked to the type of RNA recognition (shape-specific vs. sequence-specific).
  • The ff12SB force field showed improved tyrosine side-chain dynamics compared to ff99SB.

Conclusions:

  • Simulating protein-RNA complexes is challenging and requires individualized approaches.
  • The type of protein-RNA recognition mechanism significantly impacts complex stability in simulations.
  • Force field choice and starting structure quality are critical factors, with system-specific properties dominating simulation outcomes.