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

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...
Retrovirus Life Cycles01:10

Retrovirus Life Cycles

Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the retrovirus to...
Viruses with RNA Genomes01:29

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
Inhibitors of Virion Maturation and Assembly01:19

Inhibitors of Virion Maturation and Assembly

As part of their replication cycle, certain viruses synthesize long precursor proteins called polyproteins within infected host cells. In human immunodeficiency virus (HIV), two major polyproteins are produced: Gag and Gag-Pol. The Gag polyprotein supplies the structural components of the virus, while Gag-Pol includes essential viral enzymes such as reverse transcriptase, integrase, and protease. After synthesis, these polyproteins move to the host cell membrane, where they assemble into an...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Viral Mutations00:36

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...

You might also read

Related Articles

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

Sort by
Same author

The Interstellar Mapping And Acceleration Probe High Energy (IMAP-Hi) Neutral Atom Imager.

Space science reviews·2026
Same author

The Solar Wind Electron (SWE) Instrument for the Interstellar Mapping and Acceleration Probe Mission.

Space science reviews·2026
Same author

Unveiling the enzymatic pathway of UMG-SP2 urethanase: insights into polyurethane degradation at the atomic level.

Chemical science·2025
Same author

Atomistic adsorption of PETase onto large-scale PET 3D-models that mimic reality.

Physical chemistry chemical physics : PCCP·2025
Same author

Sub-Bandgap Sensitization of Perovskite Semiconductors via Colloidal Quantum Dots Incorporation.

Nanomaterials (Basel, Switzerland)·2023
Same author

A selective p53 activator and anticancer agent to improve colorectal cancer therapy.

Cell reports·2021

Related Experiment Video

Updated: Jul 19, 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

Molecular dynamics model of unliganded HIV-1 reverse transcriptase.

A T P Carvalho1, P A Fernandes, M J Ramos

  • 1Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.

Medicinal Chemistry (Shariqah (United Arab Emirates))
|October 5, 2006
PubMed
Summary

This study presents a stable computational model of the unliganded HIV-1 RT enzyme, crucial for AIDS treatment. The model reveals key structural dynamics, aiding the design of new anti-HIV drugs.

More Related Videos

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells
13:07

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

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

Related Experiment Videos

Last Updated: Jul 19, 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

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells
13:07

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

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

Area of Science:

  • Structural biology
  • Computational chemistry
  • Virology

Background:

  • HIV-1 reverse transcriptase (RT) is a key target for AIDS treatment.
  • Existing X-ray structures of HIV-1 RT are often incomplete or low-resolution, especially for the unliganded enzyme.
  • The precise conformation of the p66 thumb in unliganded HIV-1 RT has been a subject of debate.

Purpose of the Study:

  • To develop a reliable computational model of the unliganded HIV-1 RT enzyme.
  • To analyze the structural stability and dynamics of the modeled enzyme.
  • To investigate the conformation of the p66 thumb and the nucleotide binding site.

Main Methods:

  • Homology modeling was used to build the initial RT model.
  • Molecular dynamics (MD) simulations with explicit solvent were employed for refinement and validation.
  • Analysis included Root Mean Square Deviation (RMSD), Ramachandran plots, contact maps, and hydration site studies.

Main Results:

  • The computational model of HIV-1 RT demonstrated structural stability during MD simulations (RMSD of 2 Angstrom).
  • The p66 thumb maintained a closed conformation throughout the simulation.
  • Intra-domain and inter-domain movements were observed, along with insights into nucleotide binding site solvation.

Conclusions:

  • A validated computational model of unliganded HIV-1 RT was successfully generated.
  • The model provides a stable platform for studying enzyme dynamics and interactions.
  • Findings contribute to structure-based drug design for novel anti-HIV retrovirals.