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A proton-coupled dynamic conformational switch in the HIV-1 dimerization initiation site kissing complex
Mihaela-Rita Mihailescu1, John P Marino
1Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and National Institute for Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
Summary
Protonation of a specific RNA base in HIV-1
Area of Science:
- Molecular Biology
- Virology
- Structural Biology
Background:
- The dimerization initiation site (DIS) in HIV-1 genomic RNA is crucial for viral assembly.
- DIS forms a kissing dimer, which rearranges into an extended duplex during viral maturation, a process involving the HIV-1 nucleocapsid protein (NCp7).
Purpose of the Study:
- To investigate the role of base protonation in the conformational dynamics of the DIS kissing dimer.
- To elucidate the mechanism by which NCp7 catalyzes the structural rearrangement of the DIS.
Main Methods:
- Utilized biophysical techniques to study the conformational dynamics of the DIS kissing dimer.
- Investigated the effect of pH and base protonation on DIS structure and NCp7 interaction.
Main Results:
- Demonstrated that protonation of A272 in the DIS loop at near-physiological pH induces localized conformational dynamics.
- Showed a direct correlation between the rate of NCp7-catalyzed DIS maturation and these proton-coupled dynamics.
- NCp7 accelerates the conversion of the dynamic, protonated A272 state.
Conclusions:
- Revealed a novel role for base protonation in modulating local RNA structure.
- Established a mechanism for NCp7-mediated structural rearrangement of kinetically trapped RNA states via base protonation.