ArticleProceedings of the National Academy of Sciences of the United States of America2021
Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- A Practical Guide to Transition State Analysis in Biomolecular Simulations with TS-DAR.The journal of physical chemistry. B · 2025Article
- Memory kernel minimization-based neural networks for discovering slow collective variables of biomolecular dynamics.Nature computational science · 2025Article
- AMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular Dynamics.Journal of chemical theory and computation · 2025Article
- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Markov-Type State Models to Describe Non-Markovian Dynamics.Journal of chemical theory and computation · 2025Article
- Deciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization.RSC advances · 2025Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.Nature structural & molecular biology · 2024Article
- Information Bottleneck Approach for Markov Model Construction.Journal of chemical theory and computation · 2024Article
- Article
- Transient interactions modulate the affinity of NF-κB transcription factors for DNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes.The Journal of chemical physics · 2024Article
- Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.bioRxiv : the preprint server for biology · 2024Article
- Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels.The Journal of chemical physics · 2023Article
- An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.Journal of chemical theory and computation · 2023Article
- Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Automated Path Searching Reveals the Mechanism of Hydrolysis Enhancement by T4 Lysozyme Mutants.International journal of molecular sciences · 2022Article
- DNA opening during transcription initiation by RNA polymerase II in atomic detail.Biophysical journal · 2022Article
- Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding.Nature communications · 2022Article
- Rotational Mechanism of FFrontiers in microbiology · 2022Review
- Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex.Communications biology · 2021Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.