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Updated: Sep 9, 2025
07:02
An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
6.7K
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, United States.
Elife
|September 2, 2025
Summary
Cryptic pockets in viral protein 35 (VP35) are functional, not accidental. Their opening influences double-stranded RNA (dsRNA) binding, suggesting these pockets are key targets for antiviral drugs.
Area of Science:
- Structural biology
- Virology
- Drug discovery
Background:
- Cryptic pockets are potential drug targets for protein-nucleic acid interactions.
- Their functional significance and potential for drug resistance evolution are unclear.
Purpose of the Study:
- Investigate if a cryptic pocket in viral protein 35 (VP35) of Zaire ebolavirus aids double-stranded RNA (dsRNA) binding.
- Explore the role of cryptic pocket opening in dsRNA binding across different filovirus homologs.
Main Methods:
- Molecular simulations
- Thiol-labeling experiments
- dsRNA-binding assays
- Point mutation analysis
Main Results:
- Filovirus Interferon Inhibitory Domains (IIDs) exhibit varying probabilities of cryptic pocket opening.
- Closed pocket conformations preferentially bind dsRNA blunt ends.
- Open pocket conformations preferentially bind the dsRNA backbone.
Conclusions:
- The cryptic pocket in VP35 is functional and influences dsRNA binding.
- Cryptic pockets are likely under selective pressure and may be resistant to drug resistance evolution.
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