To initiate transcription, the holoenzyme (RNA polymerase [RNAP] in complex with σ factor) loads the promoter DNA via the flexible loading gate created by the clamp and β-lobe, yet their roles in DNA loading have not been characterized. We used a quasi-Markov State Model (qMSM) built from extensive molecular dynamics simulations to elucidate the dynamics of Thermus aquaticus holoenzyme’s gate opening. We showed that during gate opening, β-lobe oscillates four orders of magnitude faster than the clamp, whose opening depends on the Switch 2’s structure. Myxopyronin, an antibiotic that binds to Switch 2, was shown to undergo a conformational selection mechanism to inhibit clamp opening. Importantly, we reveal a critical but undiscovered role of β-lobe, whose opening is sufficient for DNA loading even when the clamp is partially closed. These findings open the opportunity for the development of antibiotics targeting β-lobe of RNAP. Finally, we have shown that our qMSMs, which encode non-Markovian dynamics based on the generalized master equation formalism, hold great potential to be widely applied to study biomolecular dynamics.
|Original language||English (US)|
|Journal||Proceedings of the National Academy of Sciences of the United States of America|
|State||Published - Apr 22 2021|
Bibliographical noteKAUST Repository Item: Exported on 2021-04-26
Acknowledged KAUST grant number(s): FCC/1/1976-23, FCC/1/1976-26, REI/1/0018-01-01, URF/1/4098-01-01
Acknowledgements: X.H. was supported by the Hong Kong Research Grant Council (16303919, 16307718, AoE/P-705/16, AoE/M-09/12, and T13-605/18-W)
and the Hong Kong Innovation and Technology Commission (ITCPD/17-9 and ITC-CNERC14SC01). X.G. was supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research under Awards FCC/1/1976-23, FCC/1/1976-26, URF/1/4098-01-01, and REI/1/0018-01-01. This research made use of the computing resources of the Supercomputing Laboratory at KAUST and the X-GPU cluster supported by the Hong Kong Research Grant Council Collaborative Research Fund C6021-19EF.
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