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Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
Published on: February 12, 2022
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Opening and closing of a cryptic pocket in VP35 toggles it between two different RNA-binding modes
Upasana L Mallimadugula1, Matthew A Cruz1, Neha Vithani1
1Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Biorxiv : the Preprint Server for Biology
|September 4, 2024
Summary
Cryptic pockets in viral proteins are functional, not accidental. Their opening influences double-stranded RNA binding, suggesting these targets are hard to evade for drug resistance.
Area of Science:
- Virology
- Structural Biology
- Drug Discovery
Background:
- Cryptic pockets are potential drug targets for protein-nucleic acid interactions.
- It is unclear if cryptic pockets are functional or easily evolved away.
Purpose of the Study:
- Investigate if a cryptic pocket in the Interferon Inhibitory Domain (IID) of viral protein 35 (VP35) aids double-stranded RNA (dsRNA) binding.
- Explore the link between cryptic pocket opening and dsRNA binding in filovirus IIDs.
Main Methods:
- Utilized simulations and thiol-labeling experiments to assess pocket opening probabilities in filovirus IIDs.
- Conducted dsRNA-binding assays to correlate pocket conformation with binding preference (blunt ends vs. backbone).
- Employed point mutations to modulate pocket opening and confirm functional impact.
Main Results:
- Filovirus IIDs exhibit varying probabilities of cryptic pocket opening.
- Closed pocket conformations preferentially bind dsRNA blunt ends.
- Open pocket conformations show a preference for binding the dsRNA backbone.
Conclusions:
- The open cryptic pocket in VP35 IID is functional, influencing dsRNA binding.
- Cryptic pockets are likely under selective pressure.
- These findings suggest cryptic pockets may present a challenge for evolving drug resistance.
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