Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations
Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the second...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-09-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/10/9/1289 |
| _version_ | 1797554361408159744 |
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| author | Nicolas E. J. Génin Robert O. J. Weinzierl |
| author_facet | Nicolas E. J. Génin Robert O. J. Weinzierl |
| author_sort | Nicolas E. J. Génin |
| collection | DOAJ |
| description | Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary channel (CH2) or selection to downstream sites in the main channel (CH1) prior to catalysis, have been proposed. In this study, accelerated molecular dynamics simulations of freely diffusing NTPs about RNAPII were applied to refine the CH2 model and uncover atomic details on the CH1 model that previously lacked a persuasive structural framework to illustrate its mechanism of action. Diffusion and binding of NTPs to downstream DNA, and the transfer of a preselected NTP to the active site, are simulated for the first time. All-atom simulations further support that CH1 loading is transcription factor IIF (TFIIF) dependent and impacts catalytic isomerization. Altogether, the alternative nucleotide loading systems may allow distinct transcriptional landscapes to be expressed. |
| first_indexed | 2024-03-10T16:30:57Z |
| format | Article |
| id | doaj.art-adbc9368db32426c9fb75674528637ee |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T16:30:57Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-adbc9368db32426c9fb75674528637ee2023-11-20T12:52:48ZengMDPI AGBiomolecules2218-273X2020-09-01109128910.3390/biom10091289Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular SimulationsNicolas E. J. Génin0Robert O. J. Weinzierl1Institut de Chimie Organique et Analytique, Université d’Orléans, 45100 Orléans, FranceDepartment of Life Sciences, Imperial College London, London SW7 2AZ, UKMapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary channel (CH2) or selection to downstream sites in the main channel (CH1) prior to catalysis, have been proposed. In this study, accelerated molecular dynamics simulations of freely diffusing NTPs about RNAPII were applied to refine the CH2 model and uncover atomic details on the CH1 model that previously lacked a persuasive structural framework to illustrate its mechanism of action. Diffusion and binding of NTPs to downstream DNA, and the transfer of a preselected NTP to the active site, are simulated for the first time. All-atom simulations further support that CH1 loading is transcription factor IIF (TFIIF) dependent and impacts catalytic isomerization. Altogether, the alternative nucleotide loading systems may allow distinct transcriptional landscapes to be expressed.https://www.mdpi.com/2218-273X/10/9/1289RNA polymerasenucleoside triphosphatemain channelsecondary channeltertiary channeldownstream bubble |
| spellingShingle | Nicolas E. J. Génin Robert O. J. Weinzierl Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations Biomolecules RNA polymerase nucleoside triphosphate main channel secondary channel tertiary channel downstream bubble |
| title | Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations |
| title_full | Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations |
| title_fullStr | Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations |
| title_full_unstemmed | Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations |
| title_short | Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations |
| title_sort | nucleotide loading modes of human rna polymerase ii as deciphered by molecular simulations |
| topic | RNA polymerase nucleoside triphosphate main channel secondary channel tertiary channel downstream bubble |
| url | https://www.mdpi.com/2218-273X/10/9/1289 |
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