ArticleJournal of the American Chemical Society2012
Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed.
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- Higher-order epistasis within Pol II trigger loop haplotypes.bioRxiv : the preprint server for biology · 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
- 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
- Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A.The Journal of chemical physics · 2023Article
- Colorimetry-Based Phosphate Measurement for Polymerase Elongation.BioMed research international · 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
- Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process.Acta biochimica et biophysica Sinica · 2022Review
- Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2.Chem catalysis · 2022Article
- Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex.Communications biology · 2021Article
13 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Pyrophosphate ion (PP(i)) release after nucleotide incorporation is a necessary step for RNA polymerase II (pol II) to enter the next nucleotide addition cycle during transcription elongation. However, the role of pol II residues in PP(i) release and the mechanistic relationship between PP(i) release and the conformational change of the trigger loop remain unclear. In this study, we constructed a Markov state model (MSM) from extensive all-atom molecular dynamics (MD) simulations in the explicit solvent to simulate the PP(i) release process along the pol II secondary channel. Our results show that the trigger loop has significantly larger intrinsic motion after catalysis and formation of PP(i), which in turn aids PP(i) release mainly through the hydrogen bonding between the trigger loop residue H1085 and the (Mg-PP(i))(2-) group. Once PP(i) leaves the active site, it adopts a hopping model through several highly conserved positively charged residues such as K752 and K619 to release from the pol II pore region of the secondary channel. These positive hopping sites form favorable interactions with PP(i) and generate four kinetically metastable states as identified by our MSM. Furthermore, our single-mutant simulations suggest that H1085 and K752 aid PP(i) exit from the active site after catalysis, whereas K619 facilitates its passage through the secondary channel. Finally, we suggest that PP(i) release could help the opening motion of the trigger loop, even though PP(i) release precedes full opening of the trigger loop due to faster PP(i) dynamics. Our simulations provide predictions to guide future experimental tests.
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