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Microsecond Dynamics of the Pyrophosphate Ion Release in SARS-CoV‑2 RNA Polymerase
Tiantian Xu1,2, Lin Yang3,4, Xinzhou Xu3,4
1State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.
JACS Au
|March 27, 2026
Summary
The release of pyrophosphate (PPi) from viral RNA-dependent RNA polymerase (RdRp) is crucial for replication. This study reveals a distinct PPi release mechanism in SARS-CoV-2 RdRp involving conserved residues and a stepwise process.
Area of Science:
- Molecular Biology
- Virology
- Biochemistry
Background:
- RNA-dependent RNA polymerase (RdRp) is essential for viral replication and transcription.
- The mechanism of pyrophosphate ion (PPi) release from viral RdRp is not fully understood, hindering comprehension of viral replication and transcription.
- Understanding PPi release is critical for developing antiviral strategies.
Purpose of the Study:
- To elucidate the molecular mechanism of PPi release in SARS-CoV-2 RdRp.
- To identify key residues involved in the PPi release process.
- To compare the PPi release mechanism in SARS-CoV-2 RdRp with other polymerases.
Main Methods:
- Extensive molecular dynamics simulations were employed.
- A tailor-made Markov state model was constructed.
- Two-step NTP incorporation and PPi-mediated cleavage assays were performed.
Main Results:
- Three metastable states representing stepwise PPi release over 3.6 μs were identified.
- Four conserved residues (K551, R553, R555, K798) were found to mediate PPi release.
- Experimental assays validated the role of these residues in PPi release and pyrophosphorolysis.
Conclusions:
- A distinctive PPi release model for SARS-CoV-2 RdRp was revealed.
- The identified conserved residues play a crucial role in coronavirus transcription and replication.
- This study advances the understanding of viral RdRp mechanisms, particularly PPi dynamics.
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