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

Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

632
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
632

You might also read

Related Articles

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

Sort by
Same author

AutoSTOP-RT-TDDFT: Adaptive and Selected Real-Time Time-Dependent Density Functional Theory for Simulation of X-Ray Absorptions.

Journal of computational chemistry·2026
Same author

Hydrogen evolution electrocatalysts in high-fold degenerate topological semimetals with chiral structures.

Communications chemistry·2026
Same author

Unified MPI Parallelization of Wave Function Methods: iCIPT2 as a Showcase.

Journal of chemical theory and computation·2026
Same author

Theoretical investigation of the excited-state dynamics in the CH4 + O(3P) → CH3 + OH reaction.

The Journal of chemical physics·2026
Same author

Distinguishing Aromaticity from Antiaromaticity with Information-Theoretic and Energetic Information Quantities and Their Links to Molecular Properties.

The journal of physical chemistry. A·2025
Same author

Machine Learned Fock Matrix.

JACS Au·2025

Related Experiment Video

Updated: Jan 11, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

2.1K

Unbinding Dynamics of Large HIV Non-Nucleoside Reverse Transcriptase Inhibitors Revealed by Atomistic Milestoning

Ying Liu1, Ru Wang1, Hao Wang1

  • 1Qingdao Institute for Theoretical and Computational Sciences and Center for Optics Research and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China.

The Journal of Physical Chemistry. B
|November 17, 2025
PubMed
Summary
This summary is machine-generated.

Large flexible non-nucleoside reverse transcriptase inhibitors (NNRTIs) like JLJ636 use a "tunnel" channel to unbind from HIV reverse transcriptase. This differs from smaller NNRTIs that use an "entrance" channel.

More Related Videos

Nucleocapsid Annealing-Mediated Electrophoresis NAME Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors
08:33

Nucleocapsid Annealing-Mediated Electrophoresis NAME Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors

Published on: January 19, 2015

9.3K
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

9.9K

Related Experiment Videos

Last Updated: Jan 11, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

2.1K
Nucleocapsid Annealing-Mediated Electrophoresis NAME Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors
08:33

Nucleocapsid Annealing-Mediated Electrophoresis NAME Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors

Published on: January 19, 2015

9.3K
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

9.9K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are crucial for anti-HIV therapy.
  • Large, flexible NNRTIs may overcome drug resistance mutations in HIV reverse transcriptase.
  • Dissociation pathways of large NNRTIs from the enzyme are not well understood.

Purpose of the Study:

  • To investigate the unbinding dynamics and pathways of the large NNRTI, JLJ636, from HIV reverse transcriptase.
  • To identify the preferred dissociation routes and estimate the mean residence time of JLJ636.
  • To compare the unbinding behavior of JLJ636 with smaller NNRTIs.

Main Methods:

  • Atomistic simulations were employed to study the unbinding process.
  • Random acceleration molecular dynamics and Milestoning simulations were used.
  • Free energy profiles and dissociation pathways were computed.

Main Results:

  • Three potential exit routes were identified: "entrance", "tunnel", and "groove" channels.
  • The "tunnel" channel was found to be the most favorable dissociation pathway for JLJ636.
  • The "groove" channel was the second most favorable, while the "entrance" channel was rarely used.
  • This unbinding behavior contrasts with smaller NNRTIs that primarily use the "entrance" channel.

Conclusions:

  • The dissociation pathway of large, flexible NNRTIs like JLJ636 is distinct from smaller NNRTIs.
  • The "tunnel" channel represents a key route for JLJ636 unbinding, offering insights into inhibitor-enzyme interactions.
  • Understanding these pathways is vital for designing next-generation anti-HIV drugs effective against resistant strains.