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

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

Published on: May 9, 2025

Solution structural dynamics of HIV-1 reverse transcriptase heterodimer.

James M Seckler¹, Kathryn J Howard, Mary D Barkley

¹Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA.

|July 15, 2009

Summary

Structural dynamics of HIV-1 reverse transcriptase (RT) were investigated. The study reveals that a key beta-sheet in the p66 subunit undergoes slow unfolding, impacting enzyme function and drug binding.

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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

Area of Science:

Biochemistry
Structural Biology
Virology

Background:

HIV-1 reverse transcriptase (RT) is a crucial enzyme for viral replication.
RT is an asymmetric heterodimer composed of p66 and p51 subunits.
Conformational changes are vital for RT function.

Purpose of the Study:

To investigate the structural dynamics of HIV-1 RT using hydrogen exchange mass spectrometry (H/X MS).
To elucidate the flexibility and stability of different RT subdomains.
To understand the dynamics of the beta12-beta13-beta14 sheet in relation to template/primer and NNRTI binding.

Main Methods:

Hydrogen exchange mass spectrometry (H/X MS) was employed to probe structural dynamics.
Analysis of H/D exchange patterns to determine subdomain flexibility.
Investigation of slowly interconverting species using H/X MS capabilities.

Main Results:

The fingers and palm subdomains form the stable core of the heterodimer.
The RNase H domain of the p66 subunit is highly flexible.
The beta12-beta13-beta14 beta-sheet in p66 undergoes slow cooperative unfolding (t(1/2) < 20 s).

Conclusions:

The structural dynamics of HIV-1 RT, particularly the flexibility of the RNase H domain and the unfolding of the beta12-beta13-beta14 sheet, are critical for its function.
These findings provide insights into template/primer binding and NNRTI interactions.
H/X MS is a powerful tool for studying enzyme dynamics and conformational changes.