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- W2911332512 abstract "RNA polymerase (RNAP) is an essential enzyme that transcribes DNA into messenger RNA to further express proteins. Bacteriophage T7 RNAP is widely utilized in lab gene expression system and synthetic circuit as it transcribes self-sufficiently, without transcription factors, and with high promoter activity. We have investigated T7 RNAP on both its mechano-chemical couplings and fidelity control during transcription, combining physical modeling with structural dynamics simulations. In particular, we have implemented extensive atomistic molecular dynamics (MD) simulations and constructed the Markov state model (MSM) to investigate product release and translocation process of T7 RNAP, as it couples Brownian thermal motions with essential structural elements to assist PPi release, to facilitate the RNAP translocation, and to prevent backtracking. Meanwhile, we systematically quantified the nucleotide selectivity of this non-proofreading RNAP at multiple kinetic checkpoints prior to the full nucleotide incorporation. Essential selection against the non-cognate nucleotide species appears to happen at early checkpoints at the pre-insertion and right after, with a critical amino acid serving as a paw for selective ratcheting RNAP along the DNA. In addition, we also model the complete transcription process along with RNAP traffic, as positive supercoiling is accumulated in front of a leading RNAP to inhibit the transcription, and then being resolved gradually to allow transcriptional bursting." @default.
- W2911332512 created "2019-02-21" @default.
- W2911332512 creator A5000122134 @default.
- W2911332512 date "2019-02-01" @default.
- W2911332512 modified "2023-09-25" @default.
- W2911332512 title "Transcription Machine Studied in a Nutshell on T7 RNA Polymerase Mechanochemistry, Fidelity Control, and Bursting Activity" @default.
- W2911332512 doi "https://doi.org/10.1016/j.bpj.2018.11.1155" @default.
- W2911332512 hasPublicationYear "2019" @default.
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